Mercurial > repos > iuc > metabuli
changeset 0:b01d6b38f779 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli commit d093bc33200eb4b4332e0b5845ef189e48fdb37a
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,18 @@ +<macros> + <token name="@VERSION@">1.0.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">metabuli</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>metabuli | grep Version | sed 's/metabuli Version: //g'</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41592-024-02273-y</citation> + </citations> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metabuli.xml Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,221 @@ +<tool id="metabuli_classify" name="metabuli classify" version="@VERSION@+galaxy0" profile="20.01"> + <description> + metagenomic sequences + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + if [ -z "\$GALAXY_MEMORY_MB" ] ; then + METABULI_GALAXY_MEMORY_GB=8 ; + else + METABULI_GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024) - 1) ; + fi ; + #set ext = '.fastq' + #if str($library.lib_type) == "paired" + #if $library.r1.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set read1_file = 'r1' + $ext + #set read2_file = 'r2' + $ext + ln -s '$library.r1' $read1_file && + ln -s '$library.r2' $read2_file && + #else if str($library.lib_type) == "single" + #if $library.single.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set se_read = 'sr' + $ext + ln -s '$library.single' $se_read && + #else if str($library.lib_type) == "collection" + #set ext = '.fastq' + #if $library.input1.forward.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set read1_file = 'r1' + $ext + #set read2_file = 'r2' + $ext + ln -s '$library.input1.forward' $read1_file && + ln -s '$library.input1.reverse' $read2_file && + #end if + + metabuli classify + + #if str($library.lib_type) == "paired" + $read1_file + $read2_file + #else if str($library.lib_type) == "single" + $se_read + --mask $library.mask + #else if str($library.lib_type) == "collection" + $read1_file + $read2_file + #end if + '$metabuli_databases.fields.path' + out + mtbl + #if str($taxonomy_options.taxonomy_path) == 'local' + --taxonomy-path '$taxonomy_options.taxonomy.fields.path' + #end if + --threads \${GALAXY_SLOTS:-4} + --min-score $min_score + --min-cov $min_cov + --min-cons-cnt $min_cons_cnt + --min-cons-cnt-euk $min_cons_cnt_euk + --min-sp-score $min_sp_score + --hamming-margin $hamming_margin + --match-per-kmer $match_per_kmer + #if $accession_level + --accession-level 1 + #end if + #if str($library.lib_type) == "single" + --seq-mode $library.seq_mode + #end if + --max-ram \${METABULI_GALAXY_MEMORY_GB:-8} + > + '$log' + + ]]> </command> + <inputs> + <conditional name="library"> + <param name="lib_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> + <option value="paired" selected="true">Paired End</option> + <option value="single">Single End</option> + <option value="collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="r1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> + <param name="r2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> + </when> + <when value="single"> + <param name="single" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Read" help="Single end/long read"/> + <param name="seq_mode" type="select" label="Sequence Mode"> + <option value="3" selected="true">Long Read</option> + <option value="1">Single End Short Read</option> + </param> + <param argument="--mask" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Mask low complexity sequences in k-mer stage"/> + </when> + <when value="collection"> + <param name="input1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> + </when> + </conditional> + + <!-- DATABASE INPUT--> + <param label="Select a database" name="metabuli_databases" type="select"> + <options from_data_table="metabuli_databases"> + <validator message="No database is available" type="no_options" /> + </options> + </param> + + <conditional name="taxonomy_options"> + <param name="taxonomy_path" type="select" label="Select taxonomy path from either local or accompanied metabuli db?"> + <option value="local">Use a local taxonomy</option> + <option value="embed" selected="true">Use one from a metabuli database</option> + </param> + <when value="local"> + <param name="taxonomy" label="Select taxonomy" type="select"> + <options from_data_table="taxonomy"> + <validator message="No database is available" type="no_options" /> + </options> + </param> + </when> + <when value="embed"> + </when> + </conditional> + <param argument="--min-score" type="float" min="0" max="1" value="0.000" label="Min sequence similarity score." help="Value for precision mode: ONT(0.008), PacBio Sequel II (0.005), PacBio HiFi (0.07), Illumina (0.15)"/> + <param argument="--min-sp-score" type="float" min="0" max="1" value="0.0" label="Min. score for species-level or lower-level classification." help="Value for precision mode: PacBio HiFi (0.3), Illumina (0.5)"/> + <param argument="--min-cov" type="float" min="0" max="1" value="0.0" label="Min query coverage."/> + <param argument="--min-cons-cnt" type="integer" min="0" max="100" value="4" label="Min. number of consecutive matches for prokaryote/virus classification."/> + <param argument="--min-cons-cnt-euk" type="integer" min="0" max="100" value="9" label="Min. number of consecutive matches for eukaryote classification."/> + <param argument="--hamming-margin" type="integer" min="0" max="100" value="0" label="It allows extra Hamming distance than the minimum distance."/> + <param argument="--match-per-kmer" type="integer" min="0" max="100" value="0" label="Num. of matches per query k-mer. Larger values assign more memory for storing k-mer matches."/> + <param argument="--accession-level" type="boolean" truevalue="1" falsevalue="0" checked="false" label="search a database for accession-level classification."/> + </inputs> + + <outputs> + <data format="tabular" name="report" label="${tool.name} on ${on_string} report file" from_work_dir="out/mtbl_report.tsv" /> + <data format="tabular" name="classification" label="${tool.name} on ${on_string}: classification" from_work_dir="out/mtbl_classifications.tsv"/> + <data format="html" name="krona" label="${tool.name} on ${on_string}: Krona report" from_work_dir="out/mtbl_krona.html"/> + <data format="txt" name="log" label="${tool.name} on ${on_string}: Log file"/> + </outputs> + + <tests> + <!-- PE Illumina --> + <test expect_num_outputs="4"> + <param name="lib_type" value="paired"/> + <param name="r1" value="reads/illumina_R1.fastq.gz" ftype="fastqsanger.gz"/> + <param name="r2" value="reads/illumina_R2.fastq.gz" ftype="fastqsanger.gz" /> + <param name="metabuli_databases" value="RefSeqTest"/> + <param name="taxonomy_path" value="local" /> + <param name="taxonomy" value="taxonomy"/> + <output name="report"> + <assert_contents> + <has_text text="Escherichia coli str. K-12 substr. MG1655"/> + <has_text text="511145"/> + <has_text text="66.6667"/> + </assert_contents> + </output> + </test> + <!-- Long read ONT --> + <test expect_num_outputs="4"> + <param name="lib_type" value="single"/> + <param name="single" value="reads/ont.r10.4.1.fastq.gz" ftype="fastq.gz"/> + <param name="metabuli_databases" value="RefSeqTest"/> + <param name="taxonomy_path" value="local" /> + <param name="taxonomy" value="taxonomy"/> + <output name="report"> + <assert_contents> + <has_text text="Escherichia coli str. K-12 substr. MG1655"/> + <has_text text="30.4348"/> + </assert_contents> + </output> + </test> + <!-- Long read ONT Precision mode --> + <test expect_num_outputs="4"> + <param name="lib_type" value="single"/> + <param name="single" value="reads/ont.r10.4.1.fastq.gz" ftype="fastq.gz"/> + <param name="min_score" value="0.008" /> + <param name="metabuli_databases" value="RefSeqTest"/> + <param name="taxonomy_path" value="local" /> + <param name="taxonomy" value="taxonomy"/> + <output name="report"> + <assert_contents> + <has_text text="21.7391"/> + <has_text text="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"/> + </assert_contents> + </output> + </test> + <!-- Long read Pacbio HiFi --> + <test expect_num_outputs="4"> + <param name="lib_type" value="single"/> + <param name="single" value="reads/pacbio.hifi.fastq.gz" ftype="fastq.gz"/> + <param name="metabuli_databases" value="RefSeqTest"/> + <param name="taxonomy_path" value="local" /> + <param name="taxonomy" value="taxonomy"/> + <output name="report"> + <assert_contents> + <has_text text="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"/> + <has_text text="32.5000"/> + </assert_contents> + </output> + <output name="classification"> + <assert_contents> + <has_text text="a4d8d18d-afde-b01a-d552-476bc9831614"/> + <has_text text="208964:931"/> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ + + Metabuli_ specific and sensitive metagenomic classification via joint analysis of DNA and amino acid. + + .. _Metabuli: https://github.com/steineggerlab/Metabuli/tree/master?tab=readme-ov-file#classification + + ]]> + </help> + + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeqTest/acc2taxid.map Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +NC_003197.2 99287 +NC_000913.3 511145 +AE004091.2 208964
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeqTest/db.parameters Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,8 @@ +DB_name RefSeqTest +Creation_date 2024-5-31 +Metabuli commit used to create the DB 1.0.5 +Reduced_alphabet 0 +Spaced_kmer_mask 11111111 +Accession_level 0 +Mask_mode 1 +Mask_prob 0.900000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeqTest/taxID_list Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +208964 +511145 +99287
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metabuli_databases.loc Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,4 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}GTDB{tab}/path/to/GTDB +RefSeqTest RefSeqTest 2024 ${__HERE__}/RefSeqTest \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10.precision_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,46 @@ +1 6afed69c-0764-187d-7701-25dbaa56fa4d 208964 14214 0.700577 strain 208964:2340 +1 cc0f07c9-8e86-392e-f794-1a4252e9fb38 99287 6180 0.657362 strain 99287:970 +1 f6611dfa-6896-0371-efec-a60a01132e83 99287 27942 0.864756 strain 99287:6265 +1 581fe12a-4956-fa3b-f64f-31d99c708716 511145 9627 0.791056 no rank 511145:1855 +1 2f1a09bf-c558-a8cc-b071-83128761e14f 208964 1812 0.584713 strain 208964:276 +1 956740a3-5b26-133c-d1a2-d2bde75f68da 511145 45297 0.301311 no rank 511145:3124 +1 c277097d-f2a7-010a-ee05-3c93b5f2b6fb 99287 15564 0.650186 strain 99287:2309 +1 7f94a381-1546-7827-286c-5800d7b14fce 511145 8064 0.645957 no rank 511145:1197 +0 42479fca-23da-2161-c636-4a3efa727e79 0 33 0 no rank +1 ee825b81-860f-2bca-1f5e-90339434a8a4 99287 28722 0.666301 strain 99287:4529 +1 fb11ddfb-d32f-5d75-f1c3-41724b7e594e 208964 19653 0.582659 strain 208964:2557 +1 91c09038-76cc-cc91-c19a-7a47204708d4 208964 10176 0.491794 strain 208964:1095 +1 d9237302-7ca1-1cb0-87b5-9bef45b7dafe 511145 15885 0.874032 no rank 511145:3671 +1 7957d890-cc56-1ca8-d0a8-674deb4f96a1 208964 633 0.775671 strain 208964:123 +1 db0e608c-27b4-198c-e5b1-ff9f70153a96 208964 1014 0.425542 strain 208964:82 +1 008b9f35-e6a4-170b-d7f4-3ff9ecc8c875 511145 6864 0.909528 no rank 511145:1785 +1 8f08681a-4a01-0c54-2dd0-3618e772370b 511145 35853 0.790659 no rank 511145:7122 +1 2c199f0c-2601-a3ec-5bff-0c33f1f18bfd 99287 3690 0.814499 strain 99287:770 +1 cd61a49b-d049-b767-3ac3-add014fe2895 208964 19470 0.759553 strain 208964:3718 +1 1f672421-5585-fb71-f73c-40283fb95a51 511145 19251 0.427328 no rank 511145:1851 +1 e5a03490-b6d8-d771-2029-fa165cc02486 208964 10941 0.734713 strain 208964:1858 +1 90d5e8c9-9992-ccad-ed13-50ae9e1f01ed 208964 6183 0.609009 strain 208964:892 +1 fcf8a78c-007a-340b-1dc2-aa07cd4f74e2 208964 10812 0.823899 strain 208964:2242 +1 3bcf93b0-d23f-dc99-60b0-58925d04121e 208964 9777 0.619617 strain 208964:1365 +1 4106b3dc-8d38-d435-04af-22a8a13519ec 511145 4356 0.789256 no rank 511145:839 +1 9419850f-7037-20f0-71c8-c37470e44974 208964 4002 0.824713 strain 208964:812 +1 16e12407-f1ea-d31c-1e78-159997a22af2 208964 4896 0.659518 strain 208964:711 +1 8160d594-20b5-54bf-3185-b420f94f2c3e 99287 2547 0.447978 strain 99287:240 +1 f60e7dc2-d87b-4689-7105-0bce5603d146 511145 17982 0.74708 no rank 511145:3307 +1 b860a965-3998-8602-b83d-1e9a17046940 208964 1122 0.530749 strain 208964:152 +1 b5411913-b5a4-6bfa-30a4-7c956ef32b3a 511145 3300 0.350152 no rank 511145:273 +1 879e0f5f-0bcb-f145-86b2-fa35b9d469a0 99287 34836 0.901323 strain 99287:8652 +1 d8a48a7d-947c-29e9-f7bc-4560053600aa 511145 1392 0.871049 no rank 511145:296 +1 d2c318b8-3227-032b-bfe1-fb011cfc260e 208964 7233 0.772155 strain 208964:1328 +1 a2a7b030-bf46-e658-60e4-949f0980b1ba 511145 3966 0.403681 no rank 511145:333 +1 d17a0751-b32c-c486-066e-4f2d0a23a25a 208964 13539 0.866201 strain 208964:3103 +1 3ab721e1-e301-4c80-8b8a-7483a2fd0619 99287 44919 0.531679 strain 99287:5404 +1 7c3c58f1-8745-92cb-6065-70ab62ac2afe 99287 4866 0.643444 strain 99287:735 +1 dd99b942-6109-7a63-2d38-7a272be96e27 511145 71058 0.482929 no rank 511145:7648 +1 20757211-06ab-db4f-e089-30d4c1aa72fa 511145 7911 0.633991 no rank 511145:1153 +1 ed31326f-5b4b-de9e-d3d7-a246a0790ea7 208964 5883 0.800697 strain 208964:1215 +1 f779b5ad-5375-ab6e-a07b-c5b8f3156bcf 208964 1110 0.633784 strain 208964:158 +1 ff46ad1a-56ec-fff8-0094-135fb400942d 208964 8154 0.610559 strain 208964:1106 +1 c8915e98-895d-b0ca-3eea-c031c9ff1918 208964 20103 0.692484 strain 208964:3358 +1 4f405c5a-5f00-7e8f-7cde-bec88c36d3cf 208964 8181 0.814631 strain 208964:1698 +1 0a5f9965-3e92-d697-cc36-cf18fb1a64a4 99287 1302 0.217742 strain 99287:78
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10.precision_krona.html Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,6620 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta charset="utf-8"/> + <link rel="shortcut icon" 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+ <script id="notfound">window.onload=function(){document.body.innerHTML=""}</script> + <script language="javascript" type="text/javascript"> +{//----------------------------------------------------------------------------- +// +// PURPOSE +// +// Krona is a flexible tool for exploring the relative proportions of +// hierarchical data, such as metagenomic classifications, using a +// radial, space-filling display. It is implemented using HTML5 and +// JavaScript, allowing charts to be explored locally or served over the +// Internet, requiring only a current version of any major web +// browser. Krona charts can be created using an Excel template or from +// common bioinformatic formats using the provided conversion scripts. +// +// +// COPYRIGHT LICENSE +// +// Copyright (c) 2011, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and +// Adam Phillippy +// +// This Software was prepared for the Department of Homeland Security +// (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as +// part of contract HSHQDC-07-C-00020 to manage and operate the National +// Biodefense Analysis and Countermeasures Center (NBACC), a Federally +// Funded Research and Development Center. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// * Neither the name of the Battelle National Biodefense Institute nor +// the names of its contributors may be used to endorse or promote +// products derived from this software without specific prior written +// permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// +// TRADEMARK LICENSE +// +// KRONA(TM) is a trademark of the Department of Homeland Security, and use +// of the trademark is subject to the following conditions: +// +// * Distribution of the unchanged, official code/software using the +// KRONA(TM) mark is hereby permitted by the Department of Homeland +// Security, provided that the software is distributed without charge +// and modification. +// +// * Distribution of altered source code/software using the KRONA(TM) mark +// is not permitted unless written permission has been granted by the +// Department of Homeland Security. +// +// +// FOR MORE INFORMATION VISIT +// +// https://github.com/marbl/Krona/wiki/ +// +//----------------------------------------------------------------------------- +} + + +var canvas; +var context; +var svg; // for snapshot mode +var collapse = true; +var collapseCheckBox; +var collapseLast; +var compress; +var compressCheckBox; +var maxAbsoluteDepthText; +var maxAbsoluteDepthButtonDecrease; +var maxAbsoluteDepthButtonIncrease; +var fontSize = 11; +var fontSizeText; +var fontSizeButtonDecrease; +var fontSizeButtonIncrease; +var fontSizeLast; +var radiusButtonDecrease; +var radiusButtonIncrease; +var shorten; +var shortenCheckBox; +var maxAbsoluteDepth; +var backButton; +var upButton; +var forwardButton; +var snapshotButton; +var snapshotMode = false; +var details; +var detailsName; +var search; +var searchResults; +var nSearchResults; +var useHueCheckBox; +var useHueDiv; +var datasetDropDown; +var datasetButtonLast; +var datasetButtonPrev; +var datasetButtonNext; +var keyControl; +var showKeys = true; +var linkButton; +var linkText; +var frame; + +// Node references. Note that the meanings of 'selected' and 'focused' are +// swapped in the docs. +// +var head; // the root of the entire tree +var selectedNode = 0; // the root of the current view +var focusNode = 0; // a node chosen for more info (single-click) +var highlightedNode = 0; // mouse hover node +var highlightingHidden = false; +var nodes = new Array(); +var currentNodeID = 0; // to iterate while loading + +var nodeHistory = new Array(); +var nodeHistoryPosition = 0; + +var dataEnabled = false; // true when supplemental files are present + +// store non-Krona GET variables so they can be passed on to links +// +var getVariables = new Array(); + +// selectedNodeLast is separate from the history, since we need to check +// properties of the last node viewed when browsing through the history +// +var selectedNodeLast = 0; +var zoomOut = false; + +// temporary zoom-in while holding the mouse button on a wedge +// +var quickLook = false; // true when in quick look state +var mouseDown = false; +var mouseDownTime; // to detect mouse button hold +var quickLookHoldLength = 200; + +var imageWidth; +var imageHeight; +var centerX; +var centerY; +var gRadius; +var updateViewNeeded = false; + +// Determines the angle that the pie chart starts at. 90 degrees makes the +// center label consistent with the children. +// +var rotationOffset = Math.PI / 2; + +var buffer; +var bufferFactor = .1; + +// The maps are the small pie charts showing the current slice being viewed. +// +var mapBuffer = 10; +var mapRadius = 0; +var maxMapRadius = 25; +var mapWidth = 150; +var maxLabelOverhang = Math.PI * 4.18; + +// Keys are the labeled boxes for slices in the highest level that are too thin +// to label. +// +var maxKeySizeFactor = 2; // will be multiplied by font size +var keySize; +var keys; +var keyBuffer = 10; +var currentKey; +var keyMinTextLeft; +var keyMinAngle; + +var minRingWidthFactor = 5; // will be multiplied by font size +var maxPossibleDepth; // the theoretical max that can be displayed +var maxDisplayDepth; // the actual depth that will be displayed +var headerHeight = 0;//document.getElementById('options').clientHeight; +var historySpacingFactor = 1.6; // will be multiplied by font size +var historyAlphaDelta = .25; + +// appearance +// +var lineOpacity = 0.3; +var saturation = 0.5; +var lightnessBase = 0.6; +var lightnessMax = .8; +var thinLineWidth = .3; +var highlightLineWidth = 1.5; +var labelBoxBuffer = 6; +var labelBoxRounding = 15; +var labelWidthFudge = 1.05; // The width of unshortened labels are set slightly + // longer than the name width so the animation + // finishes faster. +var fontNormal; +var fontBold; +var fontFamily = 'sans-serif'; +//var fontFaceBold = 'bold Arial'; +var nodeRadius; +var angleFactor; +var tickLength; +var compressedRadii; + +// colors +// +var highlightFill = 'rgba(255, 255, 255, .3)'; +var colorUnclassified = 'rgb(220,220,220)'; + +// label staggering +// +var labelOffsets; // will store the current offset at each depth +// +// This will store pointers to the last node that had a label in each offset (or "track") of a +// each depth. These will be used to shorten neighboring labels that would overlap. +// The [nLabelNodes] index will store the last node with a radial label. +// labelFirstNodes is the same, but to check for going all the way around and +// overlapping the first labels. +// +var labelLastNodes; +var labelFirstNodes; +// +var nLabelOffsets = 3; // the number of offsets to use + +var mouseX = -1; +var mouseY = -1; +var mouseXRel = -1; +var mouseYRel = -1; + +// tweening +// +var progress = 0; // for tweening; goes from 0 to 1. +var progressLast = 0; +var tweenFactor = 0; // progress converted by a curve for a smoother effect. +var tweenLength = 850; // in ms +var tweenCurvature = 13; +// +// tweenMax is used to scale the sigmoid function so its range is [0,1] for the +// domain [0,1] +// +var tweenMax = 1 / (1 + Math.exp(-tweenCurvature / 2)); +// +var tweenStartTime; + +// for framerate debug +// +var tweenFrames = 0; +var fpsDisplay = document.getElementById('frameRate'); + +// Arrays to translate xml attribute names into displayable attribute names +// +var attributes = new Array(); +// +var magnitudeIndex; // the index of attribute arrays used for magnitude +var membersAssignedIndex; +var membersSummaryIndex; + +// For defining gradients +// +var hueDisplayName; +var hueStopPositions; +var hueStopHues; +var hueStopText; + +// multiple datasets +// +var currentDataset = 0; +var lastDataset = 0; +var datasets = 1; +var datasetNames; +var datasetSelectSize = 30; +var datasetAlpha = new Tween(0, 0); +var datasetWidths = new Array(); +var datasetChanged; +var datasetSelectWidth = 50; + +window.onload = load; + +var image; +var hiddenPattern; +var loadingImage; +var logoImage; + +function backingScale() +{ + if ('devicePixelRatio' in window) + { + if (window.devicePixelRatio > 1) + { + return window.devicePixelRatio; + } + } + + return 1; +} + +function resize() +{ + imageWidth = window.innerWidth; + imageHeight = window.innerHeight; + + if ( ! snapshotMode ) + { + context.canvas.width = imageWidth * backingScale(); + context.canvas.height = imageHeight * backingScale(); + context.canvas.style.width = imageWidth + "px" + context.canvas.style.height = imageHeight + "px" + context.scale(backingScale(), backingScale()); + } + + if ( datasetDropDown ) + { + var ratio = + (datasetDropDown.offsetTop + datasetDropDown.clientHeight) * 2 / + imageHeight; + + if ( ratio > 1 ) + { + ratio = 1; + } + + ratio = Math.sqrt(ratio); + + datasetSelectWidth = + (datasetDropDown.offsetLeft + datasetDropDown.clientWidth) * ratio; + } + var leftMargin = datasets > 1 ? datasetSelectWidth + 30 : 0; + var minDimension = imageWidth - mapWidth - leftMargin > imageHeight ? + imageHeight : + imageWidth - mapWidth - leftMargin; + + maxMapRadius = minDimension * .03; + buffer = minDimension * bufferFactor; + margin = minDimension * .015; + centerX = (imageWidth - mapWidth - leftMargin) / 2 + leftMargin; + centerY = imageHeight / 2; + gRadius = minDimension / 2 - buffer; + //context.font = '11px sans-serif'; +} + +function handleResize() +{ + updateViewNeeded = true; +} + +function Attribute() +{ +} + +function Tween(start, end) +{ + this.start = start; + this.end = end; + this.current = this.start; + + this.current = function() + { + if ( progress == 1 || this.start == this.end ) + { + return this.end; + } + else + { + return this.start + tweenFactor * (this.end - this.start); + } + }; + + this.setTarget = function(target) + { + this.start = this.current(); + this.end = target; + } +} + +function Node() +{ + this.id = currentNodeID; + currentNodeID++; + nodes[this.id] = this; + + this.angleStart = new Tween(Math.PI, 0); + this.angleEnd = new Tween(Math.PI, 0); + this.radiusInner = new Tween(1, 1); + this.labelRadius = new Tween(1, 1); + this.labelWidth = new Tween(0, 0); + this.scale = new Tween(1, 1); // TEMP + this.radiusOuter = new Tween(1, 1); + + this.r = new Tween(255, 255); + this.g = new Tween(255, 255); + this.b = new Tween(255, 255); + + this.alphaLabel = new Tween(0, 1); + this.alphaLine = new Tween(0, 1); + this.alphaArc = new Tween(0, 0); + this.alphaWedge = new Tween(0, 1); + this.alphaOther = new Tween(0, 1); + this.alphaPattern = new Tween(0, 0); + this.children = Array(); + this.parent = 0; + + this.attributes = new Array(attributes.length); + + this.addChild = function(child) + { + this.children.push(child); + }; + + this.addLabelNode = function(depth, labelOffset) + { + if ( labelHeadNodes[depth][labelOffset] == 0 ) + { + // this will become the head node for this list + + labelHeadNodes[depth][labelOffset] = this; + this.labelPrev = this; + } + + var head = labelHeadNodes[depth][labelOffset]; + + this.labelNext = head; + this.labelPrev = head.labelPrev; + head.labelPrev.labelNext = this; + head.labelPrev = this; + } + + this.canDisplayDepth = function() + { + // whether this node is at a depth that can be displayed, according + // to the max absolute depth + + return this.depth <= maxAbsoluteDepth; + } + + this.canDisplayHistory = function() + { + var radiusInner; + + if ( compress ) + { + radiusInner = compressedRadii[0]; + } + else + { + radiusInner = nodeRadius; + } + + return ( + -this.labelRadius.end * gRadius + + historySpacingFactor * fontSize / 2 < + radiusInner * gRadius + ); + } + + this.canDisplayLabelCurrent = function() + { + return ( + (this.angleEnd.current() - this.angleStart.current()) * + (this.radiusInner.current() * gRadius + gRadius) >= + minWidth()); + } + + this.checkHighlight = function() + { + if ( this.children.length == 0 && this == focusNode ) + { + //return false; + } + + if ( this.hide ) + { + return false; + } + + if ( this.radiusInner.end == 1 ) + { + // compressed to the outside; don't check + + return false; + } + + var highlighted = false; + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + for ( var i = 0; i < this.children.length; i++ ) + { + highlighted = this.children[i].checkHighlight(); + + if ( highlighted ) + { + return true; + } + } + + if ( this.radial ) + { + var angleText = (angleStartCurrent + angleEndCurrent) / 2; + var radiusText = (gRadius + radiusInner) / 2; + + context.rotate(angleText); + context.beginPath(); + context.moveTo(radiusText, -fontSize); + context.lineTo(radiusText, fontSize); + context.lineTo(radiusText + centerX, fontSize); + context.lineTo(radiusText + centerX, -fontSize); + context.closePath(); + context.rotate(-angleText); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(this.getPercentage()) + '%' + ' ' + this.name; + + if ( this.searchResultChildren() ) + { + label += searchResultString(this.searchResultChildren()); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + radiusText + measureText(label) + ) + { + highlighted = true; + } + } + } + else + { + for ( var i = 0; i < this.hiddenLabels.length; i++ ) + { + var hiddenLabel = this.hiddenLabels[i]; + + context.rotate(hiddenLabel.angle); + context.beginPath(); + context.moveTo(gRadius, -fontSize); + context.lineTo(gRadius, fontSize); + context.lineTo(gRadius + centerX, fontSize); + context.lineTo(gRadius + centerX, -fontSize); + context.closePath(); + context.rotate(-hiddenLabel.angle); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(hiddenLabel.value) + ' more'; + + if ( hiddenLabel.search ) + { + label += searchResultString(hiddenLabel.search); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + gRadius + fontSize + measureText(label) + ) + { + highlighted = true; + break; + } + } + } + } + + if ( ! highlighted && this != selectedNode && ! this.getCollapse() ) + { + context.beginPath(); + context.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false); + context.arc(0, 0, gRadius, angleEndCurrent, angleStartCurrent, true); + context.closePath(); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + highlighted = true; + } + + if + ( + ! highlighted && + (angleEndCurrent - angleStartCurrent) * + (radiusInner + gRadius) < + minWidth() && + this.getDepth() == selectedNode.getDepth() + 1 + ) + { + if ( showKeys && this.checkHighlightKey() ) + { + highlighted = true; + } + } + } + + if ( highlighted ) + { + if ( this != highlightedNode ) + { + // document.body.style.cursor='pointer'; + } + + highlightedNode = this; + } + + return highlighted; + } + + this.checkHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + var cx = centerX; + var cy = centerY - this.labelRadius.end * gRadius; + //var dim = context.measureText(this.name); + + var width = this.nameWidth; + + if ( this.searchResultChildren() ) + { + var results = searchResultString(this.searchResultChildren()); + var dim = context.measureText(results); + width += dim.width; + } + + if + ( + mouseX > cx - width / 2 && + mouseX < cx + width / 2 && + mouseY > cy - historySpacingFactor * fontSize / 2 && + mouseY < cy + historySpacingFactor * fontSize / 2 + ) + { + highlightedNode = this; + return; + } + + if ( this.getParent() ) + { + this.getParent().checkHighlightCenter(); + } + } + + this.checkHighlightKey = function() + { + var offset = keyOffset(); + + var xMin = imageWidth - keySize - margin - this.keyNameWidth - keyBuffer; + var xMax = imageWidth - margin; + var yMin = offset; + var yMax = offset + keySize; + + currentKey++; + + return ( + mouseX > xMin && + mouseX < xMax && + mouseY > yMin && + mouseY < yMax); + } + + this.checkHighlightMap = function() + { + if ( this.parent ) + { + this.parent.checkHighlightMap(); + } + + if ( this.getCollapse() || this == focusNode ) + { + return; + } + + var box = this.getMapPosition(); + + if + ( + mouseX > box.x - mapRadius && + mouseX < box.x + mapRadius && + mouseY > box.y - mapRadius && + mouseY < box.y + mapRadius + ) + { + highlightedNode = this; + } + } + +/* this.collapse = function() + { + for (var i = 0; i < this.children.length; i++ ) + { + this.children[i] = this.children[i].collapse(); + } + + if + ( + this.children.length == 1 && + this.children[0].magnitude == this.magnitude + ) + { + this.children[0].parent = this.parent; + this.children[0].getDepth() = this.parent.getDepth() + 1; + return this.children[0]; + } + else + { + return this; + } + } +*/ + this.draw = function(labelMode, selected, searchHighlighted) + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; +// var hidden = false; + + if ( selectedNode == this ) + { + selected = true; + } + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + var canDisplayLabelCurrent = this.canDisplayLabelCurrent(); + var hiddenSearchResults = false; + +/* if ( ! this.hide ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.children[i].hide && this.children[i].searchResults ) + { + hiddenSearchResults = true; + } + } + } +*/ + var drawChildren = + ( ! this.hide || ! this.hidePrev && progress < 1 ) && + ( ! this.hideAlone || ! this.hideAlonePrev && progress < 1 ); + +// if ( this.alphaWedge.current() > 0 || this.alphaLabel.current() > 0 ) + { + var lastChildAngleEnd = angleStartCurrent; + + if ( this.hasChildren() )//canDisplayChildren ) + { + lastChildAngleEnd = + this.children[this.children.length - 1].angleEnd.current() + + rotationOffset; + } + + if ( labelMode ) + { + var drawRadial = + !( + this.parent && + this.parent != selectedNode && + angleEndCurrent == this.parent.angleEnd.current() + rotationOffset + ); + + //if ( angleStartCurrent != angleEndCurrent ) + { + this.drawLines(angleStartCurrent, angleEndCurrent, radiusInner, drawRadial, selected); + } + + var alphaOtherCurrent = this.alphaOther.current(); + var childRadiusInner; + + if ( this == selectedNode || alphaOtherCurrent ) + { + childRadiusInner = + this.children.length ? + this.children[this.children.length - 1].radiusInner.current() * gRadius + : radiusInner + } + + if ( this == selectedNode ) + { + this.drawReferenceRings(childRadiusInner); + } + + if + ( + selected && + ! searchHighlighted && + this != selectedNode && + ( + this.isSearchResult || + this.hideAlone && this.searchResultChildren() || + false +// this.hide && +// this.containsSearchResult + ) + ) + { + context.globalAlpha = this.alphaWedge.current(); + + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + + if + ( + this.keyed && + ! showKeys && + this.searchResults && + ! searchHighlighted && + this != highlightedNode && + this != focusNode + ) + { + var angle = (angleEndCurrent + angleStartCurrent) / 2; + this.drawLabel(angle, true, false, true, true); + } + + //this.drawHighlight(false); + searchHighlighted = true; + } + + if + ( + this == selectedNode || +// true + //(canDisplayLabelCurrent) && + this != highlightedNode && + this != focusNode + ) + { + if ( this.radial != this.radialPrev && this.alphaLabel.end == 1 ) + { + context.globalAlpha = tweenFactor; + } + else + { + context.globalAlpha = this.alphaLabel.current(); + } + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + this.hideAlone && this.searchResultChildren() || + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNode && ! this.radial, + selected, + this.radial + ); + + if ( this.radial != this.radialPrev && this.alphaLabel.start == 1 && progress < 1 ) + { + context.globalAlpha = 1 - tweenFactor; + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNodeLast && ! this.radialPrev, + selected, + this.radialPrev + ); + } + } + + if + ( + alphaOtherCurrent && + lastChildAngleEnd != null + ) + { + if + ( + (angleEndCurrent - lastChildAngleEnd) * + (childRadiusInner + gRadius) >= + minWidth() + ) + { + //context.font = fontNormal; + context.globalAlpha = this.alphaOther.current(); + + drawTextPolar + ( + this.getUnclassifiedText(), + this.getUnclassifiedPercentage(), + (lastChildAngleEnd + angleEndCurrent) / 2, + (childRadiusInner + gRadius) / 2, + true, + false, + false, + 0, + 0 + ); + } + } + + if ( this == selectedNode && this.keyUnclassified && showKeys ) + { + this.drawKey + ( + (lastChildAngleEnd + angleEndCurrent) / 2, + false, + false + ); + } + } + else + { + var alphaWedgeCurrent = this.alphaWedge.current(); + + if ( alphaWedgeCurrent || this.alphaOther.current() ) + { + var currentR = this.r.current(); + var currentG = this.g.current(); + var currentB = this.b.current(); + + var fill = rgbText(currentR, currentG, currentB); + + var radiusOuter; + var lastChildAngle; + var truncateWedge = + ( + (this.hasChildren() || this == selectedNode ) && + ! this.keyed && + (compress || depth < maxDisplayDepth) && + drawChildren + ); + + if ( truncateWedge ) + { + radiusOuter = this.children.length ? this.children[0].radiusInner.current() * gRadius : radiusInner; + } + else + { + radiusOuter = gRadius; + } + /* + if ( this.hasChildren() ) + { + radiusOuter = this.children[0].getUncollapsed().radiusInner.current() * gRadius + 1; + } + else + { // TEMP + radiusOuter = radiusInner + nodeRadius * gRadius; + + if ( radiusOuter > gRadius ) + { + radiusOuter = gRadius; + } + } + */ + context.globalAlpha = alphaWedgeCurrent; + + if ( radiusInner != radiusOuter || truncateWedge ) + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + radiusOuter,//this.radiusOuter.current() * gRadius, + //'rgba(0, 200, 0, .1)', + fill, + this.alphaPattern.current() + ); + + if ( truncateWedge ) + { + // fill in the extra space if the sum of our childrens' + // magnitudes is less than ours + + if ( lastChildAngleEnd < angleEndCurrent )//&& false) // TEMP + { + if ( radiusOuter > 1 ) + { + // overlap slightly to hide the seam + + // radiusOuter -= 1; + } + + if ( alphaWedgeCurrent < 1 ) + { + context.globalAlpha = this.alphaOther.current(); + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius, + colorUnclassified, + 0 + ); + context.globalAlpha = alphaWedgeCurrent; + } + + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius,//this.radiusOuter.current() * gRadius, + //'rgba(200, 0, 0, .1)', + fill, + this.alphaPattern.current() + ); + } + } + + if ( radiusOuter < gRadius ) + { + // patch up the seam + // + context.beginPath(); + context.arc(0, 0, radiusOuter, angleStartCurrent/*lastChildAngleEnd*/, angleEndCurrent, false); + context.strokeStyle = fill; + context.lineWidth = 1; + context.stroke(); + } + } + + if ( this.keyed && selected && showKeys )//&& progress == 1 ) + { + this.drawKey + ( + (angleStartCurrent + angleEndCurrent) / 2, + ( + this == highlightedNode || + this == focusNode || + this.searchResults + ), + this == highlightedNode || this == focusNode + ); + } + } + } + } + + this.hiddenLabels = Array(); + + if ( drawChildren ) + { + // draw children + // + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.drawHiddenChildren(i, selected, labelMode, searchHighlighted) ) + { + i = this.children[i].hiddenEnd; + } + else + { + this.children[i].draw(labelMode, selected, searchHighlighted); + } + } + } + }; + + this.drawHiddenChildren = function + ( + firstHiddenChild, + selected, + labelMode, + searchHighlighted + ) + { + var firstChild = this.children[firstHiddenChild]; + + if ( firstChild.hiddenEnd == null || firstChild.radiusInner.current() == 1 ) + { + return false; + } + + for ( var i = firstHiddenChild; i < firstChild.hiddenEnd; i++ ) + { + if ( ! this.children[i].hide || ! this.children[i].hidePrev && progress < 1 ) + { + return false; + } + } + + var angleStart = firstChild.angleStart.current() + rotationOffset; + var lastChild = this.children[firstChild.hiddenEnd]; + var angleEnd = lastChild.angleEnd.current() + rotationOffset; + var radiusInner = gRadius * firstChild.radiusInner.current(); + var hiddenChildren = firstChild.hiddenEnd - firstHiddenChild + 1; + + if ( labelMode ) + { + var hiddenSearchResults = 0; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + hiddenSearchResults += this.children[i].searchResults; + + if ( this.children[i].magnitude == 0 ) + { + hiddenChildren--; + } + } + + if + ( + selected && + (angleEnd - angleStart) * + (gRadius + gRadius) >= + minWidth() || + this == highlightedNode && + hiddenChildren || + hiddenSearchResults + ) + { + context.globalAlpha = this.alphaWedge.current(); + + this.drawHiddenLabel + ( + angleStart, + angleEnd, + hiddenChildren, + hiddenSearchResults + ); + } + } + + var drawWedges = true; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + // all hidden children must be completely hidden to draw together + + if ( this.children[i].alphaPattern.current() != this.children[i].alphaWedge.current() ) + { + drawWedges = false; + break; + } + } + + if ( labelMode ) + { + if ( drawWedges ) + { + var drawRadial = (angleEnd < this.angleEnd.current() + rotationOffset); + this.drawLines(angleStart, angleEnd, radiusInner, drawRadial); + } + + if ( hiddenSearchResults && ! searchHighlighted ) + { + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + highlightFill, + 0, + true + ); + } + } + else if ( drawWedges ) + { + context.globalAlpha = this.alphaWedge.current(); + + var fill = rgbText + ( + firstChild.r.current(), + firstChild.g.current(), + firstChild.b.current() + ); + + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + fill, + context.globalAlpha, + false + ); + } + + return drawWedges; + } + + this.drawHiddenLabel = function(angleStart, angleEnd, value, hiddenSearchResults) + { + var textAngle = (angleStart + angleEnd) / 2; + var labelRadius = gRadius + fontSize;//(radiusInner + radius) / 2; + + var hiddenLabel = Array(); + + hiddenLabel.value = value; + hiddenLabel.angle = textAngle; + hiddenLabel.search = hiddenSearchResults; + + this.hiddenLabels.push(hiddenLabel); + + drawTick(gRadius - fontSize * .75, fontSize * 1.5, textAngle); + drawTextPolar + ( + value.toString() + ' more', + 0, // inner text + textAngle, + labelRadius, + true, // radial + hiddenSearchResults, // bubble + this == highlightedNode || this == focusNode, // bold + false, + hiddenSearchResults + ); + } + + this.drawHighlight = function(bold) + { + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + //this.setHighlightStyle(); + + if ( this == focusNode && this == highlightedNode && this.hasChildren() ) + { +// context.fillStyle = "rgba(255, 255, 255, .3)"; + arrow + ( + angleStartCurrent, + angleEndCurrent, + radiusInner + ); + } + else + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + } + + // check if hidden children should be highlighted + // + for ( var i = 0; i < this.children.length; i++ ) + { + if + ( + this.children[i].getDepth() - selectedNode.getDepth() + 1 <= + maxDisplayDepth && + this.children[i].hiddenEnd != null + ) + { + var firstChild = this.children[i]; + var lastChild = this.children[firstChild.hiddenEnd]; + var hiddenAngleStart = firstChild.angleStart.current() + rotationOffset; + var hiddenAngleEnd = lastChild.angleEnd.current() + rotationOffset; + var hiddenRadiusInner = gRadius * firstChild.radiusInner.current(); + + drawWedge + ( + hiddenAngleStart, + hiddenAngleEnd, + hiddenRadiusInner, + gRadius, + 'rgba(255, 255, 255, .3)', + 0, + true + ); + + if ( false && ! this.searchResults ) + { + this.drawHiddenLabel + ( + hiddenAngleStart, + hiddenAngleEnd, + firstChild.hiddenEnd - i + 1 + ); + } + + i = firstChild.hiddenEnd; + } + } + +// context.strokeStyle = 'black'; + context.fillStyle = 'black'; + + var highlight = ! ( progress < 1 && zoomOut && this == selectedNodeLast ); + + var angle = (angleEndCurrent + angleStartCurrent) / 2; + + if ( ! (this.keyed && showKeys) ) + { + this.drawLabel(angle, true, bold, true, this.radial); + } + } + + this.drawHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + context.lineWidth = highlightLineWidth; + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .6)"; + + context.fillStyle = 'black'; + this.drawLabel(3 * Math.PI / 2, true, true, false); + context.font = fontNormal; + } + + this.drawKey = function(angle, highlight, bold) + { + var offset = keyOffset(); + var color; + var colorText = this.magnitude == 0 ? 'gray' : 'black'; + var patternAlpha = this.alphaPattern.end; + var boxLeft = imageWidth - keySize - margin; + var textY = offset + keySize / 2; + + var label; + var keyNameWidth; + + if ( this == selectedNode ) + { + color = colorUnclassified; + label = + this.getUnclassifiedText() + + ' ' + + this.getUnclassifiedPercentage(); + keyNameWidth = measureText(label, false); + } + else + { + label = this.keyLabel; + color = rgbText(this.r.end, this.g.end, this.b.end); + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + label = label + searchResultString(this.searchResultChildren()); + } + + keyNameWidth = measureText(label, bold); + } + else + { + keyNameWidth = this.keyNameWidth; + } + } + + var textLeft = boxLeft - keyBuffer - keyNameWidth - fontSize / 2; + var labelLeft = textLeft; + + if ( labelLeft > keyMinTextLeft - fontSize / 2 ) + { + keyMinTextLeft -= fontSize / 2; + + if ( keyMinTextLeft < centerX - gRadius + fontSize / 2 ) + { + keyMinTextLeft = centerX - gRadius + fontSize / 2; + } + + labelLeft = keyMinTextLeft; + } + + var lineX = new Array(); + var lineY = new Array(); + + var bendRadius; + var keyAngle = Math.atan((textY - centerY) / (labelLeft - centerX)); + var arcAngle; + + if ( keyAngle < 0 ) + { + keyAngle += Math.PI; + } + + if ( keyMinAngle == 0 || angle < keyMinAngle ) + { + keyMinAngle = angle; + } + + if ( angle > Math.PI && keyMinAngle > Math.PI ) + { + // allow lines to come underneath the chart + + angle -= Math.PI * 2; + } + + lineX.push(Math.cos(angle) * gRadius); + lineY.push(Math.sin(angle) * gRadius); + + if ( angle < keyAngle && textY > centerY + Math.sin(angle) * (gRadius + buffer * (currentKey - 1) / (keys + 1) / 2 + buffer / 2) ) + { + bendRadius = gRadius + buffer - buffer * currentKey / (keys + 1) / 2; + } + else + { + bendRadius = gRadius + buffer * currentKey / (keys + 1) / 2 + buffer / 2; + } + + var outside = + Math.sqrt + ( + Math.pow(labelLeft - centerX, 2) + + Math.pow(textY - centerY, 2) + ) > bendRadius; + + if ( ! outside ) + { + arcAngle = Math.asin((textY - centerY) / bendRadius); + + keyMinTextLeft = min(keyMinTextLeft, centerX + bendRadius * Math.cos(arcAngle) - fontSize / 2); + + if ( labelLeft < textLeft && textLeft > centerX + bendRadius * Math.cos(arcAngle) ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + else + { + keyMinTextLeft = min(keyMinTextLeft, labelLeft - fontSize / 2); + + if ( angle < keyAngle ) + { + // flip everything over y = x + // + arcAngle = Math.PI / 2 - keyLineAngle + ( + Math.PI / 2 - angle, + Math.PI / 2 - keyAngle, + bendRadius, + textY - centerY, + labelLeft - centerX, + lineY, + lineX + ); + + } + else + { + arcAngle = keyLineAngle + ( + angle, + keyAngle, + bendRadius, + labelLeft - centerX, + textY - centerY, + lineX, + lineY + ); + } + } + + if ( labelLeft > centerX + bendRadius * Math.cos(arcAngle) || + textY > centerY + bendRadius * Math.sin(arcAngle) + .01) +// if ( outside || ) + { + lineX.push(labelLeft - centerX); + lineY.push(textY - centerY); + + if ( textLeft != labelLeft ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + + context.globalAlpha = this.alphaWedge.current(); + + if ( snapshotMode ) + { + var labelSVG; + + if ( this == selectedNode ) + { + labelSVG = + this.getUnclassifiedText() + + spacer() + + this.getUnclassifiedPercentage(); + } + else + { + labelSVG = this.name + spacer() + this.getPercentage() + '%'; + } + + svg += + '<rect fill="' + color + '" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + + if ( patternAlpha ) + { + svg += + '<rect fill="url(#hiddenPattern)" style="stroke:none" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + } + + svg += + '<path class="line' + + (highlight ? ' highlight' : '') + + '" d="M ' + (lineX[0] + centerX) + ',' + + (lineY[0] + centerY); + + if ( angle != arcAngle ) + { + svg += + ' L ' + (centerX + bendRadius * Math.cos(angle)) + ',' + + (centerY + bendRadius * Math.sin(angle)) + + ' A ' + bendRadius + ',' + bendRadius + ' 0 ' + + '0,' + (angle > arcAngle ? '0' : '1') + ' ' + + (centerX + bendRadius * Math.cos(arcAngle)) + ',' + + (centerY + bendRadius * Math.sin(arcAngle)); + } + + for ( var i = 1; i < lineX.length; i++ ) + { + svg += + ' L ' + (centerX + lineX[i]) + ',' + + (centerY + lineY[i]); + } + + svg += '"/>'; + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + labelSVG = labelSVG + searchResultString(this.searchResultChildren()); + } + + drawBubbleSVG + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + svg += svgText(labelSVG, boxLeft - keyBuffer, textY, 'end', bold, colorText); + } + else + { + context.fillStyle = color; + context.translate(-centerX, -centerY); + context.strokeStyle = 'black'; + context.globalAlpha = 1;//this.alphaWedge.current(); + + context.fillRect(boxLeft, offset, keySize, keySize); + + if ( patternAlpha ) + { + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + + // make clipping box for Firefox performance + context.beginPath(); + context.moveTo(boxLeft, offset); + context.lineTo(boxLeft + keySize, offset); + context.lineTo(boxLeft + keySize, offset + keySize); + context.lineTo(boxLeft, offset + keySize); + context.closePath(); + context.save(); + context.clip(); + + context.fillRect(boxLeft, offset, keySize, keySize); + context.fillRect(boxLeft, offset, keySize, keySize); + + context.restore(); // remove clipping region + } + + if ( highlight ) + { + this.setHighlightStyle(); + context.fillRect(boxLeft, offset, keySize, keySize); + } + else + { + context.lineWidth = thinLineWidth; + } + + context.strokeRect(boxLeft, offset, keySize, keySize); + + if ( lineX.length ) + { + context.beginPath(); + context.moveTo(lineX[0] + centerX, lineY[0] + centerY); + + context.arc(centerX, centerY, bendRadius, angle, arcAngle, angle > arcAngle); + + for ( var i = 1; i < lineX.length; i++ ) + { + context.lineTo(lineX[i] + centerX, lineY[i] + centerY); + } + + context.globalAlpha = this == selectedNode ? + this.children[0].alphaWedge.current() : + this.alphaWedge.current(); + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.stroke(); + context.globalAlpha = 1; + } + + if ( highlight ) + { + drawBubbleCanvas + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + drawText(label, boxLeft - keyBuffer, offset + keySize / 2, 0, 'end', bold, colorText); + + context.translate(centerX, centerY); + } + + currentKey++; + } + + this.drawLabel = function(angle, bubble, bold, selected, radial) + { + if ( context.globalAlpha == 0 ) + { + return; + } + + var innerText; + var label; + var radius; + + if ( radial ) + { + radius = (this.radiusInner.current() + 1) * gRadius / 2; + } + else + { + radius = this.labelRadius.current() * gRadius; + } + + if ( radial && (selected || bubble ) ) + { + var percentage = this.getPercentage(); + innerText = percentage + '%'; + } + + if + ( + ! radial && + this != selectedNode && + ! bubble && + ( !zoomOut || this != selectedNodeLast) + ) + { + label = this.shortenLabel(); + } + else + { + label = this.name; + } + + var flipped = drawTextPolar + ( + label, + innerText, + angle, + radius, + radial, + bubble, + bold, +// this.isSearchResult && this.shouldAddSearchResultsString() && (!selected || this == selectedNode || highlight), + this.isSearchResult && (!selected || this == selectedNode || bubble), + (this.hideAlone || !selected || this == selectedNode ) ? this.searchResultChildren() : 0 + ); + + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + if + ( + ! radial && + ! bubble && + this != selectedNode && + this.angleEnd.end != this.angleStart.end && + nLabelOffsets[depth - 2] > 2 && + this.labelWidth.current() > (this.angleEnd.end - this.angleStart.end) * Math.abs(radius) && + ! ( zoomOut && this == selectedNodeLast ) && + this.labelRadius.end > 0 + ) + { + // name extends beyond wedge; draw tick mark towards the central + // radius for easier identification + + var radiusCenter = compress ? + (compressedRadii[depth - 1] + compressedRadii[depth - 2]) / 2 : + (depth - .5) * nodeRadius; + + if ( this.labelRadius.end > radiusCenter ) + { + if ( flipped ) + { + drawTick(radius - tickLength * 1.4 , tickLength, angle); + } + else + { + drawTick(radius - tickLength * 1.7, tickLength, angle); + } + } + else + { + if ( flipped ) + { + drawTick(radius + tickLength * .7, tickLength, angle); + } + else + { + drawTick(radius + tickLength * .4, tickLength, angle); + } + } + } + } + + this.drawLines = function(angleStart, angleEnd, radiusInner, drawRadial, selected) + { + if ( snapshotMode ) + { + if ( this != selectedNode) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + if ( this.alphaArc.end ) + { + var dArray = + [ + " M ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, + " 0 ", x1, ",", y1 + ]; + + svg += '<path class="line" d="' + dArray.join('') + '"/>'; + } + + if ( drawRadial && this.alphaLine.end ) + { + svg += '<line x1="' + x3 + '" y1="' + y3 + '" x2="' + x4 + '" y2="' + y4 + '"/>'; + } + } + } + else + { + context.lineWidth = thinLineWidth; + context.strokeStyle = 'black'; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.globalAlpha = this.alphaArc.current(); + context.stroke(); + + if ( drawRadial ) + { + var x1 = radiusInner * Math.cos(angleEnd); + var y1 = radiusInner * Math.sin(angleEnd); + var x2 = gRadius * Math.cos(angleEnd); + var y2 = gRadius * Math.sin(angleEnd); + + context.beginPath(); + context.moveTo(x1, y1); + context.lineTo(x2, y2); + +// if ( this.getCollapse() )//( selected && this != selectedNode ) + { + context.globalAlpha = this.alphaLine.current(); + } + + context.stroke(); + } + } + } + + this.drawMap = function(child) + { + if ( this.parent ) + { + this.parent.drawMap(child); + } + + if ( this.getCollapse() && this != child || this == focusNode ) + { + return; + } + + var angleStart = + (child.baseMagnitude - this.baseMagnitude) / this.magnitude * Math.PI * 2 + + rotationOffset; + var angleEnd = + (child.baseMagnitude - this.baseMagnitude + child.magnitude) / + this.magnitude * Math.PI * 2 + + rotationOffset; + + var box = this.getMapPosition(); + + context.save(); + context.fillStyle = 'black'; + context.textAlign = 'end'; + context.textBaseline = 'middle'; + + var textX = box.x - mapRadius - mapBuffer; + var percentage = getPercentage(child.magnitude / this.magnitude); + + var highlight = this == selectedNode || this == highlightedNode; + + if ( highlight ) + { + context.font = fontBold; + } + else + { + context.font = fontNormal; + } + + context.fillText(percentage + '% of', textX, box.y - mapRadius / 3); + context.fillText(this.name, textX, box.y + mapRadius / 3); + + if ( highlight ) + { + context.font = fontNormal; + } + + if ( this == highlightedNode && this != selectedNode ) + { + context.fillStyle = 'rgb(245, 245, 245)'; +// context.fillStyle = 'rgb(200, 200, 200)'; + } + else + { + context.fillStyle = 'rgb(255, 255, 255)'; + } + + context.beginPath(); + context.arc(box.x, box.y, mapRadius, 0, Math.PI * 2, true); + context.closePath(); + context.fill(); + + if ( this == selectedNode ) + { + context.lineWidth = 1; + context.fillStyle = 'rgb(100, 100, 100)'; + } + else + { + if ( this == highlightedNode ) + { + context.lineWidth = .2; + context.fillStyle = 'rgb(190, 190, 190)'; + } + else + { + context.lineWidth = .2; + context.fillStyle = 'rgb(200, 200, 200)'; + } + } + + var maxDepth = this.getMaxDepth(); + + if ( ! compress && maxDepth > maxPossibleDepth + this.getDepth() - 1 ) + { + maxDepth = maxPossibleDepth + this.getDepth() - 1; + } + + if ( this.getDepth() < selectedNode.getDepth() ) + { + if ( child.getDepth() - 1 >= maxDepth ) + { + maxDepth = child.getDepth(); + } + } + + var radiusInner; + + if ( compress ) + { + radiusInner = 0; +// Math.atan(child.getDepth() - this.getDepth()) / +// Math.PI * 2 * .9; + } + else + { + radiusInner = + (child.getDepth() - this.getDepth()) / + (maxDepth - this.getDepth() + 1); + } + + context.stroke(); + context.beginPath(); + + if ( radiusInner == 0 ) + { + context.moveTo(box.x, box.y); + } + else + { + context.arc(box.x, box.y, mapRadius * radiusInner, angleEnd, angleStart, true); + } + + context.arc(box.x, box.y, mapRadius, angleStart, angleEnd, false); + context.closePath(); + context.fill(); + + if ( this == highlightedNode && this != selectedNode ) + { + context.lineWidth = 1; + context.stroke(); + } + + context.restore(); + } + + this.drawReferenceRings = function(childRadiusInner) + { + if ( snapshotMode ) + { + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + childRadiusInner + '"/>'; + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + gRadius + '"/>'; + } + else + { + context.globalAlpha = 1 - this.alphaLine.current();//this.getUncollapsed().alphaLine.current(); + context.beginPath(); + context.arc(0, 0, childRadiusInner, 0, Math.PI * 2, false); + context.stroke(); + context.beginPath(); + context.arc(0, 0, gRadius, 0, Math.PI * 2, false); + context.stroke(); + } + } + + this.getCollapse = function() + { + return ( + collapse && + this.collapse && + this.depth != maxAbsoluteDepth + ); + } + + this.getDepth = function() + { + if ( collapse ) + { + return this.depthCollapsed; + } + else + { + return this.depth; + } + } + + this.getMagnitude = function() + { + return this.attributes[magnitudeIndex][currentDataset]; + } + + this.getMapPosition = function() + { + return { + x : (details.offsetLeft + details.clientWidth - mapRadius), + y : ((focusNode.getDepth() - this.getDepth()) * + (mapBuffer + mapRadius * 2) - mapRadius) + + details.clientHeight + details.offsetTop + }; + } + + this.getMaxDepth = function(limit) + { + var max; + + if ( collapse ) + { + return this.maxDepthCollapsed; + } + else + { + if ( this.maxDepth > maxAbsoluteDepth ) + { + return maxAbsoluteDepth; + } + else + { + return this.maxDepth; + } + } + } + + this.getData = function(index, summary) + { + var files = new Array(); + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null && + this.attributes[index][currentDataset] != '' + ) + { + files.push + ( + document.location + + '.files/' + + this.attributes[index][currentDataset] + ); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + files = files.concat(this.children[i].getData(index, true)); + } + } + + return files; + } + + this.getList = function(index, summary) + { + var list; + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null + ) + { + list = this.attributes[index][currentDataset]; + } + else + { + list = new Array(); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + list = list.concat(this.children[i].getList(index, true)); + } + } + + return list; + } + + this.getParent = function() + { + // returns parent, accounting for collapsing or 0 if doesn't exist + + var parent = this.parent; + + while ( parent != 0 && parent.getCollapse() ) + { + parent = parent.parent; + } + + return parent; + } + + this.getPercentage = function() + { + return getPercentage(this.magnitude / selectedNode.magnitude); + } + + this.getUnclassifiedPercentage = function() + { + if ( this.children.length ) + { + var lastChild = this.children[this.children.length - 1]; + + return getPercentage + ( + ( + this.baseMagnitude + + this.magnitude - + lastChild.magnitude - + lastChild.baseMagnitude + ) / this.magnitude + ) + '%'; + } + else + { + return '100%'; + } + } + + this.getUnclassifiedText = function() + { + return '[other '+ this.name + ']'; + } + + this.getUncollapsed = function() + { + // recurse through collapsed children until uncollapsed node is found + + if ( this.getCollapse() ) + { + return this.children[0].getUncollapsed(); + } + else + { + return this; + } + } + + this.hasChildren = function() + { + return this.children.length && this.depth < maxAbsoluteDepth && this.magnitude; + } + + this.hasParent = function(parent) + { + if ( this.parent ) + { + if ( this.parent == parent ) + { + return true; + } + else + { + return this.parent.hasParent(parent); + } + } + else + { + return false; + } + } + + this.maxVisibleDepth = function(maxDepth) + { + var childInnerRadius; + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var currentMaxDepth = depth; + + if ( this.hasChildren() && depth < maxDepth) + { + var lastChild = this.children[this.children.length - 1]; + + if ( this.name == 'Pseudomonadaceae' ) + { + var x = 3; + } + + if + ( + lastChild.baseMagnitude + lastChild.magnitude < + this.baseMagnitude + this.magnitude + ) + { + currentMaxDepth++; + } + + if ( compress ) + { + childInnerRadius = compressedRadii[depth - 1]; + } + else + { + childInnerRadius = (depth) / maxDepth; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + if + (//true || + this.children[i].magnitude * + angleFactor * + (childInnerRadius + 1) * + gRadius >= + minWidth() + ) + { + var childMaxDepth = this.children[i].maxVisibleDepth(maxDepth); + + if ( childMaxDepth > currentMaxDepth ) + { + currentMaxDepth = childMaxDepth; + } + } + } + } + + return currentMaxDepth; + } + + this.resetLabelWidth = function() + { + var nameWidthOld = this.nameWidth; + + if ( true || ! this.radial )//&& fontSize != fontSizeLast ) + { + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + } + + if ( fontSize != fontSizeLast && this.labelWidth.end == nameWidthOld * labelWidthFudge ) + { + // font size changed; adjust start of tween to match + + this.labelWidth.start = this.nameWidth * labelWidthFudge; + } + else + { + this.labelWidth.start = this.labelWidth.current(); + } + + this.labelWidth.end = this.nameWidth * labelWidthFudge; + } + + this.restrictLabelWidth = function(width) + { + if ( width < this.labelWidth.end ) + { + this.labelWidth.end = width; + } + } + + this.search = function() + { + this.isSearchResult = false; + this.searchResults = 0; + + if + ( + ! this.getCollapse() && + search.value != '' && + this.name.toLowerCase().indexOf(search.value.toLowerCase()) != -1 + ) + { + this.isSearchResult = true; + this.searchResults = 1; + nSearchResults++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.searchResults += this.children[i].search(); + } + + return this.searchResults; + } + + this.searchResultChildren = function() + { + if ( this.isSearchResult ) + { + return this.searchResults - 1; + } + else + { + return this.searchResults; + } + } + + this.setDepth = function(depth, depthCollapsed) + { + this.depth = depth; + this.depthCollapsed = depthCollapsed; + + if + ( + this.children.length == 1 && +// this.magnitude > 0 && + this.children[0].magnitude == this.magnitude && + ( head.children.length > 1 || this.children[0].children.length ) + ) + { + this.collapse = true; + } + else + { + this.collapse = false; + depthCollapsed++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setDepth(depth + 1, depthCollapsed); + } + } + + this.setHighlightStyle = function() + { + context.lineWidth = highlightLineWidth; + + if ( this.hasChildren() || this != focusNode || this != highlightedNode ) + { + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .3)"; + } + else + { + context.strokeStyle = 'rgb(90,90,90)'; + context.fillStyle = "rgba(155, 155, 155, .3)"; + } + } + + this.setLabelWidth = function(node) + { + if ( ! shorten || this.radial ) + { + return; // don't need to set width + } + + if ( node.hide ) + { + alert('wtf'); + return; + } + + var angle = (this.angleStart.end + this.angleEnd.end) / 2; + var a; // angle difference + + if ( node == selectedNode ) + { + a = Math.abs(angle - node.angleOther); + } + else + { + a = Math.abs(angle - (node.angleStart.end + node.angleEnd.end) / 2); + } + + if ( a == 0 ) + { + return; + } + + if ( a > Math.PI ) + { + a = 2 * Math.PI - a; + } + + if ( node.radial || node == selectedNode ) + { + var nodeLabelRadius; + + if ( node == selectedNode ) + { + // radial 'other' label + + nodeLabelRadius = (node.children[0].radiusInner.end + 1) / 2; + } + else + { + nodeLabelRadius = (node.radiusInner.end + 1) / 2; + } + + if ( a < Math.PI / 2 ) + { + var r = this.labelRadius.end * gRadius + .5 * fontSize + var hypotenuse = r / Math.cos(a); + var opposite = r * Math.tan(a); + var fontRadius = .8 * fontSize; + + if + ( + nodeLabelRadius * gRadius < hypotenuse && + this.labelWidth.end / 2 + fontRadius > opposite + ) + { + this.labelWidth.end = 2 * (opposite - fontRadius); + } + } + } + else if + ( + this.labelRadius.end == node.labelRadius.end && + a < Math.PI / 4 + ) + { + // same radius with small angle; use circumferential approximation + + var dist = a * this.labelRadius.end * gRadius - fontSize * (1 - a * 4 / Math.PI) * 1.3; + + if ( this.labelWidth.end < dist ) + { + node.restrictLabelWidth((dist - this.labelWidth.end / 2) * 2); + } + else if ( node.labelWidth.end < dist ) + { + this.restrictLabelWidth((dist - node.labelWidth.end / 2) * 2); + } + else + { + // both labels reach halfway point; restrict both + + this.labelWidth.end = dist; + node.labelWidth.end = dist + } + } + else + { + var r1 = this.labelRadius.end * gRadius; + var r2 = node.labelRadius.end * gRadius; + + // first adjust the radii to account for the height of the font by shifting them + // toward each other + // + var fontFudge = .35 * fontSize; + // + if ( this.labelRadius.end < node.labelRadius.end ) + { + r1 += fontFudge; + r2 -= fontFudge; + } + else if ( this.labelRadius.end > node.labelRadius.end ) + { + r1 -= fontFudge; + r2 += fontFudge; + } + else + { + r1 -= fontFudge; + r2 -= fontFudge; + } + + var r1s = r1 * r1; + var r2s = r2 * r2; + + // distance between the centers of the two labels + // + var dist = Math.sqrt(r1s + r2s - 2 * r1 * r2 * Math.cos(a)); + + // angle at our label center between our radius and the line to the other label center + // + var b = Math.acos((r1s + dist * dist - r2s) / (2 * r1 * dist)); + + // distance from our label center to the intersection of the two tangents + // + var l1 = Math.sin(a + b - Math.PI / 2) * dist / Math.sin(Math.PI - a); + + // distance from other label center the the intersection of the two tangents + // + var l2 = Math.sin(Math.PI / 2 - b) * dist / Math.sin(Math.PI - a); + + l1 = Math.abs(l1) - .4 * fontSize; + l2 = Math.abs(l2) - .4 * fontSize; +/* + // amount to shorten the distances because of the height of the font + // + var l3 = 0; + var fontRadius = fontSize * .55; + // + if ( l1 < 0 || l2 < 0 ) + { + var l4 = fontRadius / Math.tan(a); + l1 = Math.abs(l1); + l2 = Math.abs(l2); + + l1 -= l4; + l2 -= l4; + } + else + { + var c = Math.PI - a; + + l3 = fontRadius * Math.tan(c / 2); + } +*/ + if ( this.labelWidth.end / 2 > l1 && node.labelWidth.end / 2 > l2 ) + { + // shorten the farthest one from the intersection + + if ( l1 > l2 ) + { + this.restrictLabelWidth(2 * (l1));// - l3 - fontRadius)); + } + else + { + node.restrictLabelWidth(2 * (l2));// - l3 - fontRadius)); + } + }/* + else if ( this.labelWidth.end / 2 > l1 + l3 && node.labelWidth.end / 2 > l2 - l3 ) + { + node.restrictLabelWidth(2 * (l2 - l3)); + } + else if ( this.labelWidth.end / 2 > l1 - l3 && node.labelWidth.end / 2 > l2 + l3 ) + { + this.restrictLabelWidth(2 * (l1 - l3)); + }*/ + } + } + + this.setMagnitudes = function(baseMagnitude) + { + this.magnitude = this.getMagnitude(); + this.baseMagnitude = baseMagnitude; + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setMagnitudes(baseMagnitude); + baseMagnitude += this.children[i].magnitude; + } + + this.maxChildMagnitude = baseMagnitude; + } + + this.setMaxDepths = function() + { + this.maxDepth = this.depth; + this.maxDepthCollapsed = this.depthCollapsed; + + for ( i in this.children ) + { + var child = this.children[i]; + + child.setMaxDepths(); + + if ( child.maxDepth > this.maxDepth ) + { + this.maxDepth = child.maxDepth; + } + + if + ( + child.maxDepthCollapsed > this.maxDepthCollapsed && + (child.depth <= maxAbsoluteDepth || maxAbsoluteDepth == 0) + ) + { + this.maxDepthCollapsed = child.maxDepthCollapsed; + } + } + } + + this.setTargetLabelRadius = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var index = depth - 2; + var labelOffset = labelOffsets[index]; + + if ( this.radial ) + { + //this.labelRadius.setTarget((this.radiusInner.end + 1) / 2); + var max = + depth == maxDisplayDepth ? + 1 : + compressedRadii[index + 1]; + + this.labelRadius.setTarget((compressedRadii[index] + max) / 2); + } + else + { + var radiusCenter; + var width; + + if ( compress ) + { + if ( nLabelOffsets[index] > 1 ) + { + this.labelRadius.setTarget + ( + lerp + ( + labelOffset + .75, + 0, + nLabelOffsets[index] + .5, + compressedRadii[index], + compressedRadii[index + 1] + ) + ); + } + else + { + this.labelRadius.setTarget((compressedRadii[index] + compressedRadii[index + 1]) / 2); + } + } + else + { + radiusCenter = + nodeRadius * (depth - 1) + + nodeRadius / 2; + width = nodeRadius; + + this.labelRadius.setTarget + ( + radiusCenter + width * ((labelOffset + 1) / (nLabelOffsets[index] + 1) - .5) + ); + } + } + + if ( ! this.hide && ! this.keyed && nLabelOffsets[index] ) + { + // check last and first labels in each track for overlap + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + var last = labelLastNodes[i][j]; + var first = labelFirstNodes[i][j]; + + if ( last ) + { + if ( j == nLabelOffsets[i] ) + { + // last is radial + this.setLabelWidth(last); + } + else + { + last.setLabelWidth(this); + } + } + + if ( first ) + { + if ( j == nLabelOffsets[i] ) + { + this.setLabelWidth(first); + } + else + { + first.setLabelWidth(this); + } + } + } + } + + if ( selectedNode.canDisplayLabelOther ) + { + this.setLabelWidth(selectedNode); // in case there is an 'other' label + } + + if ( this.radial ) + { + // use the last 'track' of this depth for radial + + labelLastNodes[index][nLabelOffsets[index]] = this; + + if ( labelFirstNodes[index][nLabelOffsets[index]] == 0 ) + { + labelFirstNodes[index][nLabelOffsets[index]] = this; + } + } + else + { + labelLastNodes[index][labelOffset] = this; + + // update offset + + labelOffsets[index] += 1; + + if ( labelOffsets[index] > nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]--; + } + } + else if ( labelOffsets[index] == nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( false && !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]++; + } + } + + if ( labelFirstNodes[index][labelOffset] == 0 ) + { + labelFirstNodes[index][labelOffset] = this; + } + } + } + else if ( this.hide ) + { + this.labelWidth.end = 0; + } + } + + this.setTargets = function() + { + if ( this == selectedNode ) + { + this.setTargetsSelected + ( + 0, + 1, + lightnessBase, + false, + false + ); + return; + } + + var depthRelative = this.getDepth() - selectedNode.getDepth(); + + var parentOfSelected = selectedNode.hasParent(this); +/* ( +// ! this.getCollapse() && + this.baseMagnitude <= selectedNode.baseMagnitude && + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ); +*/ + if ( parentOfSelected ) + { + this.resetLabelWidth(); + } + else + { + //context.font = fontNormal; + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + //this.labelWidth.setTarget(this.labelWidth.end); + this.labelWidth.setTarget(0); + } + + // set angles + // + if ( this.baseMagnitude <= selectedNode.baseMagnitude ) + { + this.angleStart.setTarget(0); + } + else + { + this.angleStart.setTarget(Math.PI * 2); + } + // + if + ( + parentOfSelected || + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ) + { + this.angleEnd.setTarget(Math.PI * 2); + } + else + { + this.angleEnd.setTarget(0); + } + + // children + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargets(); + } + + if ( this.getDepth() <= selectedNode.getDepth() ) + { + // collapse in + + this.radiusInner.setTarget(0); + + if ( parentOfSelected ) + { + this.labelRadius.setTarget + ( + (depthRelative) * + historySpacingFactor * fontSize / gRadius + ); + //this.scale.setTarget(1 - (selectedNode.getDepth() - this.getDepth()) / 18); // TEMP + } + else + { + this.labelRadius.setTarget(0); + //this.scale.setTarget(1); // TEMP + } + } + else if ( depthRelative + 1 > maxDisplayDepth ) + { + // collapse out + + this.radiusInner.setTarget(1); + this.labelRadius.setTarget(1); + //this.scale.setTarget(1); // TEMP + } + else + { + // don't collapse + + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depthRelative - 1]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depthRelative)); + } + + //this.scale.setTarget(1); // TEMP + + if ( this == selectedNode ) + { + this.labelRadius.setTarget(0); + } + else + { + if ( compress ) + { + this.labelRadius.setTarget + ( + (compressedRadii[depthRelative - 1] + compressedRadii[depthRelative]) / 2 + ); + } + else + { + this.labelRadius.setTarget(nodeRadius * (depthRelative) + nodeRadius / 2); + } + } + } + +// this.r.start = this.r.end; +// this.g.start = this.g.end; +// this.b.start = this.b.end; + + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + + this.alphaLine.setTarget(0); + this.alphaArc.setTarget(0); + this.alphaWedge.setTarget(0); + this.alphaPattern.setTarget(0); + this.alphaOther.setTarget(0); + + if ( parentOfSelected && ! this.getCollapse() ) + { + var alpha = + ( + 1 - + (selectedNode.getDepth() - this.getDepth()) / + (Math.floor((compress ? compressedRadii[0] : nodeRadius) * gRadius / (historySpacingFactor * fontSize) - .5) + 1) + ); + + if ( alpha < 0 ) + { + alpha = 0; + } + + this.alphaLabel.setTarget(alpha); + this.radial = false; + } + else + { + this.alphaLabel.setTarget(0); + } + + this.hideAlonePrev = this.hideAlone; + this.hidePrev = this.hide; + + if ( parentOfSelected ) + { + this.hideAlone = false; + this.hide = false; + } + + if ( this.getParent() == selectedNode.getParent() ) + { + this.hiddenEnd = null; + } + + this.radialPrev = this.radial; + } + + this.setTargetsSelected = function(hueMin, hueMax, lightness, hide, nextSiblingHidden) + { + var collapse = this.getCollapse(); + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var canDisplayChildLabels = false; + var lastChild; + + if ( this.hasChildren() )//&& ! hide ) + { + lastChild = this.children[this.children.length - 1]; + this.hideAlone = true; + } + else + { + this.hideAlone = false; + } + + // set child wedges + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargetWedge(); + + if + ( + ! this.children[i].hide && + ( collapse || depth < maxDisplayDepth ) && + this.depth < maxAbsoluteDepth + ) + { + canDisplayChildLabels = true; + this.hideAlone = false; + } + } + + if ( this == selectedNode || lastChild && lastChild.angleEnd.end < this.angleEnd.end - .01) + { + this.hideAlone = false; + } + + if ( this.hideAlonePrev == undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + if ( this == selectedNode ) + { + var otherArc = + this.children.length ? + angleFactor * + ( + this.baseMagnitude + this.magnitude - + lastChild.baseMagnitude - lastChild.magnitude + ) + : this.baseMagnitude + this.magnitude; + this.canDisplayLabelOther = + this.children.length ? + otherArc * + (this.children[0].radiusInner.end + 1) * gRadius >= + minWidth() + : true; + + this.keyUnclassified = false; + + if ( this.canDisplayLabelOther ) + { + this.angleOther = Math.PI * 2 - otherArc / 2; + } + else if ( otherArc > 0.0000000001 ) + { + this.keyUnclassified = true; + keys++; + } + + this.angleStart.setTarget(0); + this.angleEnd.setTarget(Math.PI * 2); + + if ( this.children.length ) + { + this.radiusInner.setTarget(0); + } + else + { + this.radiusInner.setTarget(compressedRadii[0]); + } + + this.hidePrev = this.hide; + this.hide = false; + this.hideAlonePrev = this.hideAlone; + this.hideAlone = false; + this.keyed = false; + } + + if ( hueMax - hueMin > 1 / 12 ) + { + hueMax = hueMin + 1 / 12; + } + + // set lightness + // + if ( ! ( hide || this.hideAlone ) ) + { + if ( useHue() ) + { + lightness = (lightnessBase + lightnessMax) / 2; + } + else + { + lightness = lightnessBase + (depth - 1) * lightnessFactor; + + if ( lightness > lightnessMax ) + { + lightness = lightnessMax; + } + } + } + + if ( hide ) + { + this.hide = true; + } + + if ( this.hidePrev == undefined ) + { + this.hidePrev = this.hide; + } + + var hiddenStart = -1; + var hiddenHueNumer = 0; + var hiddenHueDenom = 0; + var i = 0; + + if ( ! this.hide ) + { + this.hiddenEnd = null; + } + + while ( true ) + { + if ( ! this.hideAlone && ! hide && ( i == this.children.length || ! this.children[i].hide ) ) + { + // reached a non-hidden child or the end; set targets for + // previous group of hidden children (if any) using their + // average hue + + if ( hiddenStart != -1 ) + { + var hiddenHue = hiddenHueDenom ? hiddenHueNumer / hiddenHueDenom : hueMin; + + for ( var j = hiddenStart; j < i; j++ ) + { + this.children[j].setTargetsSelected + ( + hiddenHue, + null, + lightness, + false, + j < i - 1 + ); + + this.children[j].hiddenEnd = null; + } + + this.children[hiddenStart].hiddenEnd = i - 1; + } + } + + if ( i == this.children.length ) + { + break; + } + + var child = this.children[i]; + var childHueMin; + var childHueMax; + + if ( this.magnitude > 0 && ! this.hide && ! this.hideAlone ) + { + if ( useHue() ) + { + childHueMin = child.hues[currentDataset]; + } + else if ( this == selectedNode ) + { + var min = 0.0; + var max = 1.0; + + if ( this.children.length > 6 ) + { + childHueMin = lerp((1 - Math.pow(1 - i / this.children.length, 1.4)) * .95, 0, 1, min, max); + childHueMax = lerp((1 - Math.pow(1 - (i + .55) / this.children.length, 1.4)) * .95, 0, 1, min, max); + } + else + { + childHueMin = lerp(i / this.children.length, 0, 1, min, max); + childHueMax = lerp((i + .55) / this.children.length, 0, 1, min, max); + } + } + else + { + childHueMin = lerp + ( + child.baseMagnitude, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + childHueMax = lerp + ( + child.baseMagnitude + child.magnitude * .99, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + } + } + else + { + childHueMin = hueMin; + childHueMax = hueMax; + } + + if ( ! this.hideAlone && ! hide && ! this.hide && child.hide ) + { + if ( hiddenStart == -1 ) + { + hiddenStart = i; + } + + if ( useHue() ) + { + hiddenHueNumer += childHueMin * child.magnitude; + hiddenHueDenom += child.magnitude; + } + else + { + hiddenHueNumer += childHueMin; + hiddenHueDenom++; + } + } + else + { + hiddenStart = -1; + + this.children[i].setTargetsSelected + ( + childHueMin, + childHueMax, + lightness, + hide || this.keyed || this.hideAlone || this.hide && ! collapse, + false + ); + } + + i++; + } + + if ( this.hue && this.magnitude ) + { + this.hue.setTarget(this.hues[currentDataset]); + + if ( this.attributes[magnitudeIndex][lastDataset] == 0 ) + { + this.hue.start = this.hue.end; + } + } + + this.radialPrev = this.radial; + + if ( this == selectedNode ) + { + this.resetLabelWidth(); + this.labelWidth.setTarget(this.nameWidth * labelWidthFudge); + this.alphaWedge.setTarget(0); + this.alphaLabel.setTarget(1); + this.alphaOther.setTarget(1); + this.alphaArc.setTarget(0); + this.alphaLine.setTarget(0); + this.alphaPattern.setTarget(0); + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + this.radial = false; + this.labelRadius.setTarget(0); + } + else + { + var rgb = hslToRgb + ( + hueMin, + saturation, + lightness + ); + + this.r.setTarget(rgb.r); + this.g.setTarget(rgb.g); + this.b.setTarget(rgb.b); + this.alphaOther.setTarget(0); + + this.alphaWedge.setTarget(1); + + if ( this.hide || this.hideAlone ) + { + this.alphaPattern.setTarget(1); + } + else + { + this.alphaPattern.setTarget(0); + } + + // set radial + // + if ( ! ( hide || this.hide ) )//&& ! this.keyed ) + { + if ( this.hideAlone ) + { + this.radial = true; + } + else if ( false && canDisplayChildLabels ) + { + this.radial = false; + } + else + { + this.radial = true; + + if ( this.hasChildren() && depth < maxDisplayDepth ) + { + var lastChild = this.children[this.children.length - 1]; + + if + ( + lastChild.angleEnd.end == this.angleEnd.end || + ( + (this.angleStart.end + this.angleEnd.end) / 2 - + lastChild.angleEnd.end + ) * (this.radiusInner.end + 1) * gRadius * 2 < + minWidth() + ) + { + this.radial = false; + } + } + } + } + + // set alphaLabel + // + if + ( + collapse || + hide || + this.hide || + this.keyed || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLabel.setTarget(0); + } + else + { + if + ( + (this.radial || nLabelOffsets[depth - 2]) + ) + { + this.alphaLabel.setTarget(1); + } + else + { + this.alphaLabel.setTarget(0); + + if ( this.radialPrev ) + { + this.alphaLabel.start = 0; + } + } + } + + // set alphaArc + // + if + ( + collapse || + hide || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaArc.setTarget(0); + } + else + { + this.alphaArc.setTarget(1); + } + + // set alphaLine + // + if + ( + hide || + this.hide && nextSiblingHidden || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLine.setTarget(0); + } + else + { + this.alphaLine.setTarget(1); + } + + //if ( ! this.radial ) + { + this.resetLabelWidth(); + } + + // set labelRadius target + // + if ( collapse ) + { + this.labelRadius.setTarget(this.radiusInner.end); + } + else + { + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.labelRadius.setTarget(1); + } + else + { + this.setTargetLabelRadius(); + } + } + } + } + + this.setTargetWedge = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + // set angles + // + var baseMagnitudeRelative = this.baseMagnitude - selectedNode.baseMagnitude; + // + this.angleStart.setTarget(baseMagnitudeRelative * angleFactor); + this.angleEnd.setTarget((baseMagnitudeRelative + this.magnitude) * angleFactor); + + // set radiusInner + // + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.radiusInner.setTarget(1); + } + else + { + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depth - 2]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depth - 1)); + } + } + + if ( this.hide != undefined ) + { + this.hidePrev = this.hide; + } + + if ( this.hideAlone != undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + // set hide + // + if + ( + (this.angleEnd.end - this.angleStart.end) * + (this.radiusInner.end * gRadius + gRadius) < + minWidth() + ) + { + if ( depth == 2 && ! this.getCollapse() && this.depth <= maxAbsoluteDepth ) + { + this.keyed = true; + keys++; + this.hide = false; + + var percentage = this.getPercentage(); + this.keyLabel = this.name + ' ' + percentage + '%'; + var dim = context.measureText(this.keyLabel); + this.keyNameWidth = dim.width; + } + else + { + this.keyed = false; + this.hide = depth > 2; + } + } + else + { + this.keyed = false; + this.hide = false; + } + } + + this.shortenLabel = function() + { + var label = this.name; + + var labelWidth = this.nameWidth; + var maxWidth = this.labelWidth.current(); + var minEndLength = 0; + + if ( labelWidth > maxWidth && label.length > minEndLength * 2 ) + { + var endLength = + Math.floor((label.length - 1) * maxWidth / labelWidth / 2); + + if ( endLength < minEndLength ) + { + endLength = minEndLength; + } + + return ( + label.substring(0, endLength) + + '...' + + label.substring(label.length - endLength)); + } + else + { + return label; + } + } + +/* this.shouldAddSearchResultsString = function() + { + if ( this.isSearchResult ) + { + return this.searchResults > 1; + } + else + { + return this.searchResults > 0; + } + } +*/ + this.sort = function() + { + this.children.sort(function(a, b){return b.getMagnitude() - a.getMagnitude()}); + + for (var i = 0; i < this.children.length; i++) + { + this.children[i].sort(); + } + } +} + +var options; + +function addOptionElement(position, innerHTML, title) +{ + var div = document.createElement("div"); +// div.style.position = 'absolute'; +// div.style.top = position + 'px'; + div.innerHTML = innerHTML; +// div.style.display = 'block'; + div.style.padding = '2px'; + + if ( title ) + { + div.title = title; + } + + options.appendChild(div); + var height = 0;//div.clientHeight; + return position + height; +} + +function addOptionElements(hueName, hueDefault) +{ + options = document.createElement('div'); + options.style.position = 'absolute'; + options.style.top = '0px'; + options.addEventListener('mousedown', function(e) {mouseClick(e)}, false); +// options.onmouseup = function(e) {mouseUp(e)} + document.body.appendChild(options); + + document.body.style.font = '11px sans-serif'; + var position = 5; + + details = document.createElement('div'); + details.style.position = 'absolute'; + details.style.top = '1%'; + details.style.right = '2%'; + details.style.textAlign = 'right'; + document.body.insertBefore(details, canvas); +// <div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"> + + details.innerHTML = '\ +<span id="detailsName" style="font-weight:bold"></span> \ +<input type="button" id="detailsExpand" onclick="expand(focusNode);"\ +value="↔" title="Expand this wedge to become the new focus of the chart"/><br/>\ +<div id="detailsInfo" style="float:right"></div>'; + + keyControl = document.createElement('input'); + keyControl.type = 'button'; + keyControl.value = showKeys ? 'x' : '…'; + keyControl.style.position = ''; + keyControl.style.position = 'fixed'; + keyControl.style.visibility = 'hidden'; + + document.body.insertBefore(keyControl, canvas); + + var logoElement = document.getElementById('logo'); + + if ( logoElement ) + { + logoImage = logoElement.src; + } + else + { + logoImage = 'http://marbl.github.io/Krona/img/logo-med.png'; + } + +// document.getElementById('options').style.fontSize = '9pt'; + position = addOptionElement + ( + position, +'<a style="margin:2px" target="_blank" href="https://github.com/marbl/Krona/wiki"><img style="vertical-align:middle;width:108px;height:30px;" src="' + logoImage + '" alt="Logo of Krona"/></a><input type="button" id="back" value="←" title="Go back (Shortcut: ←)"/>\ +<input type="button" id="forward" value="→" title="Go forward (Shortcut: →)"/> \ + Search: <input type="text" id="search"/>\ +<input id="searchClear" type="button" value="x" onclick="clearSearch()"/> \ +<span id="searchResults"></span>' + ); + + if ( datasets > 1 ) + { + var size = datasets < datasetSelectSize ? datasets : datasetSelectSize; + + var select = + '<table style="border-collapse:collapse;padding:0px"><tr><td style="padding:0px">' + + '<select id="datasets" style="min-width:100px" size="' + size + '" onchange="onDatasetChange()">'; + + for ( var i = 0; i < datasetNames.length; i++ ) + { + select += '<option>' + datasetNames[i] + '</option>'; + } + + select += + '</select></td><td style="vertical-align:top;padding:1px;">' + + '<input style="display:block" title="Previous dataset (Shortcut: ↑)" id="prevDataset" type="button" value="↑" onclick="prevDataset()" disabled="true"/>' + + '<input title="Next dataset (Shortcut: ↓)" id="nextDataset" type="button" value="↓" onclick="nextDataset()"/><br/></td>' + + '<td style="padding-top:1px;vertical-align:top"><input title="Switch to the last dataset that was viewed (Shortcut: TAB)" id="lastDataset" type="button" style="font:11px Times new roman" value="last" onclick="selectLastDataset()"/></td></tr></table>'; + + position = addOptionElement(position + 5, select); + + datasetDropDown = document.getElementById('datasets'); + datasetButtonLast = document.getElementById('lastDataset'); + datasetButtonPrev = document.getElementById('prevDataset'); + datasetButtonNext = document.getElementById('nextDataset'); + + position += datasetDropDown.clientHeight; + } + + position = addOptionElement + ( + position + 5, +'<input type="button" id="maxAbsoluteDepthDecrease" value="-"/>\ +<span id="maxAbsoluteDepth"></span>\ + <input type="button" id="maxAbsoluteDepthIncrease" value="+"/> Max depth', +'Maximum depth to display, counted from the top level \ +and including collapsed wedges.' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="fontSizeDecrease" value="-"/>\ +<span id="fontSize"></span>\ + <input type="button" id="fontSizeIncrease" value="+"/> Font size' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="radiusDecrease" value="-"/>\ +<input type="button" id="radiusIncrease" value="+"/> Chart size' + ); + + if ( hueName ) + { + hueDisplayName = attributes[attributeIndex(hueName)].displayName; + + position = addOptionElement + ( + position + 5, + '<input type="checkbox" id="useHue" style="float:left" ' + + '/><div>Color by<br/>' + hueDisplayName + + '</div>' + ); + + useHueCheckBox = document.getElementById('useHue'); + useHueCheckBox.checked = hueDefault; + useHueCheckBox.onclick = handleResize; + useHueCheckBox.onmousedown = suppressEvent; + } + /* + position = addOptionElement + ( + position + 5, + ' <input type="checkbox" id="shorten" checked="checked" />Shorten labels</div>', + 'Prevent labels from overlapping by shortening them' + ); + + position = addOptionElement + ( + position, + ' <input type="checkbox" id="compress" checked="checked" />Compress', + 'Compress wedges if needed to show the entire depth' + ); + */ + position = addOptionElement + ( + position, + '<input type="checkbox" id="collapse" checked="checked" />Collapse', + 'Collapse wedges that are redundant (entirely composed of another wedge)' + ); + + position = addOptionElement + ( + position + 5, + '<input type="button" id="snapshot" value="Snapshot"/>', +'Render the current view as SVG (Scalable Vector Graphics), a publication-\ +quality format that can be printed and saved (see Help for browser compatibility)' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="linkButton" value="Link"/>\ +<input type="text" size="30" id="linkText"/>', +'Show a link to this view that can be copied for bookmarking or sharing' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="help" value="?"\ +onclick="window.open(\'https://github.com/marbl/Krona/wiki/Browsing%20Krona%20charts\', \'help\')"/>', +'Help' + ); +} + +function arrow(angleStart, angleEnd, radiusInner) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + var angleCenter = (angleStart + angleEnd) / 2; + var radiusArrowInner = radiusInner - gRadius / 10;//nodeRadius * gRadius; + var radiusArrowOuter = gRadius * 1.1;//(1 + nodeRadius); + var radiusArrowCenter = (radiusArrowInner + radiusArrowOuter) / 2; + var pointLength = (radiusArrowOuter - radiusArrowInner) / 5; + + context.fillStyle = highlightFill; + context.lineWidth = highlightLineWidth; + + // First, mask out the first half of the arrow. This will prevent the tips + // from superimposing if the arrow goes most of the way around the circle. + // Masking is done by setting the clipping region to the inverse of the + // half-arrow, which is defined by cutting the half-arrow out of a large + // rectangle + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter, true); + context.closePath(); + context.moveTo(-imageWidth, -imageHeight); + context.lineTo(imageWidth, -imageHeight); + context.lineTo(imageWidth, imageHeight); + context.lineTo(-imageWidth, imageHeight); + context.closePath(); + context.save(); + context.clip(); + + // Next, draw the other half-arrow with the first half masked out + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleStart, true); + context.lineTo + ( + radiusArrowInner * Math.cos(angleStart), + radiusArrowInner * Math.sin(angleStart) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleStart) + pointLength * Math.sin(angleStart), + radiusArrowCenter * Math.sin(angleStart) - pointLength * Math.cos(angleStart) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleStart), + radiusArrowOuter * Math.sin(angleStart) + ); + context.arc(0, 0, gRadius, angleStart, angleCenter, false); + context.fill(); + context.stroke(); + + // Finally, remove the clipping region and draw the first half-arrow. This + // half is extended slightly to fill the seam. + // + context.restore(); + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter - 2 / (2 * Math.PI * radiusInner), angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter - 2 / (2 * Math.PI * gRadius), true); + context.fill(); + context.stroke(); +} + +function attributeIndex(aname) +{ + for ( var i = 0 ; i < attributes.length; i++ ) + { + if ( aname == attributes[i].name ) + { + return i; + } + } + + return null; +} + +function checkHighlight() +{ + var lastHighlightedNode = highlightedNode; + var lastHighlightingHidden = highlightingHidden; + + highlightedNode = selectedNode; + resetKeyOffset(); + + if ( progress == 1 ) + { + selectedNode.checkHighlight(); + if ( selectedNode.getParent() ) + { + selectedNode.getParent().checkHighlightCenter(); + } + + focusNode.checkHighlightMap(); + } + + if ( highlightedNode != selectedNode ) + { + if ( highlightedNode == focusNode ) + { +// canvas.style.display='none'; +// window.resizeBy(1,0); +// canvas.style.cursor='ew-resize'; +// window.resizeBy(-1,0); +// canvas.style.display='inline'; + } + else + { +// canvas.style.cursor='pointer'; + } + } + else + { +// canvas.style.cursor='auto'; + } + + if + ( + ( + true || + highlightedNode != lastHighlightedNode || + highlightingHidden != highlightingHiddenLast + ) && + progress == 1 + ) + { + draw(); // TODO: handle in update() + } +} + +function checkSelectedCollapse() +{ + var newNode = selectedNode; + + while ( newNode.getCollapse() ) + { + newNode = newNode.children[0]; + } + + if ( newNode.children.length == 0 && newNode.getParent() ) + { + newNode = newNode.getParent(); + } + + if ( newNode != selectedNode ) + { + selectNode(newNode); + } +} + +function clearSearch() +{ + if ( search.value != '' ) + { + search.value = ''; + onSearchChange(); + } +} + +function createSVG() +{ + svgNS = "http://www.w3.org/2000/svg"; + var SVG = {}; + SVG.xlinkns = "http://www.w3.org/1999/xlink"; + + var newSVG = document.createElementNS(svgNS, "svg:svg"); + + newSVG.setAttribute("id", "canvas"); + // How big is the canvas in pixels + newSVG.setAttribute("width", '100%'); + newSVG.setAttribute("height", '100%'); + // Set the coordinates used by drawings in the canvas +// newSVG.setAttribute("viewBox", "0 0 " + imageWidth + " " + imageHeight); + // Define the XLink namespace that SVG uses + newSVG.setAttributeNS + ( + "http://www.w3.org/2000/xmlns/", + "xmlns:xlink", + SVG.xlinkns + ); + + return newSVG; +} + +function degrees(radians) +{ + return radians * 180 / Math.PI; +} + +function draw() +{ + tweenFrames++; + //resize(); +// context.fillRect(0, 0, imageWidth, imageHeight); + context.clearRect(0, 0, imageWidth, imageHeight); + + context.font = fontNormal; + context.textBaseline = 'middle'; + + //context.strokeStyle = 'rgba(0, 0, 0, 0.3)'; + context.translate(centerX, centerY); + + resetKeyOffset(); + + head.draw(false, false); // draw pie slices + head.draw(true, false); // draw labels + + var pathRoot = selectedNode; + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + pathRoot = focusNode; + } + + if + ( + highlightedNode && + highlightedNode.getDepth() >= selectedNode.getDepth() && + highlightedNode != focusNode + ) + { + if + ( + progress == 1 && + highlightedNode != selectedNode && + ( + highlightedNode != focusNode || + focusNode.children.length > 0 + ) + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlight(true); + } + + //pathRoot = highlightedNode; + } + else if + ( + progress == 1 && + highlightedNode.getDepth() < selectedNode.getDepth() + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlightCenter(); + } + + if ( quickLook && false) // TEMP + { + context.globalAlpha = 1 - progress / 2; + selectedNode.drawHighlight(true); + } + else if ( progress < 1 )//&& zoomOut() ) + { + if ( !zoomOut)//() ) + { + context.globalAlpha = selectedNode.alphaLine.current(); + selectedNode.drawHighlight(true); + } + else if ( selectedNodeLast ) + { + context.globalAlpha = 1 - 4 * Math.pow(progress - .5, 2); + selectedNodeLast.drawHighlight(false); + } + } + + drawDatasetName(); + + //drawHistory(); + + context.translate(-centerX, -centerY); + context.globalAlpha = 1; + + mapRadius = + (imageHeight / 2 - details.clientHeight - details.offsetTop) / + (pathRoot.getDepth() - 1) * 3 / 4 / 2; + + if ( mapRadius > maxMapRadius ) + { + mapRadius = maxMapRadius; + } + + mapBuffer = mapRadius / 2; + + //context.font = fontNormal; + pathRoot.drawMap(pathRoot); + + if ( hueDisplayName && useHue() ) + { + drawLegend(); + } +} + +function drawBubble(angle, radius, width, radial, flip) +{ + var height = fontSize * 2; + var x; + var y; + + width = width + fontSize; + + if ( radial ) + { + y = -fontSize; + + if ( flip ) + { + x = radius - width + fontSize / 2; + } + else + { + x = radius - fontSize / 2; + } + } + else + { + x = -width / 2; + y = -radius - fontSize; + } + + if ( snapshotMode ) + { + drawBubbleSVG(x + centerX, y + centerY, width, height, fontSize, angle); + } + else + { + drawBubbleCanvas(x, y, width, height, fontSize, angle); + } +} + +function drawBubbleCanvas(x, y, width, height, radius, rotation) +{ + context.strokeStyle = 'black'; + context.lineWidth = highlightLineWidth; + context.fillStyle = 'rgba(255, 255, 255, .75)'; + context.rotate(rotation); + roundedRectangle(x, y, width, fontSize * 2, fontSize); + context.fill(); + context.stroke(); + context.rotate(-rotation); +} + +function drawBubbleSVG(x, y, width, height, radius, rotation) +{ + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" fill="rgba(255, 255, 255, .75)' + + '" class="highlight" ' + + 'transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; +} + +function drawDatasetName() +{ + var alpha = datasetAlpha.current(); + + if ( alpha > 0 ) + { + var radius = gRadius * compressedRadii[0] / -2; + + if ( alpha > 1 ) + { + alpha = 1; + } + + context.globalAlpha = alpha; + + drawBubble(0, -radius, datasetWidths[currentDataset], false, false); + drawText(datasetNames[currentDataset], 0, radius, 0, 'center', true); + } +} + +function drawHistory() +{ + var alpha = 1; + context.textAlign = 'center'; + + for ( var i = 0; i < nodeHistoryPosition && alpha > 0; i++ ) + { + + context.globalAlpha = alpha - historyAlphaDelta * tweenFactor; + context.fillText + ( + nodeHistory[nodeHistoryPosition - i - 1].name, + 0, + (i + tweenFactor) * historySpacingFactor * fontSize - 1 + ); + + if ( alpha > 0 ) + { + alpha -= historyAlphaDelta; + } + } + + context.globalAlpha = 1; +} + +function drawLegend() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + context.fillStyle = 'black'; + context.textAlign = 'start'; + context.font = fontNormal; +// context.fillText(valueStartText, textLeft, top + height); +// context.fillText(valueEndText, textLeft, top); + context.fillText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var gradient = context.createLinearGradient(0, top + height, 0, top); + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + gradient.addColorStop(hueStopPositions[i], hueStopHsl[i]); + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + context.fillText(hueStopText[i], textLeft, textY); + } + } + + context.fillStyle = gradient; + context.fillRect(left, top, width, height); + context.lineWidth = thinLineWidth; + context.strokeRect(left, top, width, height); +} + +function drawLegendSVG() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + var text = ''; + + text += svgText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var svgtest = '<linearGradient id="gradient" x1="0%" y1="100%" x2="0%" y2="0%">'; + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + svgtest += + '<stop offset="' + round(hueStopPositions[i] * 100) + + '%" style="stop-color:' + hueStopHsl[i] + '"/>'; + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + text += svgText(hueStopText[i], textLeft, textY); + } + } + + svgtest += '</linearGradient>'; + //alert(svgtest); + svg += svgtest; + svg += + '<rect style="fill:url(#gradient)" x="' + left + '" y="' + top + + '" width="' + width + '" height="' + height + '"/>'; + + svg += text; +} + +function drawSearchHighlights(label, bubbleX, bubbleY, rotation, center) +{ + var index = -1; + var labelLength = label.length; + + bubbleX -= fontSize / 4; + + do + { + index = label.toLowerCase().indexOf(search.value.toLowerCase(), index + 1); + + if ( index != -1 && index < labelLength ) + { + var dim = context.measureText(label.substr(0, index)); + var x = bubbleX + dim.width; + + dim = context.measureText(label.substr(index, search.value.length)); + + var y = bubbleY - fontSize * 3 / 4; + var width = dim.width + fontSize / 2; + var height = fontSize * 3 / 2; + var radius = fontSize / 2; + + if ( snapshotMode ) + { + if ( center ) + { + x += centerX; + y += centerY; + } + + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" class="searchHighlight' + + '" transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.fillStyle = 'rgb(255, 255, 100)'; + context.rotate(rotation); + roundedRectangle(x, y, width, height, radius); + context.fill(); + context.rotate(-rotation); + } + } + } + while ( index != -1 && index < labelLength ); +} + +function drawText(text, x, y, angle, anchor, bold, color) +{ + if ( color == undefined ) + { + color = 'black'; + } + + if ( snapshotMode ) + { + svg += + '<text x="' + (centerX + x) + '" y="' + (centerY + y) + + '" text-anchor="' + anchor + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" transform="rotate(' + degrees(angle) + ',' + centerX + ',' + centerY + ')">' + + text + '</text>'; + } + else + { + context.fillStyle = color; + context.textAlign = anchor; + context.font = bold ? fontBold : fontNormal; + context.rotate(angle); + context.fillText(text, x, y); + context.rotate(-angle); + } +} + +function drawTextPolar +( + text, + innerText, + angle, + radius, + radial, + bubble, + bold, + searchResult, + searchResults +) +{ + var anchor; + var textX; + var textY; + var spacer; + var totalText = text; + var flip; + + if ( snapshotMode ) + { + spacer = '   '; + } + else + { + spacer = ' '; + } + + if ( radial ) + { + flip = angle < 3 * Math.PI / 2; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + anchor = 'end'; + + if ( innerText ) + { + totalText = text + spacer + innerText; + } + } + else + { + anchor = 'start'; + + if ( innerText ) + { + totalText = innerText + spacer + text; + } + } + + textX = radius; + textY = 0; + } + else + { + flip = angle < Math.PI || angle > 2 * Math.PI; + var label; + + anchor = snapshotMode ? 'middle' : 'center'; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + } + + angle += Math.PI / 2; + textX = 0; + textY = -radius; + } + + if ( bubble ) + { + var textActual = totalText; + + if ( innerText && snapshotMode ) + { + if ( flip ) + { + textActual = text + ' ' + innerText; + } + else + { + textActual = innerText + ' ' + text; + } + } + + if ( searchResults ) + { + textActual = textActual + searchResultString(searchResults); + } + + var textWidth = measureText(textActual, bold); + + var x = textX; + + if ( anchor == 'end' ) + { + x -= textWidth; + } + else if ( anchor != 'start' ) + { + // centered + x -= textWidth / 2; + } + + drawBubble(angle, radius, textWidth, radial, flip); + + if ( searchResult ) + { + drawSearchHighlights + ( + textActual, + x, + textY, + angle, + true + ) + } + } + + if ( searchResults ) + { + totalText = totalText + searchResultString(searchResults); + } + + drawText(totalText, textX, textY, angle, anchor, bold); + + return flip; +} + +function drawTick(start, length, angle) +{ + if ( snapshotMode ) + { + svg += + '<line x1="' + (centerX + start) + + '" y1="' + centerY + + '" x2="' + (centerX + start + length) + + '" y2="' + centerY + + '" class="tick" transform="rotate(' + + degrees(angle) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.rotate(angle); + context.beginPath(); + context.moveTo(start, 0); + context.lineTo(start + length, 0); + context.lineWidth = thinLineWidth * 2; + context.stroke(); + context.rotate(-angle); + } +} + +function drawWedge +( + angleStart, + angleEnd, + radiusInner, + radiusOuter, + color, + patternAlpha, + highlight +) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + if ( snapshotMode ) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + var dArray = + [ + " M ", x1, ",", y1, + " L ", x2, ",", y2, + " A ", gRadius, ",", gRadius, " 0 ", longArc, ",1 ", x3, ",", y3, + " L ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, " 0 ", x1, ",", y1, + " Z " + ]; + + svg += + '<path class="'+ (highlight ? 'highlight' : 'wedge') + '" fill="' + color + + '" d="' + dArray.join('') + '"/>'; + + if ( patternAlpha > 0 ) + { + svg += + '<path class="wedge" fill="url(#hiddenPattern)" d="' + + dArray.join('') + '"/>'; + } + } + else + { + // fudge to prevent seams during animation + // + angleEnd += 1 / gRadius; + + context.fillStyle = color; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.arc(0, 0, radiusOuter, angleEnd, angleStart, true); + context.closePath(); + context.fill(); + + if ( patternAlpha > 0 ) + { + context.save(); + context.clip(); + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + context.fill(); + context.restore(); + } + + if ( highlight ) + { + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.strokeStyle = 'black'; + context.stroke(); + } + } +} + +function expand(node) +{ + selectNode(node); + updateView(); +} + +function focusLost() +{ + mouseX = -1; + mouseY = -1; + checkHighlight(); + document.body.style.cursor = 'auto'; +} + +function fontSizeDecrease() +{ + if ( fontSize > 1 ) + { + fontSize--; + updateViewNeeded = true; + } +} + +function fontSizeIncrease() +{ + fontSize++; + updateViewNeeded = true; +} + +function getGetString(name, value, bool) +{ + return name + '=' + (bool ? value ? 'true' : 'false' : value); +} + +function hideLink() +{ + hide(linkText); + show(linkButton); +} + +function show(object) +{ + object.style.display = 'inline'; +} + +function hide(object) +{ + object.style.display = 'none'; +} + +function showLink() +{ + var urlHalves = String(document.location).split('?'); + var newGetVariables = new Array(); + + newGetVariables.push + ( + getGetString('dataset', currentDataset, false), + getGetString('node', selectedNode.id, false), + getGetString('collapse', collapse, true), + getGetString('color', useHue(), true), + getGetString('depth', maxAbsoluteDepth - 1, false), + getGetString('font', fontSize, false), + getGetString('key', showKeys, true) + ); + + hide(linkButton); + show(linkText); + linkText.value = urlHalves[0] + '?' + getVariables.concat(newGetVariables).join('&'); + //linkText.disabled = false; + linkText.focus(); + linkText.select(); + //linkText.disabled = true; +// document.location = urlHalves[0] + '?' + getVariables.join('&'); +} + +function getFirstChild(element) +{ + element = element.firstChild; + + if ( element && element.nodeType != 1 ) + { + element = getNextSibling(element); + } + + return element; +} + +function getNextSibling(element) +{ + do + { + element = element.nextSibling; + } + while ( element && element.nodeType != 1 ); + + return element; +} + +function getPercentage(fraction) +{ + return round(fraction * 100); +} + +function hslText(hue) +{ + if ( 1 || snapshotMode ) + { + // Safari doesn't seem to allow hsl() in SVG + + var rgb = hslToRgb(hue, saturation, (lightnessBase + lightnessMax) / 2); + + return rgbText(rgb.r, rgb.g, rgb.b); + } + else + { + var hslArray = + [ + 'hsl(', + Math.floor(hue * 360), + ',', + Math.floor(saturation * 100), + '%,', + Math.floor((lightnessBase + lightnessMax) * 50), + '%)' + ]; + + return hslArray.join(''); + } +} + +function hslToRgb(h, s, l) +{ + var m1, m2; + var r, g, b; + + if (s == 0) + { + r = g = b = Math.floor((l * 255)); + } + else + { + if (l <= 0.5) + { + m2 = l * (s + 1); + } + else + { + m2 = l + s - l * s; + } + + m1 = l * 2 - m2; + + r = Math.floor(hueToRgb(m1, m2, h + 1 / 3)); + g = Math.floor(hueToRgb(m1, m2, h)); + b = Math.floor(hueToRgb(m1, m2, h - 1/3)); + } + + return {r: r, g: g, b: b}; +} + +function hueToRgb(m1, m2, hue) +{ + var v; + + while (hue < 0) + { + hue += 1; + } + + while (hue > 1) + { + hue -= 1; + } + + if (6 * hue < 1) + v = m1 + (m2 - m1) * hue * 6; + else if (2 * hue < 1) + v = m2; + else if (3 * hue < 2) + v = m1 + (m2 - m1) * (2/3 - hue) * 6; + else + v = m1; + + return 255 * v; +} + +function interpolateHue(hueStart, hueEnd, valueStart, valueEnd) +{ + // since the gradient will be RGB based, we need to add stops to hit all the + // colors in the hue spectrum + + hueStopPositions = new Array(); + hueStopHsl = new Array(); + hueStopText = new Array(); + + hueStopPositions.push(0); + hueStopHsl.push(hslText(hueStart)); + hueStopText.push(round(valueStart)); + + for + ( + var i = (hueStart > hueEnd ? 5 / 6 : 1 / 6); + (hueStart > hueEnd ? i > 0 : i < 1); + i += (hueStart > hueEnd ? -1 : 1) / 6 + ) + { + if + ( + hueStart > hueEnd ? + i > hueEnd && i < hueStart : + i > hueStart && i < hueEnd + ) + { + hueStopPositions.push(lerp(i, hueStart, hueEnd, 0, 1)); + hueStopHsl.push(hslText(i)); + hueStopText.push(round(lerp + ( + i, + hueStart, + hueEnd, + valueStart, + valueEnd + ))); + } + } + + hueStopPositions.push(1); + hueStopHsl.push(hslText(hueEnd)); + hueStopText.push(round(valueEnd)); +} + +function keyLineAngle(angle, keyAngle, bendRadius, keyX, keyY, pointsX, pointsY) +{ + if ( angle < Math.PI / 2 && keyY < bendRadius * Math.sin(angle) + || angle > Math.PI / 2 && keyY < bendRadius) + { + return Math.asin(keyY / bendRadius); + } + else + { + // find the angle of the normal to a tangent line that goes to + // the label + + var textDist = Math.sqrt + ( + Math.pow(keyX, 2) + + Math.pow(keyY, 2) + ); + + var tanAngle = Math.acos(bendRadius / textDist) + keyAngle; + + if ( angle < tanAngle || angle < Math.PI / 2 )//|| labelLeft < centerX ) + { + // angle doesn't reach far enough for tangent; collapse and + // connect directly to label + + if ( keyY / Math.tan(angle) > 0 ) + { + pointsX.push(keyY / Math.tan(angle)); + pointsY.push(keyY); + } + else + { + pointsX.push(bendRadius * Math.cos(angle)); + pointsY.push(bendRadius * Math.sin(angle)); + } + + return angle; + } + else + { + return tanAngle; + } + } +} + +function keyOffset() +{ + return imageHeight - (keys - currentKey + 1) * (keySize + keyBuffer) + keyBuffer - margin; +} + +function lerp(value, fromStart, fromEnd, toStart, toEnd) +{ + return (value - fromStart) * + (toEnd - toStart) / + (fromEnd - fromStart) + + toStart; +} + +function createCanvas() +{ + canvas = document.createElement('canvas'); + document.body.appendChild(canvas); + context = canvas.getContext('2d'); +} + +function load() +{ + document.body.style.overflow = "hidden"; + document.body.style.margin = 0; + + createCanvas(); + + if ( context == undefined ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + if ( typeof context.fillText != 'function' ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 canvas text (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + resize(); + + var kronaElement = document.getElementsByTagName('krona')[0]; + + var magnitudeName; + var hueName; + var hueDefault; + var hueStart; + var hueEnd; + var valueStart; + var valueEnd; + + if ( kronaElement.getAttribute('collapse') != undefined ) + { + collapse = kronaElement.getAttribute('collapse') == 'true'; + } + + if ( kronaElement.getAttribute('key') != undefined ) + { + showKeys = kronaElement.getAttribute('key') == 'true'; + } + + for + ( + var element = getFirstChild(kronaElement); + element; + element = getNextSibling(element) + ) + { + switch ( element.tagName.toLowerCase() ) + { + case 'attributes': + magnitudeName = element.getAttribute('magnitude'); + // + for + ( + var attributeElement = getFirstChild(element); + attributeElement; + attributeElement = getNextSibling(attributeElement) + ) + { + var tag = attributeElement.tagName.toLowerCase(); + + if ( tag == 'attribute' ) + { + var attribute = new Attribute(); + attribute.name = attributeElement.firstChild.nodeValue.toLowerCase(); + attribute.displayName = attributeElement.getAttribute('display'); + + if ( attributeElement.getAttribute('hrefBase') ) + { + attribute.hrefBase = attributeElement.getAttribute('hrefBase'); + } + + if ( attributeElement.getAttribute('target') ) + { + attribute.target = attributeElement.getAttribute('target'); + } + + if ( attribute.name == magnitudeName ) + { + magnitudeIndex = attributes.length; + } + + if ( attributeElement.getAttribute('listAll') ) + { + attribute.listAll = attributeElement.getAttribute('listAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('listNode') ) + { + attribute.listNode = attributeElement.getAttribute('listNode').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataAll') ) + { + attribute.dataAll = attributeElement.getAttribute('dataAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataNode') ) + { + attribute.dataNode = attributeElement.getAttribute('dataNode').toLowerCase(); + } + + if ( attributeElement.getAttribute('postUrl') ) + { + attribute.postUrl = attributeElement.getAttribute('postUrl'); + } + + if ( attributeElement.getAttribute('postVar') ) + { + attribute.postVar = attributeElement.getAttribute('postVar'); + } + + if ( attributeElement.getAttribute('mono') ) + { + attribute.mono = true; + } + + attributes.push(attribute); + } + else if ( tag == 'list' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.list = true; + attributes.push(attribute); + } + else if ( tag == 'data' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.data = true; + attributes.push(attribute); + + var enableScript = document.createElement('script'); + var date = new Date(); + enableScript.src = + attributeElement.getAttribute('enable') + '?' + + date.getTime(); + document.body.appendChild(enableScript); + } + } + break; + + case 'color': + hueName = element.getAttribute('attribute'); + hueStart = Number(element.getAttribute('hueStart')) / 360; + hueEnd = Number(element.getAttribute('hueEnd')) / 360; + valueStart = Number(element.getAttribute('valueStart')); + valueEnd = Number(element.getAttribute('valueEnd')); + // + interpolateHue(hueStart, hueEnd, valueStart, valueEnd); + // + if ( element.getAttribute('default') == 'true' ) + { + hueDefault = true; + } + break; + + case 'datasets': + datasetNames = new Array(); + // + for ( j = getFirstChild(element); j; j = getNextSibling(j) ) + { + datasetNames.push(j.firstChild.nodeValue); + } + datasets = datasetNames.length; + break; + + case 'node': + head = loadTreeDOM + ( + element, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + break; + } + } + + // get GET options + // + var urlHalves = String(document.location).split('?'); + var datasetDefault = 0; + var maxDepthDefault; + var nodeDefault = 0; + // + if ( urlHalves[1] ) + { + var vars = urlHalves[1].split('&'); + + for ( i = 0; i < vars.length; i++ ) + { + var pair = vars[i].split('='); + + switch ( pair[0] ) + { + case 'collapse': + collapse = pair[1] == 'true'; + break; + + case 'color': + hueDefault = pair[1] == 'true'; + break; + + case 'dataset': + datasetDefault = Number(pair[1]); + break; + + case 'depth': + maxDepthDefault = Number(pair[1]) + 1; + break; + + case 'key': + showKeys = pair[1] == 'true'; + break; + + case 'font': + fontSize = Number(pair[1]); + break; + + case 'node': + nodeDefault = Number(pair[1]); + break; + + default: + getVariables.push(pair[0] + '=' + pair[1]); + break; + } + } + } + + addOptionElements(hueName, hueDefault); + setCallBacks(); + + head.sort(); + maxAbsoluteDepth = 0; + selectDataset(datasetDefault); + + if ( maxDepthDefault && maxDepthDefault < head.maxDepth ) + { + maxAbsoluteDepth = maxDepthDefault; + } + else + { + maxAbsoluteDepth = head.maxDepth; + } + + selectNode(nodes[nodeDefault]); + + setInterval(update, 20); + + window.onresize = handleResize; + updateMaxAbsoluteDepth(); + updateViewNeeded = true; +} + +function loadTreeDOM +( + domNode, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd +) +{ + var newNode = new Node(); + + newNode.name = domNode.getAttribute('name'); + + if ( domNode.getAttribute('href') ) + { + newNode.href = domNode.getAttribute('href'); + } + + if ( hueName ) + { + newNode.hues = new Array(); + } + + for ( var i = getFirstChild(domNode); i; i = getNextSibling(i) ) + { + switch ( i.tagName.toLowerCase() ) + { + case 'node': + var newChild = loadTreeDOM + ( + i, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + newChild.parent = newNode; + newNode.children.push(newChild); + break; + + default: + var attributeName = i.tagName.toLowerCase(); + var index = attributeIndex(attributeName); + // + newNode.attributes[index] = new Array(); + // + for ( var j = getFirstChild(i); j; j = getNextSibling(j) ) + { + if ( attributes[index] == undefined ) + { + var x = 5; + } + if ( attributes[index].list ) + { + newNode.attributes[index].push(new Array()); + + for ( var k = getFirstChild(j); k; k = getNextSibling(k) ) + { + newNode.attributes[index][newNode.attributes[index].length - 1].push(k.firstChild.nodeValue); + } + } + else + { + var value = j.firstChild ? j.firstChild.nodeValue : ''; + + if ( j.getAttribute('href') ) + { + var target; + + if ( attributes[index].target ) + { + target = ' target="' + attributes[index].target + '"'; + } + + value = '<a href="' + attributes[index].hrefBase + j.getAttribute('href') + '"' + target + '>' + value + '</a>'; + } + + newNode.attributes[index].push(value); + } + } + // + if ( attributeName == magnitudeName || attributeName == hueName ) + { + for ( j = 0; j < datasets; j++ ) + { + var value = newNode.attributes[index][j] == undefined ? 0 : Number(newNode.attributes[index][j]); + + newNode.attributes[index][j] = value; + + if ( attributeName == hueName ) + { + var hue = lerp + ( + value, + valueStart, + valueEnd, + hueStart, + hueEnd + ); + + if ( hue < hueStart == hueStart < hueEnd ) + { + hue = hueStart; + } + else if ( hue > hueEnd == hueStart < hueEnd ) + { + hue = hueEnd; + } + + newNode.hues[j] = hue; + } + } + + if ( attributeName == hueName ) + { + newNode.hue = new Tween(newNode.hues[0], newNode.hues[0]); + } + } + break; + } + } + + return newNode; +} + +function maxAbsoluteDepthDecrease() +{ + if ( maxAbsoluteDepth > 2 ) + { + maxAbsoluteDepth--; + head.setMaxDepths(); + handleResize(); + } +} + +function maxAbsoluteDepthIncrease() +{ + if ( maxAbsoluteDepth < head.maxDepth ) + { + maxAbsoluteDepth++; + head.setMaxDepths(); + handleResize(); + } +} + +function measureText(text, bold) +{ + context.font = bold ? fontBold : fontNormal; + var dim = context.measureText(text); + return dim.width; +} + +function min(a, b) +{ + return a < b ? a : b; +} + +function minWidth() +{ + // Min wedge width (at center) for displaying a node (or for displaying a + // label if it's at the highest level being viewed, multiplied by 2 to make + // further calculations simpler + + return (fontSize * 2.3); +} + +function mouseMove(e) +{ + mouseX = e.pageX; + mouseY = e.pageY - headerHeight; + mouseXRel = (mouseX - centerX) * backingScale() + mouseYRel = (mouseY - centerY) * backingScale() + + if ( head && ! quickLook ) + { + checkHighlight(); + } +} + +function mouseClick(e) +{ + if ( highlightedNode == focusNode && focusNode != selectedNode || selectedNode.hasParent(highlightedNode) ) + { + if ( highlightedNode.hasChildren() ) + { + expand(highlightedNode); + } + } + else if ( progress == 1 )//( highlightedNode != selectedNode ) + { + setFocus(highlightedNode); +// document.body.style.cursor='ew-resize'; + draw(); + checkHighlight(); + var date = new Date(); + mouseDownTime = date.getTime(); + mouseDown = true; + } +} + +function mouseUp(e) +{ + if ( quickLook ) + { + navigateBack(); + quickLook = false; + } + + mouseDown = false; +} + +function navigateBack() +{ + if ( nodeHistoryPosition > 0 ) + { + nodeHistory[nodeHistoryPosition] = selectedNode; + nodeHistoryPosition--; + + if ( nodeHistory[nodeHistoryPosition].collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + setSelectedNode(nodeHistory[nodeHistoryPosition]); + updateDatasetButtons(); + updateView(); + } +} + +function navigateUp() +{ + if ( selectedNode.getParent() ) + { + selectNode(selectedNode.getParent()); + updateView(); + } +} + +function navigateForward() +{ + if ( nodeHistoryPosition < nodeHistory.length - 1 ) + { + nodeHistoryPosition++; + var newNode = nodeHistory[nodeHistoryPosition]; + + if ( newNode.collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + if ( nodeHistoryPosition == nodeHistory.length - 1 ) + { + // this will ensure the forward button is disabled + + nodeHistory.length = nodeHistoryPosition; + } + + setSelectedNode(newNode); + updateDatasetButtons(); + updateView(); + } +} + +function nextDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == datasets - 1 ) + { + newDataset = 0; + } + else + { + newDataset++; + } + } + while ( datasetDropDown.options[newDataset].disabled ) + + selectDataset(newDataset); +} + +function onDatasetChange() +{ + selectDataset(datasetDropDown.selectedIndex); +} + +function onKeyDown(event) +{ + if + ( + event.keyCode == 37 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateBack(); + event.preventDefault(); + } + else if + ( + event.keyCode == 39 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateForward(); + event.preventDefault(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { + prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { + nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 9 && datasets > 1 ) + { + selectLastDataset(); + event.preventDefault(); + } + else if ( event.keyCode == 83 ) + { + progress += .2; + } + else if ( event.keyCode == 66 ) + { + progress -= .2; + } + else if ( event.keyCode == 70 ) + { + progress = 1; + } +} + +function onKeyPress(event) +{ + if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onKeyUp(event) +{ + if ( event.keyCode == 27 && document.activeElement.id == 'search' ) + { + search.value = ''; + onSearchChange(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onSearchChange() +{ + nSearchResults = 0; + head.search(); + + if ( search.value == '' ) + { + searchResults.innerHTML = ''; + } + else + { + searchResults.innerHTML = nSearchResults + ' results'; + } + + setFocus(selectedNode); + draw(); +} + +function post(url, variable, value, postWindow) +{ + var form = document.createElement('form'); + var input = document.createElement('input'); + var inputDataset = document.createElement('input'); + + form.appendChild(input); + form.appendChild(inputDataset); + + form.method = "POST"; + form.action = url; + + if ( postWindow == undefined ) + { + form.target = '_blank'; + postWindow = window; + } + + input.type = 'hidden'; + input.name = variable; + input.value = value; + + inputDataset.type = 'hidden'; + inputDataset.name = 'dataset'; + inputDataset.value = currentDataset; + + postWindow.document.body.appendChild(form); + form.submit(); +} + +function prevDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == 0 ) + { + newDataset = datasets - 1; + } + else + { + newDataset--; + } + } + while ( datasetDropDown.options[newDataset].disabled ); + + selectDataset(newDataset); +} + +function radiusDecrease() +{ + if ( bufferFactor < .309 ) + { + bufferFactor += .03; + updateViewNeeded = true; + } +} + +function radiusIncrease() +{ + if ( bufferFactor > .041 ) + { + bufferFactor -= .03; + updateViewNeeded = true; + } +} + +function resetKeyOffset() +{ + currentKey = 1; + keyMinTextLeft = centerX + gRadius + buffer - buffer / (keys + 1) / 2 + fontSize / 2; + keyMinAngle = 0; +} + +function rgbText(r, g, b) +{ + var rgbArray = + [ + "rgb(", + Math.floor(r), + ",", + Math.floor(g), + ",", + Math.floor(b), + ")" + ]; + + return rgbArray.join(''); +} + +function round(number) +{ + if ( number >= 1 || number <= -1 ) + { + return number.toFixed(0); + } + else + { + return number.toPrecision(1); + } +} + +function roundedRectangle(x, y, width, height, radius) +{ + if ( radius * 2 > width ) + { + radius = width / 2; + } + + if ( radius * 2 > height ) + { + radius = height / 2; + } + + context.beginPath(); + context.arc(x + radius, y + radius, radius, Math.PI, Math.PI * 3 / 2, false); + context.lineTo(x + width - radius, y); + context.arc(x + width - radius, y + radius, radius, Math.PI * 3 / 2, Math.PI * 2, false); + context.lineTo(x + width, y + height - radius); + context.arc(x + width - radius, y + height - radius, radius, 0, Math.PI / 2, false); + context.lineTo(x + radius, y + height); + context.arc(x + radius, y + height - radius, radius, Math.PI / 2, Math.PI, false); + context.lineTo(x, y + radius); +} + +function passClick(e) +{ + mouseClick(e); +} + +function searchResultString(results) +{ + var searchResults = this.searchResults; + + if ( this.isSearchResult ) + { + // don't count ourselves + searchResults--; + } + + return ' - ' + results + (results > 1 ? ' results' : ' result'); +} + +function setCallBacks() +{ + canvas.onselectstart = function(){return false;} // prevent unwanted highlighting + options.onselectstart = function(){return false;} // prevent unwanted highlighting + document.onmousemove = mouseMove; + window.onblur = focusLost; + window.onmouseout = focusLost; + document.onkeyup = onKeyUp; + document.onkeydown = onKeyDown; + canvas.onmousedown = mouseClick; + document.onmouseup = mouseUp; + keyControl.onclick = toggleKeys; + collapseCheckBox = document.getElementById('collapse'); + collapseCheckBox.checked = collapse; + collapseCheckBox.onclick = handleResize; + collapseCheckBox.onmousedown = suppressEvent; + maxAbsoluteDepthText = document.getElementById('maxAbsoluteDepth'); + maxAbsoluteDepthButtonDecrease = document.getElementById('maxAbsoluteDepthDecrease'); + maxAbsoluteDepthButtonIncrease = document.getElementById('maxAbsoluteDepthIncrease'); + maxAbsoluteDepthButtonDecrease.onclick = maxAbsoluteDepthDecrease; + maxAbsoluteDepthButtonIncrease.onclick = maxAbsoluteDepthIncrease; + maxAbsoluteDepthButtonDecrease.onmousedown = suppressEvent; + maxAbsoluteDepthButtonIncrease.onmousedown = suppressEvent; + fontSizeText = document.getElementById('fontSize'); + fontSizeButtonDecrease = document.getElementById('fontSizeDecrease'); + fontSizeButtonIncrease = document.getElementById('fontSizeIncrease'); + fontSizeButtonDecrease.onclick = fontSizeDecrease; + fontSizeButtonIncrease.onclick = fontSizeIncrease; + fontSizeButtonDecrease.onmousedown = suppressEvent; + fontSizeButtonIncrease.onmousedown = suppressEvent; + radiusButtonDecrease = document.getElementById('radiusDecrease'); + radiusButtonIncrease = document.getElementById('radiusIncrease'); + radiusButtonDecrease.onclick = radiusDecrease; + radiusButtonIncrease.onclick = radiusIncrease; + radiusButtonDecrease.onmousedown = suppressEvent; + radiusButtonIncrease.onmousedown = suppressEvent; + maxAbsoluteDepth = 0; + backButton = document.getElementById('back'); + backButton.onclick = navigateBack; + backButton.onmousedown = suppressEvent; + forwardButton = document.getElementById('forward'); + forwardButton.onclick = navigateForward; + forwardButton.onmousedown = suppressEvent; + snapshotButton = document.getElementById('snapshot'); + snapshotButton.onclick = snapshot; + snapshotButton.onmousedown = suppressEvent; + detailsName = document.getElementById('detailsName'); + detailsExpand = document.getElementById('detailsExpand'); + detailsInfo = document.getElementById('detailsInfo'); + search = document.getElementById('search'); + search.onkeyup = onSearchChange; + search.onmousedown = suppressEvent; + searchResults = document.getElementById('searchResults'); + useHueDiv = document.getElementById('useHueDiv'); + linkButton = document.getElementById('linkButton'); + linkButton.onclick = showLink; + linkButton.onmousedown = suppressEvent; + linkText = document.getElementById('linkText'); + linkText.onblur = hideLink; + linkText.onmousedown = suppressEvent; + hide(linkText); + var helpButton = document.getElementById('help'); + helpButton.onmousedown = suppressEvent; + var searchClear = document.getElementById('searchClear'); + searchClear.onmousedown = suppressEvent; + if ( datasets > 1 ) + { + datasetDropDown.onmousedown = suppressEvent; + var prevDatasetButton = document.getElementById('prevDataset'); + prevDatasetButton.onmousedown = suppressEvent; + var nextDatasetButton = document.getElementById('nextDataset'); + nextDatasetButton.onmousedown = suppressEvent; + var lastDatasetButton = document.getElementById('lastDataset'); + lastDatasetButton.onmousedown = suppressEvent; + } + + image = document.getElementById('hiddenImage'); + image.onload = function() + { + hiddenPattern = context.createPattern(image, 'repeat'); + } + + var loadingImageElement = document.getElementById('loadingImage'); + + if ( loadingImageElement ) + { + loadingImage = loadingImageElement.src; + } +} + +function selectDataset(newDataset) +{ + lastDataset = currentDataset; + currentDataset = newDataset + if ( datasets > 1 ) + { + datasetDropDown.selectedIndex = currentDataset; + updateDatasetButtons(); + datasetAlpha.start = 1.5; + datasetChanged = true; + } + head.setMagnitudes(0); + head.setDepth(1, 1); + head.setMaxDepths(); + handleResize(); +} + +function selectLastDataset() +{ + selectDataset(lastDataset); + handleResize(); +} + +function selectNode(newNode) +{ + if ( selectedNode != newNode ) + { + // truncate history at current location to create a new branch + // + nodeHistory.length = nodeHistoryPosition; + + if ( selectedNode != 0 ) + { + nodeHistory.push(selectedNode); + nodeHistoryPosition++; + } + + setSelectedNode(newNode); + //updateView(); + } + + updateDatasetButtons(); +} + +function setFocus(node) +{ + if ( node == focusNode ) + { +// return; + } + + focusNode = node; + + if ( node.href ) + { + detailsName.innerHTML = + '<a target="_blank" href="' + node.href + '">' + node.name + '</a>'; + } + else + { + detailsName.innerHTML = node.name; + } + + var table = '<table>'; + //TODO: use CSS margins instead of an additional column + table += '<tr><td></td><td></td></tr>'; + + for ( var i = 0; i < node.attributes.length; i++ ) + { + if ( attributes[i].displayName && node.attributes[i] != undefined ) + { + var index = node.attributes[i].length == 1 && attributes[i].mono ? 0 : currentDataset; + + if ( typeof node.attributes[i][currentDataset] == 'number' || node.attributes[i][index] != undefined && node.attributes[i][currentDataset] != '' ) + { + var value = node.attributes[i][index]; + + if ( attributes[i].listNode != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listNode) + ',' + i + + ',false);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].listAll != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listAll) + ',' + i + + ',true);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].dataNode != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataNode) + ',' + i + + ',false);return false;" title="Show data">' + + value + '</a>'; + } + else if ( attributes[i].dataAll != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataAll) + ',' + i + + ',true);return false;" title="Show data">' + + value + '</a>'; + } + + table += + '<tr><td><strong>' + attributes[i].displayName + ':</strong></td><td>' + + value + '</td></tr>'; + } + } + } + + table += '</table>'; + detailsInfo.innerHTML = table; + + detailsExpand.disabled = !focusNode.hasChildren() || focusNode == selectedNode; +} + +function setSelectedNode(newNode) +{ + if ( selectedNode && selectedNode.hasParent(newNode) ) + { + zoomOut = true; + } + else + { + zoomOut = false; + } + + selectedNodeLast = selectedNode; + selectedNode = newNode; + + //if ( focusNode != selectedNode ) + { + setFocus(selectedNode); + } +} + +function waitForData(dataWindow, target, title, time, postUrl, postVar) +{ + if ( nodeData.length == target ) + { + if ( postUrl != undefined ) + { + for ( var i = 0; i < nodeData.length; i++ ) + { + nodeData[i] = nodeData[i].replace(/\n/g, ','); + } + + var postString = nodeData.join(''); + postString = postString.slice(0, -1); + + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + + post(postUrl, postVar, postString, dataWindow); + } + else + { + //dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + //document.body.removeChild(document.getElementById('data')); + + dataWindow.document.open(); + dataWindow.document.write('<pre>' + nodeData.join('') + '</pre>'); + dataWindow.document.close(); + } + + dataWindow.document.title = title; // replace after document.write() + } + else + { + var date = new Date(); + + if ( date.getTime() - time > 10000 ) + { + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + dataWindow.document.body.innerHTML = + 'Timed out loading supplemental files for:<br/>' + document.location; + } + else + { + setTimeout(function() {waitForData(dataWindow, target, title, time, postUrl, postVar);}, 100); + } + } +} + +function data(newData) +{ + nodeData.push(newData); +} + +function enableData() +{ + dataEnabled = true; +} + +function showData(indexData, indexAttribute, summary) +{ + var dataWindow = window.open('', '_blank'); + var title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + dataWindow.document.title = title; + + nodeData = new Array(); + + if ( dataWindow && dataWindow.document && dataWindow.document.body != null ) + { + //var loadImage = document.createElement('img'); + //loadImage.src = "file://localhost/Users/ondovb/Krona/KronaTools/img/loading.gif"; + //loadImage.id = "loading"; + //loadImage.alt = "Loading..."; + //dataWindow.document.body.appendChild(loadImage); + dataWindow.document.body.innerHTML = + '<img id="loading" src="' + loadingImage + '" alt="Loading..."></img>'; + } + + var scripts = document.createElement('div'); + scripts.id = 'data'; + document.body.appendChild(scripts); + + var files = focusNode.getData(indexData, summary); + + var date = new Date(); + var time = date.getTime(); + + for ( var i = 0; i < files.length; i++ ) + { + var script = document.createElement('script'); + script.src = files[i] + '?' + time; + scripts.appendChild(script); + } + + waitForData(dataWindow, files.length, title, time, attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar); + + return false; +} + +function showList(indexList, indexAttribute, summary) +{ + var list = focusNode.getList(indexList, summary); + + if ( attributes[indexAttribute].postUrl != undefined ) + { + post(attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar, list.join(',')); + } + else + { + var dataWindow = window.open('', '_blank'); + + if ( true || navigator.appName == 'Microsoft Internet Explorer' ) // :( + { + dataWindow.document.open(); + dataWindow.document.write('<pre>' + list.join('\n') + '</pre>'); + dataWindow.document.close(); + } + else + { + var pre = document.createElement('pre'); + dataWindow.document.body.appendChild(pre); + pre.innerHTML = list; + } + + dataWindow.document.title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + } +} + +function snapshot() +{ + svg = svgHeader(); + + resetKeyOffset(); + + snapshotMode = true; + + selectedNode.draw(false, true); + selectedNode.draw(true, true); + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + } + + if ( hueDisplayName && useHue() ) + { + drawLegendSVG(); + } + + snapshotMode = false; + + svg += svgFooter(); + + var snapshotWindow = window.open('', '_blank', '', 'replace=false'); + snapshotWindow.document.write('<html><body><a href="data:image/svg+xml,' + encodeURIComponent(svg) + '" download="snapshot.svg">Download Snapshot</a></html></body>'); + snapshotWindow.document.write(svg); +} + +function save() +{ + alert(document.body.innerHTML); +} + +function spacer() +{ + if ( snapshotMode ) + { + return '   '; + } + else + { + return ' '; + } +} + +function suppressEvent(e) +{ + e.cancelBubble = true; + if (e.stopPropagation) e.stopPropagation(); +} + +function svgFooter() +{ + return '</svg>'; +} + +function svgHeader() +{ + var patternWidth = fontSize * .6;//radius / 50; + + return '\ +<?xml version="1.0" standalone="no"?>\ +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" \ + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\ +<svg width="' + imageWidth + '" height="' + imageHeight + '" version="1.1"\ + xmlns="http://www.w3.org/2000/svg">\ +<title>Krona (snapshot) - ' + +(datasets > 1 ? datasetNames[currentDataset] + ' - ' : '') + selectedNode.name + +'</title>\ +<defs>\ + <style type="text/css">\ + text {font-size: ' + fontSize + 'px; font-family: ' + fontFamily + '; dominant-baseline:central}\ + path {stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + path.wedge {stroke:none}\ + path.line {fill:none;stroke:black;}\ + line {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + line.tick {stroke-width:' + thinLineWidth * fontSize / 6 + ';}\ + line.pattern {stroke-width:' + thinLineWidth * fontSize / 18 + ';}\ + circle {fill:none;stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + rect {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + .highlight {stroke:black;stroke-width:'+ highlightLineWidth * fontSize / 12 + ';}\ + .searchHighlight {fill:rgb(255, 255, 100);stroke:none;}\ + </style>\ +<pattern id="hiddenPattern" patternUnits="userSpaceOnUse" \ +x="0" y="0" width="' + patternWidth + '" height="' + patternWidth + '">\ +<line class="pattern" x1="0" y1="0" x2="' + patternWidth / 2 + '" y2="' + patternWidth / 2 + '"/>\ +<line class="pattern" x1="' + patternWidth / 2 + '" y1="' + patternWidth + +'" x2="' + patternWidth + '" y2="' + patternWidth / 2 + '"/>\ +</pattern>\ +</defs>\ +'; +} + +function svgText(text, x, y, anchor, bold, color) +{ + if ( typeof(anchor) == 'undefined' ) + { + anchor = 'start'; + } + + if ( color == undefined ) + { + color = 'black'; + } + + return '<text x="' + x + '" y="' + y + + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" text-anchor="' + anchor + '">' + text + '</text>'; +} + +function toggleKeys() +{ + if ( showKeys ) + { + keyControl.value = '…'; + showKeys = false; + } + else + { + keyControl.value = 'x'; + showKeys = true; + } + + updateKeyControl(); + + if ( progress == 1 ) + { + draw(); + } +} + +function update() +{ + if ( ! head ) + { + return; + } + + if ( mouseDown && focusNode != selectedNode ) + { + var date = new Date(); + + if ( date.getTime() - mouseDownTime > quickLookHoldLength ) + { + if ( focusNode.hasChildren() ) + { + expand(focusNode); + quickLook = true; + } + } + } + + if ( updateViewNeeded ) + { + resize(); + mouseX = -1; + mouseY = -1; + + collapse = collapseCheckBox.checked; + compress = true;//compressCheckBox.checked; + shorten = true;//shortenCheckBox.checked; + + checkSelectedCollapse(); + updateMaxAbsoluteDepth(); + + if ( focusNode.getCollapse() || focusNode.depth > maxAbsoluteDepth ) + { + setFocus(selectedNode); + } + else + { + setFocus(focusNode); + } + + updateView(); + + updateViewNeeded = false; + } + + var date = new Date(); + progress = (date.getTime() - tweenStartTime) / tweenLength; +// progress += .01; + + if ( progress >= 1 ) + { + progress = 1; + } + + if ( progress != progressLast ) + { + tweenFactor =// progress; + (1 / (1 + Math.exp(-tweenCurvature * (progress - .5))) - .5) / + (tweenMax - .5) / 2 + .5; + + if ( progress == 1 ) + { + snapshotButton.disabled = false; + zoomOut = false; + + //updateKeyControl(); + + if ( ! quickLook ) + { + //checkHighlight(); + } + + + if ( fpsDisplay ) + { + fpsDisplay.innerHTML = 'fps: ' + Math.round(tweenFrames * 1000 / tweenLength); + } + } + + draw(); + } + + progressLast = progress; +} + +function updateDatasetButtons() +{ + if ( datasets == 1 ) + { + return; + } + + var node = selectedNode ? selectedNode : head; + + datasetButtonLast.disabled = + node.attributes[magnitudeIndex][lastDataset] == 0; + + datasetButtonPrev.disabled = true; + datasetButtonNext.disabled = true; + + for ( var i = 0; i < datasets; i++ ) + { + var disable = node.attributes[magnitudeIndex][i] == 0; + + datasetDropDown.options[i].disabled = disable; + + if ( ! disable ) + { + if ( i != currentDataset ) + { + datasetButtonPrev.disabled = false; + datasetButtonNext.disabled = false; + } + } + } +} + +function updateDatasetWidths() +{ + if ( datasets > 1 ) + { + for ( var i = 0; i < datasets; i++ ) + { + context.font = fontBold; + var dim = context.measureText(datasetNames[i]); + datasetWidths[i] = dim.width; + } + } +} + +function updateKeyControl() +{ + if ( keys == 0 )//|| progress != 1 ) + { + keyControl.style.visibility = 'hidden'; + } + else + { + keyControl.style.visibility = 'visible'; + keyControl.style.right = margin + 'px'; + + if ( showKeys ) + { + keyControl.style.top = + imageHeight - + ( + keys * (keySize + keyBuffer) - + keyBuffer + + margin + + keyControl.clientHeight * 1.5 + ) + 'px'; + } + else + { + keyControl.style.top = + (imageHeight - margin - keyControl.clientHeight) + 'px'; + } + } +} + +function updateView() +{ + if ( selectedNode.depth > maxAbsoluteDepth - 1 ) + { + maxAbsoluteDepth = selectedNode.depth + 1; + } + + highlightedNode = selectedNode; + + angleFactor = 2 * Math.PI / (selectedNode.magnitude); + + maxPossibleDepth = Math.floor(gRadius / (fontSize * minRingWidthFactor)); + + if ( maxPossibleDepth < 4 ) + { + maxPossibleDepth = 4; + } + + var minRadiusInner = fontSize * 8 / gRadius; + var minRadiusFirst = fontSize * 6 / gRadius; + var minRadiusOuter = fontSize * 5 / gRadius; + + if ( .25 < minRadiusInner ) + { + minRadiusInner = .25; + } + + if ( .15 < minRadiusFirst ) + { + minRadiusFirst = .15; + } + + if ( .15 < minRadiusOuter ) + { + minRadiusOuter = .15; + } + + // visibility of nodes depends on the depth they are displayed at, + // so we need to set the max depth assuming they can all be displayed + // and iterate it down based on the deepest child node we can display + // + var maxDepth; + var newMaxDepth = selectedNode.getMaxDepth() - selectedNode.getDepth() + 1; + // + do + { + maxDepth = newMaxDepth; + + if ( ! compress && maxDepth > maxPossibleDepth ) + { + maxDepth = maxPossibleDepth; + } + + if ( compress ) + { + compressedRadii = new Array(maxDepth); + + compressedRadii[0] = minRadiusInner; + + var offset = 0; + + while + ( + lerp + ( + Math.atan(offset + 2), + Math.atan(offset + 1), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) - minRadiusInner > minRadiusFirst && + offset < 10 + ) + { + offset++; + } + + offset--; + + for ( var i = 1; i < maxDepth; i++ ) + { + compressedRadii[i] = lerp + ( + Math.atan(i + offset), + Math.atan(offset), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) + } + } + else + { + nodeRadius = 1 / maxDepth; + } + + newMaxDepth = selectedNode.maxVisibleDepth(maxDepth); + + if ( compress ) + { + if ( newMaxDepth <= maxPossibleDepth ) + { +// compress + } + } + else + { + if ( newMaxDepth > maxPossibleDepth ) + { + newMaxDepth = maxPossibleDepth; + } + } + } + while ( newMaxDepth < maxDepth ); + + maxDisplayDepth = maxDepth; + + lightnessFactor = (lightnessMax - lightnessBase) / (maxDepth > 8 ? 8 : maxDepth); + keys = 0; + + nLabelOffsets = new Array(maxDisplayDepth - 1); + labelOffsets = new Array(maxDisplayDepth - 1); + labelLastNodes = new Array(maxDisplayDepth - 1); + labelFirstNodes = new Array(maxDisplayDepth - 1); + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + if ( compress ) + { + if ( i == maxDisplayDepth - 1 ) + { + nLabelOffsets[i] = 0; + } + else + { + var width = + (compressedRadii[i + 1] - compressedRadii[i]) * + gRadius; + + nLabelOffsets[i] = Math.floor(width / fontSize / 1.2); + + if ( nLabelOffsets[i] > 2 ) + { + nLabelOffsets[i] = min + ( + Math.floor(width / fontSize / 1.75), + 5 + ); + } + } + } + else + { + nLabelOffsets[i] = Math.max + ( + Math.floor(Math.sqrt((nodeRadius * gRadius / fontSize)) * 1.5), + 3 + ); + } + + labelOffsets[i] = Math.floor((nLabelOffsets[i] - 1) / 2); + labelLastNodes[i] = new Array(nLabelOffsets[i] + 1); + labelFirstNodes[i] = new Array(nLabelOffsets[i] + 1); + + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + // these arrays will allow nodes with neighboring labels to link to + // each other to determine max label length + + labelLastNodes[i][j] = 0; + labelFirstNodes[i][j] = 0; + } + } + + fontSizeText.innerHTML = fontSize; + fontNormal = fontSize + 'px ' + fontFamily; + context.font = fontNormal; + fontBold = 'bold ' + fontSize + 'px ' + fontFamily; + tickLength = fontSize * .7; + + head.setTargets(0); + + keySize = ((imageHeight - margin * 3) * 1 / 2) / keys * 3 / 4; + + if ( keySize > fontSize * maxKeySizeFactor ) + { + keySize = fontSize * maxKeySizeFactor; + } + + keyBuffer = keySize / 3; + + fontSizeLast = fontSize; + + if ( datasetChanged ) + { + datasetChanged = false; + } + else + { + datasetAlpha.start = 0; + } + + var date = new Date(); + tweenStartTime = date.getTime(); + progress = 0; + tweenFrames = 0; + + updateKeyControl(); + updateDatasetWidths(); + + document.title = 'Krona - ' + selectedNode.name; + updateNavigationButtons(); + snapshotButton.disabled = true; + + maxAbsoluteDepthText.innerHTML = maxAbsoluteDepth - 1; + + maxAbsoluteDepthButtonDecrease.disabled = (maxAbsoluteDepth == 2); + maxAbsoluteDepthButtonIncrease.disabled = (maxAbsoluteDepth == head.maxDepth); + + if ( collapse != collapseLast && search.value != '' ) + { + onSearchChange(); + collapseLast = collapse; + } +} + +function updateMaxAbsoluteDepth() +{ + while ( maxAbsoluteDepth > 1 && selectedNode.depth > maxAbsoluteDepth - 1 ) + { + selectedNode = selectedNode.getParent(); + } +} + +function updateNavigationButtons() +{ + backButton.disabled = (nodeHistoryPosition == 0); +// upButton.disabled = (selectedNode.getParent() == 0); + forwardButton.disabled = (nodeHistoryPosition == nodeHistory.length); +} + +function useHue() +{ + return useHueCheckBox && useHueCheckBox.checked; +} +/* +function zoomOut() +{ + return ( + selectedNodeLast != 0 && + selectedNodeLast.getDepth() < selectedNode.getDepth()); +} +*/ + </script> +</head> +<body> +<img id="hiddenImage" src="data:image/png;base64,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" style="display:none"/> +<img id="loadingImage" 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style="display:none"/> +<noscript>Javascript must be enabled to view this page.</noscript> +<div style="display:none"> + <krona collapse="true" key="true"> + <attributes magnitude="magnitude"> + <attribute display="Total">magnitude</attribute> + </attributes> + <datasets> + <dataset>kt</dataset> + </datasets> + +<node name="all"><magnitude><val>46</val></magnitude><node name="unclassified"><magnitude><val>1</val></magnitude></node><node name="root"><magnitude><val>45</val></magnitude><node name="cellular organisms"><magnitude><val>45</val></magnitude><node name="Bacteria"><magnitude><val>45</val></magnitude><node name="Pseudomonadota"><magnitude><val>45</val></magnitude><node name="Gammaproteobacteria"><magnitude><val>45</val></magnitude><node name="Enterobacterales"><magnitude><val>24</val></magnitude><node name="Enterobacteriaceae"><magnitude><val>24</val></magnitude><node name="Escherichia"><magnitude><val>14</val></magnitude><node name="Escherichia coli"><magnitude><val>14</val></magnitude><node name="Escherichia coli K-12"><magnitude><val>14</val></magnitude><node name="Escherichia coli str. K-12 substr. MG1655"><magnitude><val>14</val></magnitude></node></node></node></node><node name="Salmonella"><magnitude><val>10</val></magnitude><node name="Salmonella enterica"><magnitude><val>10</val></magnitude><node name="Salmonella enterica subsp. enterica"><magnitude><val>10</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium"><magnitude><val>10</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"><magnitude><val>10</val></magnitude></node></node></node></node></node></node></node><node name="Pseudomonadales"><magnitude><val>21</val></magnitude><node name="Pseudomonadaceae"><magnitude><val>21</val></magnitude><node name="Pseudomonas"><magnitude><val>21</val></magnitude><node name="Pseudomonas aeruginosa group"><magnitude><val>21</val></magnitude><node name="Pseudomonas aeruginosa"><magnitude><val>21</val></magnitude><node name="Pseudomonas aeruginosa PAO1"><magnitude><val>21</val></magnitude></node></node></node></node></node></node></node></node></node></node></node></node></krona></div></body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10.precision_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,23 @@ +2.1739 1 1 no rank 0 unclassified +97.8261 45 0 no rank 1 root +97.8261 45 0 no rank 131567 cellular organisms +97.8261 45 0 superkingdom 2 Bacteria +97.8261 45 0 phylum 1224 Pseudomonadota +97.8261 45 0 class 1236 Gammaproteobacteria +52.1739 24 0 order 91347 Enterobacterales +52.1739 24 0 family 543 Enterobacteriaceae +30.4348 14 0 genus 561 Escherichia +30.4348 14 0 species 562 Escherichia coli +30.4348 14 0 strain 83333 Escherichia coli K-12 +30.4348 14 14 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +21.7391 10 0 genus 590 Salmonella +21.7391 10 0 species 28901 Salmonella enterica +21.7391 10 0 subspecies 59201 Salmonella enterica subsp. enterica +21.7391 10 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +21.7391 10 10 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +45.6522 21 0 order 72274 Pseudomonadales +45.6522 21 0 family 135621 Pseudomonadaceae +45.6522 21 0 genus 286 Pseudomonas +45.6522 21 0 species group 136841 Pseudomonas aeruginosa group +45.6522 21 0 species 287 Pseudomonas aeruginosa +45.6522 21 21 strain 208964 Pseudomonas aeruginosa PAO1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,46 @@ +1 6afed69c-0764-187d-7701-25dbaa56fa4d 208964 14214 0.700577 strain 208964:2340 +1 cc0f07c9-8e86-392e-f794-1a4252e9fb38 99287 6180 0.657362 strain 99287:970 +1 f6611dfa-6896-0371-efec-a60a01132e83 99287 27942 0.864756 strain 99287:6265 +1 581fe12a-4956-fa3b-f64f-31d99c708716 511145 9627 0.791056 no rank 511145:1855 +1 2f1a09bf-c558-a8cc-b071-83128761e14f 208964 1812 0.584713 strain 208964:276 +1 956740a3-5b26-133c-d1a2-d2bde75f68da 511145 45297 0.301311 no rank 511145:3124 +1 c277097d-f2a7-010a-ee05-3c93b5f2b6fb 99287 15564 0.650186 strain 99287:2309 +1 7f94a381-1546-7827-286c-5800d7b14fce 511145 8064 0.645957 no rank 511145:1197 +0 42479fca-23da-2161-c636-4a3efa727e79 0 33 0 no rank +1 ee825b81-860f-2bca-1f5e-90339434a8a4 99287 28722 0.666301 strain 99287:4529 +1 fb11ddfb-d32f-5d75-f1c3-41724b7e594e 208964 19653 0.582659 strain 208964:2557 +1 91c09038-76cc-cc91-c19a-7a47204708d4 208964 10176 0.491794 strain 208964:1095 +1 d9237302-7ca1-1cb0-87b5-9bef45b7dafe 511145 15885 0.874032 no rank 511145:3671 +1 7957d890-cc56-1ca8-d0a8-674deb4f96a1 208964 633 0.775671 strain 208964:123 +1 db0e608c-27b4-198c-e5b1-ff9f70153a96 208964 1014 0.425542 strain 208964:82 +1 008b9f35-e6a4-170b-d7f4-3ff9ecc8c875 511145 6864 0.909528 no rank 511145:1785 +1 8f08681a-4a01-0c54-2dd0-3618e772370b 511145 35853 0.790659 no rank 511145:7122 +1 2c199f0c-2601-a3ec-5bff-0c33f1f18bfd 99287 3690 0.814499 strain 99287:770 +1 cd61a49b-d049-b767-3ac3-add014fe2895 208964 19470 0.759553 strain 208964:3718 +1 1f672421-5585-fb71-f73c-40283fb95a51 511145 19251 0.427328 no rank 511145:1851 +1 e5a03490-b6d8-d771-2029-fa165cc02486 208964 10941 0.734713 strain 208964:1858 +1 90d5e8c9-9992-ccad-ed13-50ae9e1f01ed 208964 6183 0.609009 strain 208964:892 +1 fcf8a78c-007a-340b-1dc2-aa07cd4f74e2 208964 10812 0.823899 strain 208964:2242 +1 3bcf93b0-d23f-dc99-60b0-58925d04121e 208964 9777 0.619617 strain 208964:1365 +1 4106b3dc-8d38-d435-04af-22a8a13519ec 511145 4356 0.789256 no rank 511145:839 +1 9419850f-7037-20f0-71c8-c37470e44974 208964 4002 0.824713 strain 208964:812 +1 16e12407-f1ea-d31c-1e78-159997a22af2 208964 4896 0.659518 strain 208964:711 +1 8160d594-20b5-54bf-3185-b420f94f2c3e 99287 2547 0.447978 strain 99287:240 +1 f60e7dc2-d87b-4689-7105-0bce5603d146 511145 17982 0.74708 no rank 511145:3307 +1 b860a965-3998-8602-b83d-1e9a17046940 208964 1122 0.530749 strain 208964:152 +1 b5411913-b5a4-6bfa-30a4-7c956ef32b3a 511145 3300 0.350152 no rank 511145:273 +1 879e0f5f-0bcb-f145-86b2-fa35b9d469a0 99287 34836 0.901323 strain 99287:8652 +1 d8a48a7d-947c-29e9-f7bc-4560053600aa 511145 1392 0.871049 no rank 511145:296 +1 d2c318b8-3227-032b-bfe1-fb011cfc260e 208964 7233 0.772155 strain 208964:1328 +1 a2a7b030-bf46-e658-60e4-949f0980b1ba 511145 3966 0.403681 no rank 511145:333 +1 d17a0751-b32c-c486-066e-4f2d0a23a25a 208964 13539 0.866201 strain 208964:3103 +1 3ab721e1-e301-4c80-8b8a-7483a2fd0619 99287 44919 0.531679 strain 99287:5404 +1 7c3c58f1-8745-92cb-6065-70ab62ac2afe 99287 4866 0.643444 strain 99287:735 +1 dd99b942-6109-7a63-2d38-7a272be96e27 511145 71058 0.482929 no rank 511145:7648 +1 20757211-06ab-db4f-e089-30d4c1aa72fa 511145 7911 0.633991 no rank 511145:1153 +1 ed31326f-5b4b-de9e-d3d7-a246a0790ea7 208964 5883 0.800697 strain 208964:1215 +1 f779b5ad-5375-ab6e-a07b-c5b8f3156bcf 208964 1110 0.633784 strain 208964:158 +1 ff46ad1a-56ec-fff8-0094-135fb400942d 208964 8154 0.610559 strain 208964:1106 +1 c8915e98-895d-b0ca-3eea-c031c9ff1918 208964 20103 0.692484 strain 208964:3358 +1 4f405c5a-5f00-7e8f-7cde-bec88c36d3cf 208964 8181 0.814631 strain 208964:1698 +1 0a5f9965-3e92-d697-cc36-cf18fb1a64a4 99287 1302 0.217742 strain 99287:78
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+ <script id="notfound">window.onload=function(){document.body.innerHTML=""}</script> + <script language="javascript" type="text/javascript"> +{//----------------------------------------------------------------------------- +// +// PURPOSE +// +// Krona is a flexible tool for exploring the relative proportions of +// hierarchical data, such as metagenomic classifications, using a +// radial, space-filling display. It is implemented using HTML5 and +// JavaScript, allowing charts to be explored locally or served over the +// Internet, requiring only a current version of any major web +// browser. Krona charts can be created using an Excel template or from +// common bioinformatic formats using the provided conversion scripts. +// +// +// COPYRIGHT LICENSE +// +// Copyright (c) 2011, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and +// Adam Phillippy +// +// This Software was prepared for the Department of Homeland Security +// (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as +// part of contract HSHQDC-07-C-00020 to manage and operate the National +// Biodefense Analysis and Countermeasures Center (NBACC), a Federally +// Funded Research and Development Center. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// * Neither the name of the Battelle National Biodefense Institute nor +// the names of its contributors may be used to endorse or promote +// products derived from this software without specific prior written +// permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// +// TRADEMARK LICENSE +// +// KRONA(TM) is a trademark of the Department of Homeland Security, and use +// of the trademark is subject to the following conditions: +// +// * Distribution of the unchanged, official code/software using the +// KRONA(TM) mark is hereby permitted by the Department of Homeland +// Security, provided that the software is distributed without charge +// and modification. +// +// * Distribution of altered source code/software using the KRONA(TM) mark +// is not permitted unless written permission has been granted by the +// Department of Homeland Security. +// +// +// FOR MORE INFORMATION VISIT +// +// https://github.com/marbl/Krona/wiki/ +// +//----------------------------------------------------------------------------- +} + + +var canvas; +var context; +var svg; // for snapshot mode +var collapse = true; +var collapseCheckBox; +var collapseLast; +var compress; +var compressCheckBox; +var maxAbsoluteDepthText; +var maxAbsoluteDepthButtonDecrease; +var maxAbsoluteDepthButtonIncrease; +var fontSize = 11; +var fontSizeText; +var fontSizeButtonDecrease; +var fontSizeButtonIncrease; +var fontSizeLast; +var radiusButtonDecrease; +var radiusButtonIncrease; +var shorten; +var shortenCheckBox; +var maxAbsoluteDepth; +var backButton; +var upButton; +var forwardButton; +var snapshotButton; +var snapshotMode = false; +var details; +var detailsName; +var search; +var searchResults; +var nSearchResults; +var useHueCheckBox; +var useHueDiv; +var datasetDropDown; +var datasetButtonLast; +var datasetButtonPrev; +var datasetButtonNext; +var keyControl; +var showKeys = true; +var linkButton; +var linkText; +var frame; + +// Node references. Note that the meanings of 'selected' and 'focused' are +// swapped in the docs. +// +var head; // the root of the entire tree +var selectedNode = 0; // the root of the current view +var focusNode = 0; // a node chosen for more info (single-click) +var highlightedNode = 0; // mouse hover node +var highlightingHidden = false; +var nodes = new Array(); +var currentNodeID = 0; // to iterate while loading + +var nodeHistory = new Array(); +var nodeHistoryPosition = 0; + +var dataEnabled = false; // true when supplemental files are present + +// store non-Krona GET variables so they can be passed on to links +// +var getVariables = new Array(); + +// selectedNodeLast is separate from the history, since we need to check +// properties of the last node viewed when browsing through the history +// +var selectedNodeLast = 0; +var zoomOut = false; + +// temporary zoom-in while holding the mouse button on a wedge +// +var quickLook = false; // true when in quick look state +var mouseDown = false; +var mouseDownTime; // to detect mouse button hold +var quickLookHoldLength = 200; + +var imageWidth; +var imageHeight; +var centerX; +var centerY; +var gRadius; +var updateViewNeeded = false; + +// Determines the angle that the pie chart starts at. 90 degrees makes the +// center label consistent with the children. +// +var rotationOffset = Math.PI / 2; + +var buffer; +var bufferFactor = .1; + +// The maps are the small pie charts showing the current slice being viewed. +// +var mapBuffer = 10; +var mapRadius = 0; +var maxMapRadius = 25; +var mapWidth = 150; +var maxLabelOverhang = Math.PI * 4.18; + +// Keys are the labeled boxes for slices in the highest level that are too thin +// to label. +// +var maxKeySizeFactor = 2; // will be multiplied by font size +var keySize; +var keys; +var keyBuffer = 10; +var currentKey; +var keyMinTextLeft; +var keyMinAngle; + +var minRingWidthFactor = 5; // will be multiplied by font size +var maxPossibleDepth; // the theoretical max that can be displayed +var maxDisplayDepth; // the actual depth that will be displayed +var headerHeight = 0;//document.getElementById('options').clientHeight; +var historySpacingFactor = 1.6; // will be multiplied by font size +var historyAlphaDelta = .25; + +// appearance +// +var lineOpacity = 0.3; +var saturation = 0.5; +var lightnessBase = 0.6; +var lightnessMax = .8; +var thinLineWidth = .3; +var highlightLineWidth = 1.5; +var labelBoxBuffer = 6; +var labelBoxRounding = 15; +var labelWidthFudge = 1.05; // The width of unshortened labels are set slightly + // longer than the name width so the animation + // finishes faster. +var fontNormal; +var fontBold; +var fontFamily = 'sans-serif'; +//var fontFaceBold = 'bold Arial'; +var nodeRadius; +var angleFactor; +var tickLength; +var compressedRadii; + +// colors +// +var highlightFill = 'rgba(255, 255, 255, .3)'; +var colorUnclassified = 'rgb(220,220,220)'; + +// label staggering +// +var labelOffsets; // will store the current offset at each depth +// +// This will store pointers to the last node that had a label in each offset (or "track") of a +// each depth. These will be used to shorten neighboring labels that would overlap. +// The [nLabelNodes] index will store the last node with a radial label. +// labelFirstNodes is the same, but to check for going all the way around and +// overlapping the first labels. +// +var labelLastNodes; +var labelFirstNodes; +// +var nLabelOffsets = 3; // the number of offsets to use + +var mouseX = -1; +var mouseY = -1; +var mouseXRel = -1; +var mouseYRel = -1; + +// tweening +// +var progress = 0; // for tweening; goes from 0 to 1. +var progressLast = 0; +var tweenFactor = 0; // progress converted by a curve for a smoother effect. +var tweenLength = 850; // in ms +var tweenCurvature = 13; +// +// tweenMax is used to scale the sigmoid function so its range is [0,1] for the +// domain [0,1] +// +var tweenMax = 1 / (1 + Math.exp(-tweenCurvature / 2)); +// +var tweenStartTime; + +// for framerate debug +// +var tweenFrames = 0; +var fpsDisplay = document.getElementById('frameRate'); + +// Arrays to translate xml attribute names into displayable attribute names +// +var attributes = new Array(); +// +var magnitudeIndex; // the index of attribute arrays used for magnitude +var membersAssignedIndex; +var membersSummaryIndex; + +// For defining gradients +// +var hueDisplayName; +var hueStopPositions; +var hueStopHues; +var hueStopText; + +// multiple datasets +// +var currentDataset = 0; +var lastDataset = 0; +var datasets = 1; +var datasetNames; +var datasetSelectSize = 30; +var datasetAlpha = new Tween(0, 0); +var datasetWidths = new Array(); +var datasetChanged; +var datasetSelectWidth = 50; + +window.onload = load; + +var image; +var hiddenPattern; +var loadingImage; +var logoImage; + +function backingScale() +{ + if ('devicePixelRatio' in window) + { + if (window.devicePixelRatio > 1) + { + return window.devicePixelRatio; + } + } + + return 1; +} + +function resize() +{ + imageWidth = window.innerWidth; + imageHeight = window.innerHeight; + + if ( ! snapshotMode ) + { + context.canvas.width = imageWidth * backingScale(); + context.canvas.height = imageHeight * backingScale(); + context.canvas.style.width = imageWidth + "px" + context.canvas.style.height = imageHeight + "px" + context.scale(backingScale(), backingScale()); + } + + if ( datasetDropDown ) + { + var ratio = + (datasetDropDown.offsetTop + datasetDropDown.clientHeight) * 2 / + imageHeight; + + if ( ratio > 1 ) + { + ratio = 1; + } + + ratio = Math.sqrt(ratio); + + datasetSelectWidth = + (datasetDropDown.offsetLeft + datasetDropDown.clientWidth) * ratio; + } + var leftMargin = datasets > 1 ? datasetSelectWidth + 30 : 0; + var minDimension = imageWidth - mapWidth - leftMargin > imageHeight ? + imageHeight : + imageWidth - mapWidth - leftMargin; + + maxMapRadius = minDimension * .03; + buffer = minDimension * bufferFactor; + margin = minDimension * .015; + centerX = (imageWidth - mapWidth - leftMargin) / 2 + leftMargin; + centerY = imageHeight / 2; + gRadius = minDimension / 2 - buffer; + //context.font = '11px sans-serif'; +} + +function handleResize() +{ + updateViewNeeded = true; +} + +function Attribute() +{ +} + +function Tween(start, end) +{ + this.start = start; + this.end = end; + this.current = this.start; + + this.current = function() + { + if ( progress == 1 || this.start == this.end ) + { + return this.end; + } + else + { + return this.start + tweenFactor * (this.end - this.start); + } + }; + + this.setTarget = function(target) + { + this.start = this.current(); + this.end = target; + } +} + +function Node() +{ + this.id = currentNodeID; + currentNodeID++; + nodes[this.id] = this; + + this.angleStart = new Tween(Math.PI, 0); + this.angleEnd = new Tween(Math.PI, 0); + this.radiusInner = new Tween(1, 1); + this.labelRadius = new Tween(1, 1); + this.labelWidth = new Tween(0, 0); + this.scale = new Tween(1, 1); // TEMP + this.radiusOuter = new Tween(1, 1); + + this.r = new Tween(255, 255); + this.g = new Tween(255, 255); + this.b = new Tween(255, 255); + + this.alphaLabel = new Tween(0, 1); + this.alphaLine = new Tween(0, 1); + this.alphaArc = new Tween(0, 0); + this.alphaWedge = new Tween(0, 1); + this.alphaOther = new Tween(0, 1); + this.alphaPattern = new Tween(0, 0); + this.children = Array(); + this.parent = 0; + + this.attributes = new Array(attributes.length); + + this.addChild = function(child) + { + this.children.push(child); + }; + + this.addLabelNode = function(depth, labelOffset) + { + if ( labelHeadNodes[depth][labelOffset] == 0 ) + { + // this will become the head node for this list + + labelHeadNodes[depth][labelOffset] = this; + this.labelPrev = this; + } + + var head = labelHeadNodes[depth][labelOffset]; + + this.labelNext = head; + this.labelPrev = head.labelPrev; + head.labelPrev.labelNext = this; + head.labelPrev = this; + } + + this.canDisplayDepth = function() + { + // whether this node is at a depth that can be displayed, according + // to the max absolute depth + + return this.depth <= maxAbsoluteDepth; + } + + this.canDisplayHistory = function() + { + var radiusInner; + + if ( compress ) + { + radiusInner = compressedRadii[0]; + } + else + { + radiusInner = nodeRadius; + } + + return ( + -this.labelRadius.end * gRadius + + historySpacingFactor * fontSize / 2 < + radiusInner * gRadius + ); + } + + this.canDisplayLabelCurrent = function() + { + return ( + (this.angleEnd.current() - this.angleStart.current()) * + (this.radiusInner.current() * gRadius + gRadius) >= + minWidth()); + } + + this.checkHighlight = function() + { + if ( this.children.length == 0 && this == focusNode ) + { + //return false; + } + + if ( this.hide ) + { + return false; + } + + if ( this.radiusInner.end == 1 ) + { + // compressed to the outside; don't check + + return false; + } + + var highlighted = false; + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + for ( var i = 0; i < this.children.length; i++ ) + { + highlighted = this.children[i].checkHighlight(); + + if ( highlighted ) + { + return true; + } + } + + if ( this.radial ) + { + var angleText = (angleStartCurrent + angleEndCurrent) / 2; + var radiusText = (gRadius + radiusInner) / 2; + + context.rotate(angleText); + context.beginPath(); + context.moveTo(radiusText, -fontSize); + context.lineTo(radiusText, fontSize); + context.lineTo(radiusText + centerX, fontSize); + context.lineTo(radiusText + centerX, -fontSize); + context.closePath(); + context.rotate(-angleText); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(this.getPercentage()) + '%' + ' ' + this.name; + + if ( this.searchResultChildren() ) + { + label += searchResultString(this.searchResultChildren()); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + radiusText + measureText(label) + ) + { + highlighted = true; + } + } + } + else + { + for ( var i = 0; i < this.hiddenLabels.length; i++ ) + { + var hiddenLabel = this.hiddenLabels[i]; + + context.rotate(hiddenLabel.angle); + context.beginPath(); + context.moveTo(gRadius, -fontSize); + context.lineTo(gRadius, fontSize); + context.lineTo(gRadius + centerX, fontSize); + context.lineTo(gRadius + centerX, -fontSize); + context.closePath(); + context.rotate(-hiddenLabel.angle); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(hiddenLabel.value) + ' more'; + + if ( hiddenLabel.search ) + { + label += searchResultString(hiddenLabel.search); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + gRadius + fontSize + measureText(label) + ) + { + highlighted = true; + break; + } + } + } + } + + if ( ! highlighted && this != selectedNode && ! this.getCollapse() ) + { + context.beginPath(); + context.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false); + context.arc(0, 0, gRadius, angleEndCurrent, angleStartCurrent, true); + context.closePath(); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + highlighted = true; + } + + if + ( + ! highlighted && + (angleEndCurrent - angleStartCurrent) * + (radiusInner + gRadius) < + minWidth() && + this.getDepth() == selectedNode.getDepth() + 1 + ) + { + if ( showKeys && this.checkHighlightKey() ) + { + highlighted = true; + } + } + } + + if ( highlighted ) + { + if ( this != highlightedNode ) + { + // document.body.style.cursor='pointer'; + } + + highlightedNode = this; + } + + return highlighted; + } + + this.checkHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + var cx = centerX; + var cy = centerY - this.labelRadius.end * gRadius; + //var dim = context.measureText(this.name); + + var width = this.nameWidth; + + if ( this.searchResultChildren() ) + { + var results = searchResultString(this.searchResultChildren()); + var dim = context.measureText(results); + width += dim.width; + } + + if + ( + mouseX > cx - width / 2 && + mouseX < cx + width / 2 && + mouseY > cy - historySpacingFactor * fontSize / 2 && + mouseY < cy + historySpacingFactor * fontSize / 2 + ) + { + highlightedNode = this; + return; + } + + if ( this.getParent() ) + { + this.getParent().checkHighlightCenter(); + } + } + + this.checkHighlightKey = function() + { + var offset = keyOffset(); + + var xMin = imageWidth - keySize - margin - this.keyNameWidth - keyBuffer; + var xMax = imageWidth - margin; + var yMin = offset; + var yMax = offset + keySize; + + currentKey++; + + return ( + mouseX > xMin && + mouseX < xMax && + mouseY > yMin && + mouseY < yMax); + } + + this.checkHighlightMap = function() + { + if ( this.parent ) + { + this.parent.checkHighlightMap(); + } + + if ( this.getCollapse() || this == focusNode ) + { + return; + } + + var box = this.getMapPosition(); + + if + ( + mouseX > box.x - mapRadius && + mouseX < box.x + mapRadius && + mouseY > box.y - mapRadius && + mouseY < box.y + mapRadius + ) + { + highlightedNode = this; + } + } + +/* this.collapse = function() + { + for (var i = 0; i < this.children.length; i++ ) + { + this.children[i] = this.children[i].collapse(); + } + + if + ( + this.children.length == 1 && + this.children[0].magnitude == this.magnitude + ) + { + this.children[0].parent = this.parent; + this.children[0].getDepth() = this.parent.getDepth() + 1; + return this.children[0]; + } + else + { + return this; + } + } +*/ + this.draw = function(labelMode, selected, searchHighlighted) + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; +// var hidden = false; + + if ( selectedNode == this ) + { + selected = true; + } + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + var canDisplayLabelCurrent = this.canDisplayLabelCurrent(); + var hiddenSearchResults = false; + +/* if ( ! this.hide ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.children[i].hide && this.children[i].searchResults ) + { + hiddenSearchResults = true; + } + } + } +*/ + var drawChildren = + ( ! this.hide || ! this.hidePrev && progress < 1 ) && + ( ! this.hideAlone || ! this.hideAlonePrev && progress < 1 ); + +// if ( this.alphaWedge.current() > 0 || this.alphaLabel.current() > 0 ) + { + var lastChildAngleEnd = angleStartCurrent; + + if ( this.hasChildren() )//canDisplayChildren ) + { + lastChildAngleEnd = + this.children[this.children.length - 1].angleEnd.current() + + rotationOffset; + } + + if ( labelMode ) + { + var drawRadial = + !( + this.parent && + this.parent != selectedNode && + angleEndCurrent == this.parent.angleEnd.current() + rotationOffset + ); + + //if ( angleStartCurrent != angleEndCurrent ) + { + this.drawLines(angleStartCurrent, angleEndCurrent, radiusInner, drawRadial, selected); + } + + var alphaOtherCurrent = this.alphaOther.current(); + var childRadiusInner; + + if ( this == selectedNode || alphaOtherCurrent ) + { + childRadiusInner = + this.children.length ? + this.children[this.children.length - 1].radiusInner.current() * gRadius + : radiusInner + } + + if ( this == selectedNode ) + { + this.drawReferenceRings(childRadiusInner); + } + + if + ( + selected && + ! searchHighlighted && + this != selectedNode && + ( + this.isSearchResult || + this.hideAlone && this.searchResultChildren() || + false +// this.hide && +// this.containsSearchResult + ) + ) + { + context.globalAlpha = this.alphaWedge.current(); + + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + + if + ( + this.keyed && + ! showKeys && + this.searchResults && + ! searchHighlighted && + this != highlightedNode && + this != focusNode + ) + { + var angle = (angleEndCurrent + angleStartCurrent) / 2; + this.drawLabel(angle, true, false, true, true); + } + + //this.drawHighlight(false); + searchHighlighted = true; + } + + if + ( + this == selectedNode || +// true + //(canDisplayLabelCurrent) && + this != highlightedNode && + this != focusNode + ) + { + if ( this.radial != this.radialPrev && this.alphaLabel.end == 1 ) + { + context.globalAlpha = tweenFactor; + } + else + { + context.globalAlpha = this.alphaLabel.current(); + } + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + this.hideAlone && this.searchResultChildren() || + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNode && ! this.radial, + selected, + this.radial + ); + + if ( this.radial != this.radialPrev && this.alphaLabel.start == 1 && progress < 1 ) + { + context.globalAlpha = 1 - tweenFactor; + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNodeLast && ! this.radialPrev, + selected, + this.radialPrev + ); + } + } + + if + ( + alphaOtherCurrent && + lastChildAngleEnd != null + ) + { + if + ( + (angleEndCurrent - lastChildAngleEnd) * + (childRadiusInner + gRadius) >= + minWidth() + ) + { + //context.font = fontNormal; + context.globalAlpha = this.alphaOther.current(); + + drawTextPolar + ( + this.getUnclassifiedText(), + this.getUnclassifiedPercentage(), + (lastChildAngleEnd + angleEndCurrent) / 2, + (childRadiusInner + gRadius) / 2, + true, + false, + false, + 0, + 0 + ); + } + } + + if ( this == selectedNode && this.keyUnclassified && showKeys ) + { + this.drawKey + ( + (lastChildAngleEnd + angleEndCurrent) / 2, + false, + false + ); + } + } + else + { + var alphaWedgeCurrent = this.alphaWedge.current(); + + if ( alphaWedgeCurrent || this.alphaOther.current() ) + { + var currentR = this.r.current(); + var currentG = this.g.current(); + var currentB = this.b.current(); + + var fill = rgbText(currentR, currentG, currentB); + + var radiusOuter; + var lastChildAngle; + var truncateWedge = + ( + (this.hasChildren() || this == selectedNode ) && + ! this.keyed && + (compress || depth < maxDisplayDepth) && + drawChildren + ); + + if ( truncateWedge ) + { + radiusOuter = this.children.length ? this.children[0].radiusInner.current() * gRadius : radiusInner; + } + else + { + radiusOuter = gRadius; + } + /* + if ( this.hasChildren() ) + { + radiusOuter = this.children[0].getUncollapsed().radiusInner.current() * gRadius + 1; + } + else + { // TEMP + radiusOuter = radiusInner + nodeRadius * gRadius; + + if ( radiusOuter > gRadius ) + { + radiusOuter = gRadius; + } + } + */ + context.globalAlpha = alphaWedgeCurrent; + + if ( radiusInner != radiusOuter || truncateWedge ) + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + radiusOuter,//this.radiusOuter.current() * gRadius, + //'rgba(0, 200, 0, .1)', + fill, + this.alphaPattern.current() + ); + + if ( truncateWedge ) + { + // fill in the extra space if the sum of our childrens' + // magnitudes is less than ours + + if ( lastChildAngleEnd < angleEndCurrent )//&& false) // TEMP + { + if ( radiusOuter > 1 ) + { + // overlap slightly to hide the seam + + // radiusOuter -= 1; + } + + if ( alphaWedgeCurrent < 1 ) + { + context.globalAlpha = this.alphaOther.current(); + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius, + colorUnclassified, + 0 + ); + context.globalAlpha = alphaWedgeCurrent; + } + + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius,//this.radiusOuter.current() * gRadius, + //'rgba(200, 0, 0, .1)', + fill, + this.alphaPattern.current() + ); + } + } + + if ( radiusOuter < gRadius ) + { + // patch up the seam + // + context.beginPath(); + context.arc(0, 0, radiusOuter, angleStartCurrent/*lastChildAngleEnd*/, angleEndCurrent, false); + context.strokeStyle = fill; + context.lineWidth = 1; + context.stroke(); + } + } + + if ( this.keyed && selected && showKeys )//&& progress == 1 ) + { + this.drawKey + ( + (angleStartCurrent + angleEndCurrent) / 2, + ( + this == highlightedNode || + this == focusNode || + this.searchResults + ), + this == highlightedNode || this == focusNode + ); + } + } + } + } + + this.hiddenLabels = Array(); + + if ( drawChildren ) + { + // draw children + // + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.drawHiddenChildren(i, selected, labelMode, searchHighlighted) ) + { + i = this.children[i].hiddenEnd; + } + else + { + this.children[i].draw(labelMode, selected, searchHighlighted); + } + } + } + }; + + this.drawHiddenChildren = function + ( + firstHiddenChild, + selected, + labelMode, + searchHighlighted + ) + { + var firstChild = this.children[firstHiddenChild]; + + if ( firstChild.hiddenEnd == null || firstChild.radiusInner.current() == 1 ) + { + return false; + } + + for ( var i = firstHiddenChild; i < firstChild.hiddenEnd; i++ ) + { + if ( ! this.children[i].hide || ! this.children[i].hidePrev && progress < 1 ) + { + return false; + } + } + + var angleStart = firstChild.angleStart.current() + rotationOffset; + var lastChild = this.children[firstChild.hiddenEnd]; + var angleEnd = lastChild.angleEnd.current() + rotationOffset; + var radiusInner = gRadius * firstChild.radiusInner.current(); + var hiddenChildren = firstChild.hiddenEnd - firstHiddenChild + 1; + + if ( labelMode ) + { + var hiddenSearchResults = 0; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + hiddenSearchResults += this.children[i].searchResults; + + if ( this.children[i].magnitude == 0 ) + { + hiddenChildren--; + } + } + + if + ( + selected && + (angleEnd - angleStart) * + (gRadius + gRadius) >= + minWidth() || + this == highlightedNode && + hiddenChildren || + hiddenSearchResults + ) + { + context.globalAlpha = this.alphaWedge.current(); + + this.drawHiddenLabel + ( + angleStart, + angleEnd, + hiddenChildren, + hiddenSearchResults + ); + } + } + + var drawWedges = true; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + // all hidden children must be completely hidden to draw together + + if ( this.children[i].alphaPattern.current() != this.children[i].alphaWedge.current() ) + { + drawWedges = false; + break; + } + } + + if ( labelMode ) + { + if ( drawWedges ) + { + var drawRadial = (angleEnd < this.angleEnd.current() + rotationOffset); + this.drawLines(angleStart, angleEnd, radiusInner, drawRadial); + } + + if ( hiddenSearchResults && ! searchHighlighted ) + { + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + highlightFill, + 0, + true + ); + } + } + else if ( drawWedges ) + { + context.globalAlpha = this.alphaWedge.current(); + + var fill = rgbText + ( + firstChild.r.current(), + firstChild.g.current(), + firstChild.b.current() + ); + + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + fill, + context.globalAlpha, + false + ); + } + + return drawWedges; + } + + this.drawHiddenLabel = function(angleStart, angleEnd, value, hiddenSearchResults) + { + var textAngle = (angleStart + angleEnd) / 2; + var labelRadius = gRadius + fontSize;//(radiusInner + radius) / 2; + + var hiddenLabel = Array(); + + hiddenLabel.value = value; + hiddenLabel.angle = textAngle; + hiddenLabel.search = hiddenSearchResults; + + this.hiddenLabels.push(hiddenLabel); + + drawTick(gRadius - fontSize * .75, fontSize * 1.5, textAngle); + drawTextPolar + ( + value.toString() + ' more', + 0, // inner text + textAngle, + labelRadius, + true, // radial + hiddenSearchResults, // bubble + this == highlightedNode || this == focusNode, // bold + false, + hiddenSearchResults + ); + } + + this.drawHighlight = function(bold) + { + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + //this.setHighlightStyle(); + + if ( this == focusNode && this == highlightedNode && this.hasChildren() ) + { +// context.fillStyle = "rgba(255, 255, 255, .3)"; + arrow + ( + angleStartCurrent, + angleEndCurrent, + radiusInner + ); + } + else + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + } + + // check if hidden children should be highlighted + // + for ( var i = 0; i < this.children.length; i++ ) + { + if + ( + this.children[i].getDepth() - selectedNode.getDepth() + 1 <= + maxDisplayDepth && + this.children[i].hiddenEnd != null + ) + { + var firstChild = this.children[i]; + var lastChild = this.children[firstChild.hiddenEnd]; + var hiddenAngleStart = firstChild.angleStart.current() + rotationOffset; + var hiddenAngleEnd = lastChild.angleEnd.current() + rotationOffset; + var hiddenRadiusInner = gRadius * firstChild.radiusInner.current(); + + drawWedge + ( + hiddenAngleStart, + hiddenAngleEnd, + hiddenRadiusInner, + gRadius, + 'rgba(255, 255, 255, .3)', + 0, + true + ); + + if ( false && ! this.searchResults ) + { + this.drawHiddenLabel + ( + hiddenAngleStart, + hiddenAngleEnd, + firstChild.hiddenEnd - i + 1 + ); + } + + i = firstChild.hiddenEnd; + } + } + +// context.strokeStyle = 'black'; + context.fillStyle = 'black'; + + var highlight = ! ( progress < 1 && zoomOut && this == selectedNodeLast ); + + var angle = (angleEndCurrent + angleStartCurrent) / 2; + + if ( ! (this.keyed && showKeys) ) + { + this.drawLabel(angle, true, bold, true, this.radial); + } + } + + this.drawHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + context.lineWidth = highlightLineWidth; + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .6)"; + + context.fillStyle = 'black'; + this.drawLabel(3 * Math.PI / 2, true, true, false); + context.font = fontNormal; + } + + this.drawKey = function(angle, highlight, bold) + { + var offset = keyOffset(); + var color; + var colorText = this.magnitude == 0 ? 'gray' : 'black'; + var patternAlpha = this.alphaPattern.end; + var boxLeft = imageWidth - keySize - margin; + var textY = offset + keySize / 2; + + var label; + var keyNameWidth; + + if ( this == selectedNode ) + { + color = colorUnclassified; + label = + this.getUnclassifiedText() + + ' ' + + this.getUnclassifiedPercentage(); + keyNameWidth = measureText(label, false); + } + else + { + label = this.keyLabel; + color = rgbText(this.r.end, this.g.end, this.b.end); + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + label = label + searchResultString(this.searchResultChildren()); + } + + keyNameWidth = measureText(label, bold); + } + else + { + keyNameWidth = this.keyNameWidth; + } + } + + var textLeft = boxLeft - keyBuffer - keyNameWidth - fontSize / 2; + var labelLeft = textLeft; + + if ( labelLeft > keyMinTextLeft - fontSize / 2 ) + { + keyMinTextLeft -= fontSize / 2; + + if ( keyMinTextLeft < centerX - gRadius + fontSize / 2 ) + { + keyMinTextLeft = centerX - gRadius + fontSize / 2; + } + + labelLeft = keyMinTextLeft; + } + + var lineX = new Array(); + var lineY = new Array(); + + var bendRadius; + var keyAngle = Math.atan((textY - centerY) / (labelLeft - centerX)); + var arcAngle; + + if ( keyAngle < 0 ) + { + keyAngle += Math.PI; + } + + if ( keyMinAngle == 0 || angle < keyMinAngle ) + { + keyMinAngle = angle; + } + + if ( angle > Math.PI && keyMinAngle > Math.PI ) + { + // allow lines to come underneath the chart + + angle -= Math.PI * 2; + } + + lineX.push(Math.cos(angle) * gRadius); + lineY.push(Math.sin(angle) * gRadius); + + if ( angle < keyAngle && textY > centerY + Math.sin(angle) * (gRadius + buffer * (currentKey - 1) / (keys + 1) / 2 + buffer / 2) ) + { + bendRadius = gRadius + buffer - buffer * currentKey / (keys + 1) / 2; + } + else + { + bendRadius = gRadius + buffer * currentKey / (keys + 1) / 2 + buffer / 2; + } + + var outside = + Math.sqrt + ( + Math.pow(labelLeft - centerX, 2) + + Math.pow(textY - centerY, 2) + ) > bendRadius; + + if ( ! outside ) + { + arcAngle = Math.asin((textY - centerY) / bendRadius); + + keyMinTextLeft = min(keyMinTextLeft, centerX + bendRadius * Math.cos(arcAngle) - fontSize / 2); + + if ( labelLeft < textLeft && textLeft > centerX + bendRadius * Math.cos(arcAngle) ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + else + { + keyMinTextLeft = min(keyMinTextLeft, labelLeft - fontSize / 2); + + if ( angle < keyAngle ) + { + // flip everything over y = x + // + arcAngle = Math.PI / 2 - keyLineAngle + ( + Math.PI / 2 - angle, + Math.PI / 2 - keyAngle, + bendRadius, + textY - centerY, + labelLeft - centerX, + lineY, + lineX + ); + + } + else + { + arcAngle = keyLineAngle + ( + angle, + keyAngle, + bendRadius, + labelLeft - centerX, + textY - centerY, + lineX, + lineY + ); + } + } + + if ( labelLeft > centerX + bendRadius * Math.cos(arcAngle) || + textY > centerY + bendRadius * Math.sin(arcAngle) + .01) +// if ( outside || ) + { + lineX.push(labelLeft - centerX); + lineY.push(textY - centerY); + + if ( textLeft != labelLeft ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + + context.globalAlpha = this.alphaWedge.current(); + + if ( snapshotMode ) + { + var labelSVG; + + if ( this == selectedNode ) + { + labelSVG = + this.getUnclassifiedText() + + spacer() + + this.getUnclassifiedPercentage(); + } + else + { + labelSVG = this.name + spacer() + this.getPercentage() + '%'; + } + + svg += + '<rect fill="' + color + '" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + + if ( patternAlpha ) + { + svg += + '<rect fill="url(#hiddenPattern)" style="stroke:none" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + } + + svg += + '<path class="line' + + (highlight ? ' highlight' : '') + + '" d="M ' + (lineX[0] + centerX) + ',' + + (lineY[0] + centerY); + + if ( angle != arcAngle ) + { + svg += + ' L ' + (centerX + bendRadius * Math.cos(angle)) + ',' + + (centerY + bendRadius * Math.sin(angle)) + + ' A ' + bendRadius + ',' + bendRadius + ' 0 ' + + '0,' + (angle > arcAngle ? '0' : '1') + ' ' + + (centerX + bendRadius * Math.cos(arcAngle)) + ',' + + (centerY + bendRadius * Math.sin(arcAngle)); + } + + for ( var i = 1; i < lineX.length; i++ ) + { + svg += + ' L ' + (centerX + lineX[i]) + ',' + + (centerY + lineY[i]); + } + + svg += '"/>'; + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + labelSVG = labelSVG + searchResultString(this.searchResultChildren()); + } + + drawBubbleSVG + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + svg += svgText(labelSVG, boxLeft - keyBuffer, textY, 'end', bold, colorText); + } + else + { + context.fillStyle = color; + context.translate(-centerX, -centerY); + context.strokeStyle = 'black'; + context.globalAlpha = 1;//this.alphaWedge.current(); + + context.fillRect(boxLeft, offset, keySize, keySize); + + if ( patternAlpha ) + { + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + + // make clipping box for Firefox performance + context.beginPath(); + context.moveTo(boxLeft, offset); + context.lineTo(boxLeft + keySize, offset); + context.lineTo(boxLeft + keySize, offset + keySize); + context.lineTo(boxLeft, offset + keySize); + context.closePath(); + context.save(); + context.clip(); + + context.fillRect(boxLeft, offset, keySize, keySize); + context.fillRect(boxLeft, offset, keySize, keySize); + + context.restore(); // remove clipping region + } + + if ( highlight ) + { + this.setHighlightStyle(); + context.fillRect(boxLeft, offset, keySize, keySize); + } + else + { + context.lineWidth = thinLineWidth; + } + + context.strokeRect(boxLeft, offset, keySize, keySize); + + if ( lineX.length ) + { + context.beginPath(); + context.moveTo(lineX[0] + centerX, lineY[0] + centerY); + + context.arc(centerX, centerY, bendRadius, angle, arcAngle, angle > arcAngle); + + for ( var i = 1; i < lineX.length; i++ ) + { + context.lineTo(lineX[i] + centerX, lineY[i] + centerY); + } + + context.globalAlpha = this == selectedNode ? + this.children[0].alphaWedge.current() : + this.alphaWedge.current(); + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.stroke(); + context.globalAlpha = 1; + } + + if ( highlight ) + { + drawBubbleCanvas + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + drawText(label, boxLeft - keyBuffer, offset + keySize / 2, 0, 'end', bold, colorText); + + context.translate(centerX, centerY); + } + + currentKey++; + } + + this.drawLabel = function(angle, bubble, bold, selected, radial) + { + if ( context.globalAlpha == 0 ) + { + return; + } + + var innerText; + var label; + var radius; + + if ( radial ) + { + radius = (this.radiusInner.current() + 1) * gRadius / 2; + } + else + { + radius = this.labelRadius.current() * gRadius; + } + + if ( radial && (selected || bubble ) ) + { + var percentage = this.getPercentage(); + innerText = percentage + '%'; + } + + if + ( + ! radial && + this != selectedNode && + ! bubble && + ( !zoomOut || this != selectedNodeLast) + ) + { + label = this.shortenLabel(); + } + else + { + label = this.name; + } + + var flipped = drawTextPolar + ( + label, + innerText, + angle, + radius, + radial, + bubble, + bold, +// this.isSearchResult && this.shouldAddSearchResultsString() && (!selected || this == selectedNode || highlight), + this.isSearchResult && (!selected || this == selectedNode || bubble), + (this.hideAlone || !selected || this == selectedNode ) ? this.searchResultChildren() : 0 + ); + + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + if + ( + ! radial && + ! bubble && + this != selectedNode && + this.angleEnd.end != this.angleStart.end && + nLabelOffsets[depth - 2] > 2 && + this.labelWidth.current() > (this.angleEnd.end - this.angleStart.end) * Math.abs(radius) && + ! ( zoomOut && this == selectedNodeLast ) && + this.labelRadius.end > 0 + ) + { + // name extends beyond wedge; draw tick mark towards the central + // radius for easier identification + + var radiusCenter = compress ? + (compressedRadii[depth - 1] + compressedRadii[depth - 2]) / 2 : + (depth - .5) * nodeRadius; + + if ( this.labelRadius.end > radiusCenter ) + { + if ( flipped ) + { + drawTick(radius - tickLength * 1.4 , tickLength, angle); + } + else + { + drawTick(radius - tickLength * 1.7, tickLength, angle); + } + } + else + { + if ( flipped ) + { + drawTick(radius + tickLength * .7, tickLength, angle); + } + else + { + drawTick(radius + tickLength * .4, tickLength, angle); + } + } + } + } + + this.drawLines = function(angleStart, angleEnd, radiusInner, drawRadial, selected) + { + if ( snapshotMode ) + { + if ( this != selectedNode) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + if ( this.alphaArc.end ) + { + var dArray = + [ + " M ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, + " 0 ", x1, ",", y1 + ]; + + svg += '<path class="line" d="' + dArray.join('') + '"/>'; + } + + if ( drawRadial && this.alphaLine.end ) + { + svg += '<line x1="' + x3 + '" y1="' + y3 + '" x2="' + x4 + '" y2="' + y4 + '"/>'; + } + } + } + else + { + context.lineWidth = thinLineWidth; + context.strokeStyle = 'black'; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.globalAlpha = this.alphaArc.current(); + context.stroke(); + + if ( drawRadial ) + { + var x1 = radiusInner * Math.cos(angleEnd); + var y1 = radiusInner * Math.sin(angleEnd); + var x2 = gRadius * Math.cos(angleEnd); + var y2 = gRadius * Math.sin(angleEnd); + + context.beginPath(); + context.moveTo(x1, y1); + context.lineTo(x2, y2); + +// if ( this.getCollapse() )//( selected && this != selectedNode ) + { + context.globalAlpha = this.alphaLine.current(); + } + + context.stroke(); + } + } + } + + this.drawMap = function(child) + { + if ( this.parent ) + { + this.parent.drawMap(child); + } + + if ( this.getCollapse() && this != child || this == focusNode ) + { + return; + } + + var angleStart = + (child.baseMagnitude - this.baseMagnitude) / this.magnitude * Math.PI * 2 + + rotationOffset; + var angleEnd = + (child.baseMagnitude - this.baseMagnitude + child.magnitude) / + this.magnitude * Math.PI * 2 + + rotationOffset; + + var box = this.getMapPosition(); + + context.save(); + context.fillStyle = 'black'; + context.textAlign = 'end'; + context.textBaseline = 'middle'; + + var textX = box.x - mapRadius - mapBuffer; + var percentage = getPercentage(child.magnitude / this.magnitude); + + var highlight = this == selectedNode || this == highlightedNode; + + if ( highlight ) + { + context.font = fontBold; + } + else + { + context.font = fontNormal; + } + + context.fillText(percentage + '% of', textX, box.y - mapRadius / 3); + context.fillText(this.name, textX, box.y + mapRadius / 3); + + if ( highlight ) + { + context.font = fontNormal; + } + + if ( this == highlightedNode && this != selectedNode ) + { + context.fillStyle = 'rgb(245, 245, 245)'; +// context.fillStyle = 'rgb(200, 200, 200)'; + } + else + { + context.fillStyle = 'rgb(255, 255, 255)'; + } + + context.beginPath(); + context.arc(box.x, box.y, mapRadius, 0, Math.PI * 2, true); + context.closePath(); + context.fill(); + + if ( this == selectedNode ) + { + context.lineWidth = 1; + context.fillStyle = 'rgb(100, 100, 100)'; + } + else + { + if ( this == highlightedNode ) + { + context.lineWidth = .2; + context.fillStyle = 'rgb(190, 190, 190)'; + } + else + { + context.lineWidth = .2; + context.fillStyle = 'rgb(200, 200, 200)'; + } + } + + var maxDepth = this.getMaxDepth(); + + if ( ! compress && maxDepth > maxPossibleDepth + this.getDepth() - 1 ) + { + maxDepth = maxPossibleDepth + this.getDepth() - 1; + } + + if ( this.getDepth() < selectedNode.getDepth() ) + { + if ( child.getDepth() - 1 >= maxDepth ) + { + maxDepth = child.getDepth(); + } + } + + var radiusInner; + + if ( compress ) + { + radiusInner = 0; +// Math.atan(child.getDepth() - this.getDepth()) / +// Math.PI * 2 * .9; + } + else + { + radiusInner = + (child.getDepth() - this.getDepth()) / + (maxDepth - this.getDepth() + 1); + } + + context.stroke(); + context.beginPath(); + + if ( radiusInner == 0 ) + { + context.moveTo(box.x, box.y); + } + else + { + context.arc(box.x, box.y, mapRadius * radiusInner, angleEnd, angleStart, true); + } + + context.arc(box.x, box.y, mapRadius, angleStart, angleEnd, false); + context.closePath(); + context.fill(); + + if ( this == highlightedNode && this != selectedNode ) + { + context.lineWidth = 1; + context.stroke(); + } + + context.restore(); + } + + this.drawReferenceRings = function(childRadiusInner) + { + if ( snapshotMode ) + { + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + childRadiusInner + '"/>'; + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + gRadius + '"/>'; + } + else + { + context.globalAlpha = 1 - this.alphaLine.current();//this.getUncollapsed().alphaLine.current(); + context.beginPath(); + context.arc(0, 0, childRadiusInner, 0, Math.PI * 2, false); + context.stroke(); + context.beginPath(); + context.arc(0, 0, gRadius, 0, Math.PI * 2, false); + context.stroke(); + } + } + + this.getCollapse = function() + { + return ( + collapse && + this.collapse && + this.depth != maxAbsoluteDepth + ); + } + + this.getDepth = function() + { + if ( collapse ) + { + return this.depthCollapsed; + } + else + { + return this.depth; + } + } + + this.getMagnitude = function() + { + return this.attributes[magnitudeIndex][currentDataset]; + } + + this.getMapPosition = function() + { + return { + x : (details.offsetLeft + details.clientWidth - mapRadius), + y : ((focusNode.getDepth() - this.getDepth()) * + (mapBuffer + mapRadius * 2) - mapRadius) + + details.clientHeight + details.offsetTop + }; + } + + this.getMaxDepth = function(limit) + { + var max; + + if ( collapse ) + { + return this.maxDepthCollapsed; + } + else + { + if ( this.maxDepth > maxAbsoluteDepth ) + { + return maxAbsoluteDepth; + } + else + { + return this.maxDepth; + } + } + } + + this.getData = function(index, summary) + { + var files = new Array(); + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null && + this.attributes[index][currentDataset] != '' + ) + { + files.push + ( + document.location + + '.files/' + + this.attributes[index][currentDataset] + ); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + files = files.concat(this.children[i].getData(index, true)); + } + } + + return files; + } + + this.getList = function(index, summary) + { + var list; + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null + ) + { + list = this.attributes[index][currentDataset]; + } + else + { + list = new Array(); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + list = list.concat(this.children[i].getList(index, true)); + } + } + + return list; + } + + this.getParent = function() + { + // returns parent, accounting for collapsing or 0 if doesn't exist + + var parent = this.parent; + + while ( parent != 0 && parent.getCollapse() ) + { + parent = parent.parent; + } + + return parent; + } + + this.getPercentage = function() + { + return getPercentage(this.magnitude / selectedNode.magnitude); + } + + this.getUnclassifiedPercentage = function() + { + if ( this.children.length ) + { + var lastChild = this.children[this.children.length - 1]; + + return getPercentage + ( + ( + this.baseMagnitude + + this.magnitude - + lastChild.magnitude - + lastChild.baseMagnitude + ) / this.magnitude + ) + '%'; + } + else + { + return '100%'; + } + } + + this.getUnclassifiedText = function() + { + return '[other '+ this.name + ']'; + } + + this.getUncollapsed = function() + { + // recurse through collapsed children until uncollapsed node is found + + if ( this.getCollapse() ) + { + return this.children[0].getUncollapsed(); + } + else + { + return this; + } + } + + this.hasChildren = function() + { + return this.children.length && this.depth < maxAbsoluteDepth && this.magnitude; + } + + this.hasParent = function(parent) + { + if ( this.parent ) + { + if ( this.parent == parent ) + { + return true; + } + else + { + return this.parent.hasParent(parent); + } + } + else + { + return false; + } + } + + this.maxVisibleDepth = function(maxDepth) + { + var childInnerRadius; + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var currentMaxDepth = depth; + + if ( this.hasChildren() && depth < maxDepth) + { + var lastChild = this.children[this.children.length - 1]; + + if ( this.name == 'Pseudomonadaceae' ) + { + var x = 3; + } + + if + ( + lastChild.baseMagnitude + lastChild.magnitude < + this.baseMagnitude + this.magnitude + ) + { + currentMaxDepth++; + } + + if ( compress ) + { + childInnerRadius = compressedRadii[depth - 1]; + } + else + { + childInnerRadius = (depth) / maxDepth; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + if + (//true || + this.children[i].magnitude * + angleFactor * + (childInnerRadius + 1) * + gRadius >= + minWidth() + ) + { + var childMaxDepth = this.children[i].maxVisibleDepth(maxDepth); + + if ( childMaxDepth > currentMaxDepth ) + { + currentMaxDepth = childMaxDepth; + } + } + } + } + + return currentMaxDepth; + } + + this.resetLabelWidth = function() + { + var nameWidthOld = this.nameWidth; + + if ( true || ! this.radial )//&& fontSize != fontSizeLast ) + { + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + } + + if ( fontSize != fontSizeLast && this.labelWidth.end == nameWidthOld * labelWidthFudge ) + { + // font size changed; adjust start of tween to match + + this.labelWidth.start = this.nameWidth * labelWidthFudge; + } + else + { + this.labelWidth.start = this.labelWidth.current(); + } + + this.labelWidth.end = this.nameWidth * labelWidthFudge; + } + + this.restrictLabelWidth = function(width) + { + if ( width < this.labelWidth.end ) + { + this.labelWidth.end = width; + } + } + + this.search = function() + { + this.isSearchResult = false; + this.searchResults = 0; + + if + ( + ! this.getCollapse() && + search.value != '' && + this.name.toLowerCase().indexOf(search.value.toLowerCase()) != -1 + ) + { + this.isSearchResult = true; + this.searchResults = 1; + nSearchResults++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.searchResults += this.children[i].search(); + } + + return this.searchResults; + } + + this.searchResultChildren = function() + { + if ( this.isSearchResult ) + { + return this.searchResults - 1; + } + else + { + return this.searchResults; + } + } + + this.setDepth = function(depth, depthCollapsed) + { + this.depth = depth; + this.depthCollapsed = depthCollapsed; + + if + ( + this.children.length == 1 && +// this.magnitude > 0 && + this.children[0].magnitude == this.magnitude && + ( head.children.length > 1 || this.children[0].children.length ) + ) + { + this.collapse = true; + } + else + { + this.collapse = false; + depthCollapsed++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setDepth(depth + 1, depthCollapsed); + } + } + + this.setHighlightStyle = function() + { + context.lineWidth = highlightLineWidth; + + if ( this.hasChildren() || this != focusNode || this != highlightedNode ) + { + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .3)"; + } + else + { + context.strokeStyle = 'rgb(90,90,90)'; + context.fillStyle = "rgba(155, 155, 155, .3)"; + } + } + + this.setLabelWidth = function(node) + { + if ( ! shorten || this.radial ) + { + return; // don't need to set width + } + + if ( node.hide ) + { + alert('wtf'); + return; + } + + var angle = (this.angleStart.end + this.angleEnd.end) / 2; + var a; // angle difference + + if ( node == selectedNode ) + { + a = Math.abs(angle - node.angleOther); + } + else + { + a = Math.abs(angle - (node.angleStart.end + node.angleEnd.end) / 2); + } + + if ( a == 0 ) + { + return; + } + + if ( a > Math.PI ) + { + a = 2 * Math.PI - a; + } + + if ( node.radial || node == selectedNode ) + { + var nodeLabelRadius; + + if ( node == selectedNode ) + { + // radial 'other' label + + nodeLabelRadius = (node.children[0].radiusInner.end + 1) / 2; + } + else + { + nodeLabelRadius = (node.radiusInner.end + 1) / 2; + } + + if ( a < Math.PI / 2 ) + { + var r = this.labelRadius.end * gRadius + .5 * fontSize + var hypotenuse = r / Math.cos(a); + var opposite = r * Math.tan(a); + var fontRadius = .8 * fontSize; + + if + ( + nodeLabelRadius * gRadius < hypotenuse && + this.labelWidth.end / 2 + fontRadius > opposite + ) + { + this.labelWidth.end = 2 * (opposite - fontRadius); + } + } + } + else if + ( + this.labelRadius.end == node.labelRadius.end && + a < Math.PI / 4 + ) + { + // same radius with small angle; use circumferential approximation + + var dist = a * this.labelRadius.end * gRadius - fontSize * (1 - a * 4 / Math.PI) * 1.3; + + if ( this.labelWidth.end < dist ) + { + node.restrictLabelWidth((dist - this.labelWidth.end / 2) * 2); + } + else if ( node.labelWidth.end < dist ) + { + this.restrictLabelWidth((dist - node.labelWidth.end / 2) * 2); + } + else + { + // both labels reach halfway point; restrict both + + this.labelWidth.end = dist; + node.labelWidth.end = dist + } + } + else + { + var r1 = this.labelRadius.end * gRadius; + var r2 = node.labelRadius.end * gRadius; + + // first adjust the radii to account for the height of the font by shifting them + // toward each other + // + var fontFudge = .35 * fontSize; + // + if ( this.labelRadius.end < node.labelRadius.end ) + { + r1 += fontFudge; + r2 -= fontFudge; + } + else if ( this.labelRadius.end > node.labelRadius.end ) + { + r1 -= fontFudge; + r2 += fontFudge; + } + else + { + r1 -= fontFudge; + r2 -= fontFudge; + } + + var r1s = r1 * r1; + var r2s = r2 * r2; + + // distance between the centers of the two labels + // + var dist = Math.sqrt(r1s + r2s - 2 * r1 * r2 * Math.cos(a)); + + // angle at our label center between our radius and the line to the other label center + // + var b = Math.acos((r1s + dist * dist - r2s) / (2 * r1 * dist)); + + // distance from our label center to the intersection of the two tangents + // + var l1 = Math.sin(a + b - Math.PI / 2) * dist / Math.sin(Math.PI - a); + + // distance from other label center the the intersection of the two tangents + // + var l2 = Math.sin(Math.PI / 2 - b) * dist / Math.sin(Math.PI - a); + + l1 = Math.abs(l1) - .4 * fontSize; + l2 = Math.abs(l2) - .4 * fontSize; +/* + // amount to shorten the distances because of the height of the font + // + var l3 = 0; + var fontRadius = fontSize * .55; + // + if ( l1 < 0 || l2 < 0 ) + { + var l4 = fontRadius / Math.tan(a); + l1 = Math.abs(l1); + l2 = Math.abs(l2); + + l1 -= l4; + l2 -= l4; + } + else + { + var c = Math.PI - a; + + l3 = fontRadius * Math.tan(c / 2); + } +*/ + if ( this.labelWidth.end / 2 > l1 && node.labelWidth.end / 2 > l2 ) + { + // shorten the farthest one from the intersection + + if ( l1 > l2 ) + { + this.restrictLabelWidth(2 * (l1));// - l3 - fontRadius)); + } + else + { + node.restrictLabelWidth(2 * (l2));// - l3 - fontRadius)); + } + }/* + else if ( this.labelWidth.end / 2 > l1 + l3 && node.labelWidth.end / 2 > l2 - l3 ) + { + node.restrictLabelWidth(2 * (l2 - l3)); + } + else if ( this.labelWidth.end / 2 > l1 - l3 && node.labelWidth.end / 2 > l2 + l3 ) + { + this.restrictLabelWidth(2 * (l1 - l3)); + }*/ + } + } + + this.setMagnitudes = function(baseMagnitude) + { + this.magnitude = this.getMagnitude(); + this.baseMagnitude = baseMagnitude; + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setMagnitudes(baseMagnitude); + baseMagnitude += this.children[i].magnitude; + } + + this.maxChildMagnitude = baseMagnitude; + } + + this.setMaxDepths = function() + { + this.maxDepth = this.depth; + this.maxDepthCollapsed = this.depthCollapsed; + + for ( i in this.children ) + { + var child = this.children[i]; + + child.setMaxDepths(); + + if ( child.maxDepth > this.maxDepth ) + { + this.maxDepth = child.maxDepth; + } + + if + ( + child.maxDepthCollapsed > this.maxDepthCollapsed && + (child.depth <= maxAbsoluteDepth || maxAbsoluteDepth == 0) + ) + { + this.maxDepthCollapsed = child.maxDepthCollapsed; + } + } + } + + this.setTargetLabelRadius = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var index = depth - 2; + var labelOffset = labelOffsets[index]; + + if ( this.radial ) + { + //this.labelRadius.setTarget((this.radiusInner.end + 1) / 2); + var max = + depth == maxDisplayDepth ? + 1 : + compressedRadii[index + 1]; + + this.labelRadius.setTarget((compressedRadii[index] + max) / 2); + } + else + { + var radiusCenter; + var width; + + if ( compress ) + { + if ( nLabelOffsets[index] > 1 ) + { + this.labelRadius.setTarget + ( + lerp + ( + labelOffset + .75, + 0, + nLabelOffsets[index] + .5, + compressedRadii[index], + compressedRadii[index + 1] + ) + ); + } + else + { + this.labelRadius.setTarget((compressedRadii[index] + compressedRadii[index + 1]) / 2); + } + } + else + { + radiusCenter = + nodeRadius * (depth - 1) + + nodeRadius / 2; + width = nodeRadius; + + this.labelRadius.setTarget + ( + radiusCenter + width * ((labelOffset + 1) / (nLabelOffsets[index] + 1) - .5) + ); + } + } + + if ( ! this.hide && ! this.keyed && nLabelOffsets[index] ) + { + // check last and first labels in each track for overlap + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + var last = labelLastNodes[i][j]; + var first = labelFirstNodes[i][j]; + + if ( last ) + { + if ( j == nLabelOffsets[i] ) + { + // last is radial + this.setLabelWidth(last); + } + else + { + last.setLabelWidth(this); + } + } + + if ( first ) + { + if ( j == nLabelOffsets[i] ) + { + this.setLabelWidth(first); + } + else + { + first.setLabelWidth(this); + } + } + } + } + + if ( selectedNode.canDisplayLabelOther ) + { + this.setLabelWidth(selectedNode); // in case there is an 'other' label + } + + if ( this.radial ) + { + // use the last 'track' of this depth for radial + + labelLastNodes[index][nLabelOffsets[index]] = this; + + if ( labelFirstNodes[index][nLabelOffsets[index]] == 0 ) + { + labelFirstNodes[index][nLabelOffsets[index]] = this; + } + } + else + { + labelLastNodes[index][labelOffset] = this; + + // update offset + + labelOffsets[index] += 1; + + if ( labelOffsets[index] > nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]--; + } + } + else if ( labelOffsets[index] == nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( false && !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]++; + } + } + + if ( labelFirstNodes[index][labelOffset] == 0 ) + { + labelFirstNodes[index][labelOffset] = this; + } + } + } + else if ( this.hide ) + { + this.labelWidth.end = 0; + } + } + + this.setTargets = function() + { + if ( this == selectedNode ) + { + this.setTargetsSelected + ( + 0, + 1, + lightnessBase, + false, + false + ); + return; + } + + var depthRelative = this.getDepth() - selectedNode.getDepth(); + + var parentOfSelected = selectedNode.hasParent(this); +/* ( +// ! this.getCollapse() && + this.baseMagnitude <= selectedNode.baseMagnitude && + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ); +*/ + if ( parentOfSelected ) + { + this.resetLabelWidth(); + } + else + { + //context.font = fontNormal; + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + //this.labelWidth.setTarget(this.labelWidth.end); + this.labelWidth.setTarget(0); + } + + // set angles + // + if ( this.baseMagnitude <= selectedNode.baseMagnitude ) + { + this.angleStart.setTarget(0); + } + else + { + this.angleStart.setTarget(Math.PI * 2); + } + // + if + ( + parentOfSelected || + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ) + { + this.angleEnd.setTarget(Math.PI * 2); + } + else + { + this.angleEnd.setTarget(0); + } + + // children + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargets(); + } + + if ( this.getDepth() <= selectedNode.getDepth() ) + { + // collapse in + + this.radiusInner.setTarget(0); + + if ( parentOfSelected ) + { + this.labelRadius.setTarget + ( + (depthRelative) * + historySpacingFactor * fontSize / gRadius + ); + //this.scale.setTarget(1 - (selectedNode.getDepth() - this.getDepth()) / 18); // TEMP + } + else + { + this.labelRadius.setTarget(0); + //this.scale.setTarget(1); // TEMP + } + } + else if ( depthRelative + 1 > maxDisplayDepth ) + { + // collapse out + + this.radiusInner.setTarget(1); + this.labelRadius.setTarget(1); + //this.scale.setTarget(1); // TEMP + } + else + { + // don't collapse + + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depthRelative - 1]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depthRelative)); + } + + //this.scale.setTarget(1); // TEMP + + if ( this == selectedNode ) + { + this.labelRadius.setTarget(0); + } + else + { + if ( compress ) + { + this.labelRadius.setTarget + ( + (compressedRadii[depthRelative - 1] + compressedRadii[depthRelative]) / 2 + ); + } + else + { + this.labelRadius.setTarget(nodeRadius * (depthRelative) + nodeRadius / 2); + } + } + } + +// this.r.start = this.r.end; +// this.g.start = this.g.end; +// this.b.start = this.b.end; + + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + + this.alphaLine.setTarget(0); + this.alphaArc.setTarget(0); + this.alphaWedge.setTarget(0); + this.alphaPattern.setTarget(0); + this.alphaOther.setTarget(0); + + if ( parentOfSelected && ! this.getCollapse() ) + { + var alpha = + ( + 1 - + (selectedNode.getDepth() - this.getDepth()) / + (Math.floor((compress ? compressedRadii[0] : nodeRadius) * gRadius / (historySpacingFactor * fontSize) - .5) + 1) + ); + + if ( alpha < 0 ) + { + alpha = 0; + } + + this.alphaLabel.setTarget(alpha); + this.radial = false; + } + else + { + this.alphaLabel.setTarget(0); + } + + this.hideAlonePrev = this.hideAlone; + this.hidePrev = this.hide; + + if ( parentOfSelected ) + { + this.hideAlone = false; + this.hide = false; + } + + if ( this.getParent() == selectedNode.getParent() ) + { + this.hiddenEnd = null; + } + + this.radialPrev = this.radial; + } + + this.setTargetsSelected = function(hueMin, hueMax, lightness, hide, nextSiblingHidden) + { + var collapse = this.getCollapse(); + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var canDisplayChildLabels = false; + var lastChild; + + if ( this.hasChildren() )//&& ! hide ) + { + lastChild = this.children[this.children.length - 1]; + this.hideAlone = true; + } + else + { + this.hideAlone = false; + } + + // set child wedges + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargetWedge(); + + if + ( + ! this.children[i].hide && + ( collapse || depth < maxDisplayDepth ) && + this.depth < maxAbsoluteDepth + ) + { + canDisplayChildLabels = true; + this.hideAlone = false; + } + } + + if ( this == selectedNode || lastChild && lastChild.angleEnd.end < this.angleEnd.end - .01) + { + this.hideAlone = false; + } + + if ( this.hideAlonePrev == undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + if ( this == selectedNode ) + { + var otherArc = + this.children.length ? + angleFactor * + ( + this.baseMagnitude + this.magnitude - + lastChild.baseMagnitude - lastChild.magnitude + ) + : this.baseMagnitude + this.magnitude; + this.canDisplayLabelOther = + this.children.length ? + otherArc * + (this.children[0].radiusInner.end + 1) * gRadius >= + minWidth() + : true; + + this.keyUnclassified = false; + + if ( this.canDisplayLabelOther ) + { + this.angleOther = Math.PI * 2 - otherArc / 2; + } + else if ( otherArc > 0.0000000001 ) + { + this.keyUnclassified = true; + keys++; + } + + this.angleStart.setTarget(0); + this.angleEnd.setTarget(Math.PI * 2); + + if ( this.children.length ) + { + this.radiusInner.setTarget(0); + } + else + { + this.radiusInner.setTarget(compressedRadii[0]); + } + + this.hidePrev = this.hide; + this.hide = false; + this.hideAlonePrev = this.hideAlone; + this.hideAlone = false; + this.keyed = false; + } + + if ( hueMax - hueMin > 1 / 12 ) + { + hueMax = hueMin + 1 / 12; + } + + // set lightness + // + if ( ! ( hide || this.hideAlone ) ) + { + if ( useHue() ) + { + lightness = (lightnessBase + lightnessMax) / 2; + } + else + { + lightness = lightnessBase + (depth - 1) * lightnessFactor; + + if ( lightness > lightnessMax ) + { + lightness = lightnessMax; + } + } + } + + if ( hide ) + { + this.hide = true; + } + + if ( this.hidePrev == undefined ) + { + this.hidePrev = this.hide; + } + + var hiddenStart = -1; + var hiddenHueNumer = 0; + var hiddenHueDenom = 0; + var i = 0; + + if ( ! this.hide ) + { + this.hiddenEnd = null; + } + + while ( true ) + { + if ( ! this.hideAlone && ! hide && ( i == this.children.length || ! this.children[i].hide ) ) + { + // reached a non-hidden child or the end; set targets for + // previous group of hidden children (if any) using their + // average hue + + if ( hiddenStart != -1 ) + { + var hiddenHue = hiddenHueDenom ? hiddenHueNumer / hiddenHueDenom : hueMin; + + for ( var j = hiddenStart; j < i; j++ ) + { + this.children[j].setTargetsSelected + ( + hiddenHue, + null, + lightness, + false, + j < i - 1 + ); + + this.children[j].hiddenEnd = null; + } + + this.children[hiddenStart].hiddenEnd = i - 1; + } + } + + if ( i == this.children.length ) + { + break; + } + + var child = this.children[i]; + var childHueMin; + var childHueMax; + + if ( this.magnitude > 0 && ! this.hide && ! this.hideAlone ) + { + if ( useHue() ) + { + childHueMin = child.hues[currentDataset]; + } + else if ( this == selectedNode ) + { + var min = 0.0; + var max = 1.0; + + if ( this.children.length > 6 ) + { + childHueMin = lerp((1 - Math.pow(1 - i / this.children.length, 1.4)) * .95, 0, 1, min, max); + childHueMax = lerp((1 - Math.pow(1 - (i + .55) / this.children.length, 1.4)) * .95, 0, 1, min, max); + } + else + { + childHueMin = lerp(i / this.children.length, 0, 1, min, max); + childHueMax = lerp((i + .55) / this.children.length, 0, 1, min, max); + } + } + else + { + childHueMin = lerp + ( + child.baseMagnitude, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + childHueMax = lerp + ( + child.baseMagnitude + child.magnitude * .99, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + } + } + else + { + childHueMin = hueMin; + childHueMax = hueMax; + } + + if ( ! this.hideAlone && ! hide && ! this.hide && child.hide ) + { + if ( hiddenStart == -1 ) + { + hiddenStart = i; + } + + if ( useHue() ) + { + hiddenHueNumer += childHueMin * child.magnitude; + hiddenHueDenom += child.magnitude; + } + else + { + hiddenHueNumer += childHueMin; + hiddenHueDenom++; + } + } + else + { + hiddenStart = -1; + + this.children[i].setTargetsSelected + ( + childHueMin, + childHueMax, + lightness, + hide || this.keyed || this.hideAlone || this.hide && ! collapse, + false + ); + } + + i++; + } + + if ( this.hue && this.magnitude ) + { + this.hue.setTarget(this.hues[currentDataset]); + + if ( this.attributes[magnitudeIndex][lastDataset] == 0 ) + { + this.hue.start = this.hue.end; + } + } + + this.radialPrev = this.radial; + + if ( this == selectedNode ) + { + this.resetLabelWidth(); + this.labelWidth.setTarget(this.nameWidth * labelWidthFudge); + this.alphaWedge.setTarget(0); + this.alphaLabel.setTarget(1); + this.alphaOther.setTarget(1); + this.alphaArc.setTarget(0); + this.alphaLine.setTarget(0); + this.alphaPattern.setTarget(0); + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + this.radial = false; + this.labelRadius.setTarget(0); + } + else + { + var rgb = hslToRgb + ( + hueMin, + saturation, + lightness + ); + + this.r.setTarget(rgb.r); + this.g.setTarget(rgb.g); + this.b.setTarget(rgb.b); + this.alphaOther.setTarget(0); + + this.alphaWedge.setTarget(1); + + if ( this.hide || this.hideAlone ) + { + this.alphaPattern.setTarget(1); + } + else + { + this.alphaPattern.setTarget(0); + } + + // set radial + // + if ( ! ( hide || this.hide ) )//&& ! this.keyed ) + { + if ( this.hideAlone ) + { + this.radial = true; + } + else if ( false && canDisplayChildLabels ) + { + this.radial = false; + } + else + { + this.radial = true; + + if ( this.hasChildren() && depth < maxDisplayDepth ) + { + var lastChild = this.children[this.children.length - 1]; + + if + ( + lastChild.angleEnd.end == this.angleEnd.end || + ( + (this.angleStart.end + this.angleEnd.end) / 2 - + lastChild.angleEnd.end + ) * (this.radiusInner.end + 1) * gRadius * 2 < + minWidth() + ) + { + this.radial = false; + } + } + } + } + + // set alphaLabel + // + if + ( + collapse || + hide || + this.hide || + this.keyed || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLabel.setTarget(0); + } + else + { + if + ( + (this.radial || nLabelOffsets[depth - 2]) + ) + { + this.alphaLabel.setTarget(1); + } + else + { + this.alphaLabel.setTarget(0); + + if ( this.radialPrev ) + { + this.alphaLabel.start = 0; + } + } + } + + // set alphaArc + // + if + ( + collapse || + hide || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaArc.setTarget(0); + } + else + { + this.alphaArc.setTarget(1); + } + + // set alphaLine + // + if + ( + hide || + this.hide && nextSiblingHidden || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLine.setTarget(0); + } + else + { + this.alphaLine.setTarget(1); + } + + //if ( ! this.radial ) + { + this.resetLabelWidth(); + } + + // set labelRadius target + // + if ( collapse ) + { + this.labelRadius.setTarget(this.radiusInner.end); + } + else + { + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.labelRadius.setTarget(1); + } + else + { + this.setTargetLabelRadius(); + } + } + } + } + + this.setTargetWedge = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + // set angles + // + var baseMagnitudeRelative = this.baseMagnitude - selectedNode.baseMagnitude; + // + this.angleStart.setTarget(baseMagnitudeRelative * angleFactor); + this.angleEnd.setTarget((baseMagnitudeRelative + this.magnitude) * angleFactor); + + // set radiusInner + // + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.radiusInner.setTarget(1); + } + else + { + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depth - 2]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depth - 1)); + } + } + + if ( this.hide != undefined ) + { + this.hidePrev = this.hide; + } + + if ( this.hideAlone != undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + // set hide + // + if + ( + (this.angleEnd.end - this.angleStart.end) * + (this.radiusInner.end * gRadius + gRadius) < + minWidth() + ) + { + if ( depth == 2 && ! this.getCollapse() && this.depth <= maxAbsoluteDepth ) + { + this.keyed = true; + keys++; + this.hide = false; + + var percentage = this.getPercentage(); + this.keyLabel = this.name + ' ' + percentage + '%'; + var dim = context.measureText(this.keyLabel); + this.keyNameWidth = dim.width; + } + else + { + this.keyed = false; + this.hide = depth > 2; + } + } + else + { + this.keyed = false; + this.hide = false; + } + } + + this.shortenLabel = function() + { + var label = this.name; + + var labelWidth = this.nameWidth; + var maxWidth = this.labelWidth.current(); + var minEndLength = 0; + + if ( labelWidth > maxWidth && label.length > minEndLength * 2 ) + { + var endLength = + Math.floor((label.length - 1) * maxWidth / labelWidth / 2); + + if ( endLength < minEndLength ) + { + endLength = minEndLength; + } + + return ( + label.substring(0, endLength) + + '...' + + label.substring(label.length - endLength)); + } + else + { + return label; + } + } + +/* this.shouldAddSearchResultsString = function() + { + if ( this.isSearchResult ) + { + return this.searchResults > 1; + } + else + { + return this.searchResults > 0; + } + } +*/ + this.sort = function() + { + this.children.sort(function(a, b){return b.getMagnitude() - a.getMagnitude()}); + + for (var i = 0; i < this.children.length; i++) + { + this.children[i].sort(); + } + } +} + +var options; + +function addOptionElement(position, innerHTML, title) +{ + var div = document.createElement("div"); +// div.style.position = 'absolute'; +// div.style.top = position + 'px'; + div.innerHTML = innerHTML; +// div.style.display = 'block'; + div.style.padding = '2px'; + + if ( title ) + { + div.title = title; + } + + options.appendChild(div); + var height = 0;//div.clientHeight; + return position + height; +} + +function addOptionElements(hueName, hueDefault) +{ + options = document.createElement('div'); + options.style.position = 'absolute'; + options.style.top = '0px'; + options.addEventListener('mousedown', function(e) {mouseClick(e)}, false); +// options.onmouseup = function(e) {mouseUp(e)} + document.body.appendChild(options); + + document.body.style.font = '11px sans-serif'; + var position = 5; + + details = document.createElement('div'); + details.style.position = 'absolute'; + details.style.top = '1%'; + details.style.right = '2%'; + details.style.textAlign = 'right'; + document.body.insertBefore(details, canvas); +// <div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"> + + details.innerHTML = '\ +<span id="detailsName" style="font-weight:bold"></span> \ +<input type="button" id="detailsExpand" onclick="expand(focusNode);"\ +value="↔" title="Expand this wedge to become the new focus of the chart"/><br/>\ +<div id="detailsInfo" style="float:right"></div>'; + + keyControl = document.createElement('input'); + keyControl.type = 'button'; + keyControl.value = showKeys ? 'x' : '…'; + keyControl.style.position = ''; + keyControl.style.position = 'fixed'; + keyControl.style.visibility = 'hidden'; + + document.body.insertBefore(keyControl, canvas); + + var logoElement = document.getElementById('logo'); + + if ( logoElement ) + { + logoImage = logoElement.src; + } + else + { + logoImage = 'http://marbl.github.io/Krona/img/logo-med.png'; + } + +// document.getElementById('options').style.fontSize = '9pt'; + position = addOptionElement + ( + position, +'<a style="margin:2px" target="_blank" href="https://github.com/marbl/Krona/wiki"><img style="vertical-align:middle;width:108px;height:30px;" src="' + logoImage + '" alt="Logo of Krona"/></a><input type="button" id="back" value="←" title="Go back (Shortcut: ←)"/>\ +<input type="button" id="forward" value="→" title="Go forward (Shortcut: →)"/> \ + Search: <input type="text" id="search"/>\ +<input id="searchClear" type="button" value="x" onclick="clearSearch()"/> \ +<span id="searchResults"></span>' + ); + + if ( datasets > 1 ) + { + var size = datasets < datasetSelectSize ? datasets : datasetSelectSize; + + var select = + '<table style="border-collapse:collapse;padding:0px"><tr><td style="padding:0px">' + + '<select id="datasets" style="min-width:100px" size="' + size + '" onchange="onDatasetChange()">'; + + for ( var i = 0; i < datasetNames.length; i++ ) + { + select += '<option>' + datasetNames[i] + '</option>'; + } + + select += + '</select></td><td style="vertical-align:top;padding:1px;">' + + '<input style="display:block" title="Previous dataset (Shortcut: ↑)" id="prevDataset" type="button" value="↑" onclick="prevDataset()" disabled="true"/>' + + '<input title="Next dataset (Shortcut: ↓)" id="nextDataset" type="button" value="↓" onclick="nextDataset()"/><br/></td>' + + '<td style="padding-top:1px;vertical-align:top"><input title="Switch to the last dataset that was viewed (Shortcut: TAB)" id="lastDataset" type="button" style="font:11px Times new roman" value="last" onclick="selectLastDataset()"/></td></tr></table>'; + + position = addOptionElement(position + 5, select); + + datasetDropDown = document.getElementById('datasets'); + datasetButtonLast = document.getElementById('lastDataset'); + datasetButtonPrev = document.getElementById('prevDataset'); + datasetButtonNext = document.getElementById('nextDataset'); + + position += datasetDropDown.clientHeight; + } + + position = addOptionElement + ( + position + 5, +'<input type="button" id="maxAbsoluteDepthDecrease" value="-"/>\ +<span id="maxAbsoluteDepth"></span>\ + <input type="button" id="maxAbsoluteDepthIncrease" value="+"/> Max depth', +'Maximum depth to display, counted from the top level \ +and including collapsed wedges.' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="fontSizeDecrease" value="-"/>\ +<span id="fontSize"></span>\ + <input type="button" id="fontSizeIncrease" value="+"/> Font size' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="radiusDecrease" value="-"/>\ +<input type="button" id="radiusIncrease" value="+"/> Chart size' + ); + + if ( hueName ) + { + hueDisplayName = attributes[attributeIndex(hueName)].displayName; + + position = addOptionElement + ( + position + 5, + '<input type="checkbox" id="useHue" style="float:left" ' + + '/><div>Color by<br/>' + hueDisplayName + + '</div>' + ); + + useHueCheckBox = document.getElementById('useHue'); + useHueCheckBox.checked = hueDefault; + useHueCheckBox.onclick = handleResize; + useHueCheckBox.onmousedown = suppressEvent; + } + /* + position = addOptionElement + ( + position + 5, + ' <input type="checkbox" id="shorten" checked="checked" />Shorten labels</div>', + 'Prevent labels from overlapping by shortening them' + ); + + position = addOptionElement + ( + position, + ' <input type="checkbox" id="compress" checked="checked" />Compress', + 'Compress wedges if needed to show the entire depth' + ); + */ + position = addOptionElement + ( + position, + '<input type="checkbox" id="collapse" checked="checked" />Collapse', + 'Collapse wedges that are redundant (entirely composed of another wedge)' + ); + + position = addOptionElement + ( + position + 5, + '<input type="button" id="snapshot" value="Snapshot"/>', +'Render the current view as SVG (Scalable Vector Graphics), a publication-\ +quality format that can be printed and saved (see Help for browser compatibility)' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="linkButton" value="Link"/>\ +<input type="text" size="30" id="linkText"/>', +'Show a link to this view that can be copied for bookmarking or sharing' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="help" value="?"\ +onclick="window.open(\'https://github.com/marbl/Krona/wiki/Browsing%20Krona%20charts\', \'help\')"/>', +'Help' + ); +} + +function arrow(angleStart, angleEnd, radiusInner) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + var angleCenter = (angleStart + angleEnd) / 2; + var radiusArrowInner = radiusInner - gRadius / 10;//nodeRadius * gRadius; + var radiusArrowOuter = gRadius * 1.1;//(1 + nodeRadius); + var radiusArrowCenter = (radiusArrowInner + radiusArrowOuter) / 2; + var pointLength = (radiusArrowOuter - radiusArrowInner) / 5; + + context.fillStyle = highlightFill; + context.lineWidth = highlightLineWidth; + + // First, mask out the first half of the arrow. This will prevent the tips + // from superimposing if the arrow goes most of the way around the circle. + // Masking is done by setting the clipping region to the inverse of the + // half-arrow, which is defined by cutting the half-arrow out of a large + // rectangle + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter, true); + context.closePath(); + context.moveTo(-imageWidth, -imageHeight); + context.lineTo(imageWidth, -imageHeight); + context.lineTo(imageWidth, imageHeight); + context.lineTo(-imageWidth, imageHeight); + context.closePath(); + context.save(); + context.clip(); + + // Next, draw the other half-arrow with the first half masked out + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleStart, true); + context.lineTo + ( + radiusArrowInner * Math.cos(angleStart), + radiusArrowInner * Math.sin(angleStart) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleStart) + pointLength * Math.sin(angleStart), + radiusArrowCenter * Math.sin(angleStart) - pointLength * Math.cos(angleStart) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleStart), + radiusArrowOuter * Math.sin(angleStart) + ); + context.arc(0, 0, gRadius, angleStart, angleCenter, false); + context.fill(); + context.stroke(); + + // Finally, remove the clipping region and draw the first half-arrow. This + // half is extended slightly to fill the seam. + // + context.restore(); + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter - 2 / (2 * Math.PI * radiusInner), angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter - 2 / (2 * Math.PI * gRadius), true); + context.fill(); + context.stroke(); +} + +function attributeIndex(aname) +{ + for ( var i = 0 ; i < attributes.length; i++ ) + { + if ( aname == attributes[i].name ) + { + return i; + } + } + + return null; +} + +function checkHighlight() +{ + var lastHighlightedNode = highlightedNode; + var lastHighlightingHidden = highlightingHidden; + + highlightedNode = selectedNode; + resetKeyOffset(); + + if ( progress == 1 ) + { + selectedNode.checkHighlight(); + if ( selectedNode.getParent() ) + { + selectedNode.getParent().checkHighlightCenter(); + } + + focusNode.checkHighlightMap(); + } + + if ( highlightedNode != selectedNode ) + { + if ( highlightedNode == focusNode ) + { +// canvas.style.display='none'; +// window.resizeBy(1,0); +// canvas.style.cursor='ew-resize'; +// window.resizeBy(-1,0); +// canvas.style.display='inline'; + } + else + { +// canvas.style.cursor='pointer'; + } + } + else + { +// canvas.style.cursor='auto'; + } + + if + ( + ( + true || + highlightedNode != lastHighlightedNode || + highlightingHidden != highlightingHiddenLast + ) && + progress == 1 + ) + { + draw(); // TODO: handle in update() + } +} + +function checkSelectedCollapse() +{ + var newNode = selectedNode; + + while ( newNode.getCollapse() ) + { + newNode = newNode.children[0]; + } + + if ( newNode.children.length == 0 && newNode.getParent() ) + { + newNode = newNode.getParent(); + } + + if ( newNode != selectedNode ) + { + selectNode(newNode); + } +} + +function clearSearch() +{ + if ( search.value != '' ) + { + search.value = ''; + onSearchChange(); + } +} + +function createSVG() +{ + svgNS = "http://www.w3.org/2000/svg"; + var SVG = {}; + SVG.xlinkns = "http://www.w3.org/1999/xlink"; + + var newSVG = document.createElementNS(svgNS, "svg:svg"); + + newSVG.setAttribute("id", "canvas"); + // How big is the canvas in pixels + newSVG.setAttribute("width", '100%'); + newSVG.setAttribute("height", '100%'); + // Set the coordinates used by drawings in the canvas +// newSVG.setAttribute("viewBox", "0 0 " + imageWidth + " " + imageHeight); + // Define the XLink namespace that SVG uses + newSVG.setAttributeNS + ( + "http://www.w3.org/2000/xmlns/", + "xmlns:xlink", + SVG.xlinkns + ); + + return newSVG; +} + +function degrees(radians) +{ + return radians * 180 / Math.PI; +} + +function draw() +{ + tweenFrames++; + //resize(); +// context.fillRect(0, 0, imageWidth, imageHeight); + context.clearRect(0, 0, imageWidth, imageHeight); + + context.font = fontNormal; + context.textBaseline = 'middle'; + + //context.strokeStyle = 'rgba(0, 0, 0, 0.3)'; + context.translate(centerX, centerY); + + resetKeyOffset(); + + head.draw(false, false); // draw pie slices + head.draw(true, false); // draw labels + + var pathRoot = selectedNode; + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + pathRoot = focusNode; + } + + if + ( + highlightedNode && + highlightedNode.getDepth() >= selectedNode.getDepth() && + highlightedNode != focusNode + ) + { + if + ( + progress == 1 && + highlightedNode != selectedNode && + ( + highlightedNode != focusNode || + focusNode.children.length > 0 + ) + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlight(true); + } + + //pathRoot = highlightedNode; + } + else if + ( + progress == 1 && + highlightedNode.getDepth() < selectedNode.getDepth() + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlightCenter(); + } + + if ( quickLook && false) // TEMP + { + context.globalAlpha = 1 - progress / 2; + selectedNode.drawHighlight(true); + } + else if ( progress < 1 )//&& zoomOut() ) + { + if ( !zoomOut)//() ) + { + context.globalAlpha = selectedNode.alphaLine.current(); + selectedNode.drawHighlight(true); + } + else if ( selectedNodeLast ) + { + context.globalAlpha = 1 - 4 * Math.pow(progress - .5, 2); + selectedNodeLast.drawHighlight(false); + } + } + + drawDatasetName(); + + //drawHistory(); + + context.translate(-centerX, -centerY); + context.globalAlpha = 1; + + mapRadius = + (imageHeight / 2 - details.clientHeight - details.offsetTop) / + (pathRoot.getDepth() - 1) * 3 / 4 / 2; + + if ( mapRadius > maxMapRadius ) + { + mapRadius = maxMapRadius; + } + + mapBuffer = mapRadius / 2; + + //context.font = fontNormal; + pathRoot.drawMap(pathRoot); + + if ( hueDisplayName && useHue() ) + { + drawLegend(); + } +} + +function drawBubble(angle, radius, width, radial, flip) +{ + var height = fontSize * 2; + var x; + var y; + + width = width + fontSize; + + if ( radial ) + { + y = -fontSize; + + if ( flip ) + { + x = radius - width + fontSize / 2; + } + else + { + x = radius - fontSize / 2; + } + } + else + { + x = -width / 2; + y = -radius - fontSize; + } + + if ( snapshotMode ) + { + drawBubbleSVG(x + centerX, y + centerY, width, height, fontSize, angle); + } + else + { + drawBubbleCanvas(x, y, width, height, fontSize, angle); + } +} + +function drawBubbleCanvas(x, y, width, height, radius, rotation) +{ + context.strokeStyle = 'black'; + context.lineWidth = highlightLineWidth; + context.fillStyle = 'rgba(255, 255, 255, .75)'; + context.rotate(rotation); + roundedRectangle(x, y, width, fontSize * 2, fontSize); + context.fill(); + context.stroke(); + context.rotate(-rotation); +} + +function drawBubbleSVG(x, y, width, height, radius, rotation) +{ + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" fill="rgba(255, 255, 255, .75)' + + '" class="highlight" ' + + 'transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; +} + +function drawDatasetName() +{ + var alpha = datasetAlpha.current(); + + if ( alpha > 0 ) + { + var radius = gRadius * compressedRadii[0] / -2; + + if ( alpha > 1 ) + { + alpha = 1; + } + + context.globalAlpha = alpha; + + drawBubble(0, -radius, datasetWidths[currentDataset], false, false); + drawText(datasetNames[currentDataset], 0, radius, 0, 'center', true); + } +} + +function drawHistory() +{ + var alpha = 1; + context.textAlign = 'center'; + + for ( var i = 0; i < nodeHistoryPosition && alpha > 0; i++ ) + { + + context.globalAlpha = alpha - historyAlphaDelta * tweenFactor; + context.fillText + ( + nodeHistory[nodeHistoryPosition - i - 1].name, + 0, + (i + tweenFactor) * historySpacingFactor * fontSize - 1 + ); + + if ( alpha > 0 ) + { + alpha -= historyAlphaDelta; + } + } + + context.globalAlpha = 1; +} + +function drawLegend() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + context.fillStyle = 'black'; + context.textAlign = 'start'; + context.font = fontNormal; +// context.fillText(valueStartText, textLeft, top + height); +// context.fillText(valueEndText, textLeft, top); + context.fillText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var gradient = context.createLinearGradient(0, top + height, 0, top); + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + gradient.addColorStop(hueStopPositions[i], hueStopHsl[i]); + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + context.fillText(hueStopText[i], textLeft, textY); + } + } + + context.fillStyle = gradient; + context.fillRect(left, top, width, height); + context.lineWidth = thinLineWidth; + context.strokeRect(left, top, width, height); +} + +function drawLegendSVG() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + var text = ''; + + text += svgText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var svgtest = '<linearGradient id="gradient" x1="0%" y1="100%" x2="0%" y2="0%">'; + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + svgtest += + '<stop offset="' + round(hueStopPositions[i] * 100) + + '%" style="stop-color:' + hueStopHsl[i] + '"/>'; + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + text += svgText(hueStopText[i], textLeft, textY); + } + } + + svgtest += '</linearGradient>'; + //alert(svgtest); + svg += svgtest; + svg += + '<rect style="fill:url(#gradient)" x="' + left + '" y="' + top + + '" width="' + width + '" height="' + height + '"/>'; + + svg += text; +} + +function drawSearchHighlights(label, bubbleX, bubbleY, rotation, center) +{ + var index = -1; + var labelLength = label.length; + + bubbleX -= fontSize / 4; + + do + { + index = label.toLowerCase().indexOf(search.value.toLowerCase(), index + 1); + + if ( index != -1 && index < labelLength ) + { + var dim = context.measureText(label.substr(0, index)); + var x = bubbleX + dim.width; + + dim = context.measureText(label.substr(index, search.value.length)); + + var y = bubbleY - fontSize * 3 / 4; + var width = dim.width + fontSize / 2; + var height = fontSize * 3 / 2; + var radius = fontSize / 2; + + if ( snapshotMode ) + { + if ( center ) + { + x += centerX; + y += centerY; + } + + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" class="searchHighlight' + + '" transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.fillStyle = 'rgb(255, 255, 100)'; + context.rotate(rotation); + roundedRectangle(x, y, width, height, radius); + context.fill(); + context.rotate(-rotation); + } + } + } + while ( index != -1 && index < labelLength ); +} + +function drawText(text, x, y, angle, anchor, bold, color) +{ + if ( color == undefined ) + { + color = 'black'; + } + + if ( snapshotMode ) + { + svg += + '<text x="' + (centerX + x) + '" y="' + (centerY + y) + + '" text-anchor="' + anchor + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" transform="rotate(' + degrees(angle) + ',' + centerX + ',' + centerY + ')">' + + text + '</text>'; + } + else + { + context.fillStyle = color; + context.textAlign = anchor; + context.font = bold ? fontBold : fontNormal; + context.rotate(angle); + context.fillText(text, x, y); + context.rotate(-angle); + } +} + +function drawTextPolar +( + text, + innerText, + angle, + radius, + radial, + bubble, + bold, + searchResult, + searchResults +) +{ + var anchor; + var textX; + var textY; + var spacer; + var totalText = text; + var flip; + + if ( snapshotMode ) + { + spacer = '   '; + } + else + { + spacer = ' '; + } + + if ( radial ) + { + flip = angle < 3 * Math.PI / 2; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + anchor = 'end'; + + if ( innerText ) + { + totalText = text + spacer + innerText; + } + } + else + { + anchor = 'start'; + + if ( innerText ) + { + totalText = innerText + spacer + text; + } + } + + textX = radius; + textY = 0; + } + else + { + flip = angle < Math.PI || angle > 2 * Math.PI; + var label; + + anchor = snapshotMode ? 'middle' : 'center'; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + } + + angle += Math.PI / 2; + textX = 0; + textY = -radius; + } + + if ( bubble ) + { + var textActual = totalText; + + if ( innerText && snapshotMode ) + { + if ( flip ) + { + textActual = text + ' ' + innerText; + } + else + { + textActual = innerText + ' ' + text; + } + } + + if ( searchResults ) + { + textActual = textActual + searchResultString(searchResults); + } + + var textWidth = measureText(textActual, bold); + + var x = textX; + + if ( anchor == 'end' ) + { + x -= textWidth; + } + else if ( anchor != 'start' ) + { + // centered + x -= textWidth / 2; + } + + drawBubble(angle, radius, textWidth, radial, flip); + + if ( searchResult ) + { + drawSearchHighlights + ( + textActual, + x, + textY, + angle, + true + ) + } + } + + if ( searchResults ) + { + totalText = totalText + searchResultString(searchResults); + } + + drawText(totalText, textX, textY, angle, anchor, bold); + + return flip; +} + +function drawTick(start, length, angle) +{ + if ( snapshotMode ) + { + svg += + '<line x1="' + (centerX + start) + + '" y1="' + centerY + + '" x2="' + (centerX + start + length) + + '" y2="' + centerY + + '" class="tick" transform="rotate(' + + degrees(angle) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.rotate(angle); + context.beginPath(); + context.moveTo(start, 0); + context.lineTo(start + length, 0); + context.lineWidth = thinLineWidth * 2; + context.stroke(); + context.rotate(-angle); + } +} + +function drawWedge +( + angleStart, + angleEnd, + radiusInner, + radiusOuter, + color, + patternAlpha, + highlight +) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + if ( snapshotMode ) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + var dArray = + [ + " M ", x1, ",", y1, + " L ", x2, ",", y2, + " A ", gRadius, ",", gRadius, " 0 ", longArc, ",1 ", x3, ",", y3, + " L ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, " 0 ", x1, ",", y1, + " Z " + ]; + + svg += + '<path class="'+ (highlight ? 'highlight' : 'wedge') + '" fill="' + color + + '" d="' + dArray.join('') + '"/>'; + + if ( patternAlpha > 0 ) + { + svg += + '<path class="wedge" fill="url(#hiddenPattern)" d="' + + dArray.join('') + '"/>'; + } + } + else + { + // fudge to prevent seams during animation + // + angleEnd += 1 / gRadius; + + context.fillStyle = color; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.arc(0, 0, radiusOuter, angleEnd, angleStart, true); + context.closePath(); + context.fill(); + + if ( patternAlpha > 0 ) + { + context.save(); + context.clip(); + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + context.fill(); + context.restore(); + } + + if ( highlight ) + { + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.strokeStyle = 'black'; + context.stroke(); + } + } +} + +function expand(node) +{ + selectNode(node); + updateView(); +} + +function focusLost() +{ + mouseX = -1; + mouseY = -1; + checkHighlight(); + document.body.style.cursor = 'auto'; +} + +function fontSizeDecrease() +{ + if ( fontSize > 1 ) + { + fontSize--; + updateViewNeeded = true; + } +} + +function fontSizeIncrease() +{ + fontSize++; + updateViewNeeded = true; +} + +function getGetString(name, value, bool) +{ + return name + '=' + (bool ? value ? 'true' : 'false' : value); +} + +function hideLink() +{ + hide(linkText); + show(linkButton); +} + +function show(object) +{ + object.style.display = 'inline'; +} + +function hide(object) +{ + object.style.display = 'none'; +} + +function showLink() +{ + var urlHalves = String(document.location).split('?'); + var newGetVariables = new Array(); + + newGetVariables.push + ( + getGetString('dataset', currentDataset, false), + getGetString('node', selectedNode.id, false), + getGetString('collapse', collapse, true), + getGetString('color', useHue(), true), + getGetString('depth', maxAbsoluteDepth - 1, false), + getGetString('font', fontSize, false), + getGetString('key', showKeys, true) + ); + + hide(linkButton); + show(linkText); + linkText.value = urlHalves[0] + '?' + getVariables.concat(newGetVariables).join('&'); + //linkText.disabled = false; + linkText.focus(); + linkText.select(); + //linkText.disabled = true; +// document.location = urlHalves[0] + '?' + getVariables.join('&'); +} + +function getFirstChild(element) +{ + element = element.firstChild; + + if ( element && element.nodeType != 1 ) + { + element = getNextSibling(element); + } + + return element; +} + +function getNextSibling(element) +{ + do + { + element = element.nextSibling; + } + while ( element && element.nodeType != 1 ); + + return element; +} + +function getPercentage(fraction) +{ + return round(fraction * 100); +} + +function hslText(hue) +{ + if ( 1 || snapshotMode ) + { + // Safari doesn't seem to allow hsl() in SVG + + var rgb = hslToRgb(hue, saturation, (lightnessBase + lightnessMax) / 2); + + return rgbText(rgb.r, rgb.g, rgb.b); + } + else + { + var hslArray = + [ + 'hsl(', + Math.floor(hue * 360), + ',', + Math.floor(saturation * 100), + '%,', + Math.floor((lightnessBase + lightnessMax) * 50), + '%)' + ]; + + return hslArray.join(''); + } +} + +function hslToRgb(h, s, l) +{ + var m1, m2; + var r, g, b; + + if (s == 0) + { + r = g = b = Math.floor((l * 255)); + } + else + { + if (l <= 0.5) + { + m2 = l * (s + 1); + } + else + { + m2 = l + s - l * s; + } + + m1 = l * 2 - m2; + + r = Math.floor(hueToRgb(m1, m2, h + 1 / 3)); + g = Math.floor(hueToRgb(m1, m2, h)); + b = Math.floor(hueToRgb(m1, m2, h - 1/3)); + } + + return {r: r, g: g, b: b}; +} + +function hueToRgb(m1, m2, hue) +{ + var v; + + while (hue < 0) + { + hue += 1; + } + + while (hue > 1) + { + hue -= 1; + } + + if (6 * hue < 1) + v = m1 + (m2 - m1) * hue * 6; + else if (2 * hue < 1) + v = m2; + else if (3 * hue < 2) + v = m1 + (m2 - m1) * (2/3 - hue) * 6; + else + v = m1; + + return 255 * v; +} + +function interpolateHue(hueStart, hueEnd, valueStart, valueEnd) +{ + // since the gradient will be RGB based, we need to add stops to hit all the + // colors in the hue spectrum + + hueStopPositions = new Array(); + hueStopHsl = new Array(); + hueStopText = new Array(); + + hueStopPositions.push(0); + hueStopHsl.push(hslText(hueStart)); + hueStopText.push(round(valueStart)); + + for + ( + var i = (hueStart > hueEnd ? 5 / 6 : 1 / 6); + (hueStart > hueEnd ? i > 0 : i < 1); + i += (hueStart > hueEnd ? -1 : 1) / 6 + ) + { + if + ( + hueStart > hueEnd ? + i > hueEnd && i < hueStart : + i > hueStart && i < hueEnd + ) + { + hueStopPositions.push(lerp(i, hueStart, hueEnd, 0, 1)); + hueStopHsl.push(hslText(i)); + hueStopText.push(round(lerp + ( + i, + hueStart, + hueEnd, + valueStart, + valueEnd + ))); + } + } + + hueStopPositions.push(1); + hueStopHsl.push(hslText(hueEnd)); + hueStopText.push(round(valueEnd)); +} + +function keyLineAngle(angle, keyAngle, bendRadius, keyX, keyY, pointsX, pointsY) +{ + if ( angle < Math.PI / 2 && keyY < bendRadius * Math.sin(angle) + || angle > Math.PI / 2 && keyY < bendRadius) + { + return Math.asin(keyY / bendRadius); + } + else + { + // find the angle of the normal to a tangent line that goes to + // the label + + var textDist = Math.sqrt + ( + Math.pow(keyX, 2) + + Math.pow(keyY, 2) + ); + + var tanAngle = Math.acos(bendRadius / textDist) + keyAngle; + + if ( angle < tanAngle || angle < Math.PI / 2 )//|| labelLeft < centerX ) + { + // angle doesn't reach far enough for tangent; collapse and + // connect directly to label + + if ( keyY / Math.tan(angle) > 0 ) + { + pointsX.push(keyY / Math.tan(angle)); + pointsY.push(keyY); + } + else + { + pointsX.push(bendRadius * Math.cos(angle)); + pointsY.push(bendRadius * Math.sin(angle)); + } + + return angle; + } + else + { + return tanAngle; + } + } +} + +function keyOffset() +{ + return imageHeight - (keys - currentKey + 1) * (keySize + keyBuffer) + keyBuffer - margin; +} + +function lerp(value, fromStart, fromEnd, toStart, toEnd) +{ + return (value - fromStart) * + (toEnd - toStart) / + (fromEnd - fromStart) + + toStart; +} + +function createCanvas() +{ + canvas = document.createElement('canvas'); + document.body.appendChild(canvas); + context = canvas.getContext('2d'); +} + +function load() +{ + document.body.style.overflow = "hidden"; + document.body.style.margin = 0; + + createCanvas(); + + if ( context == undefined ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + if ( typeof context.fillText != 'function' ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 canvas text (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + resize(); + + var kronaElement = document.getElementsByTagName('krona')[0]; + + var magnitudeName; + var hueName; + var hueDefault; + var hueStart; + var hueEnd; + var valueStart; + var valueEnd; + + if ( kronaElement.getAttribute('collapse') != undefined ) + { + collapse = kronaElement.getAttribute('collapse') == 'true'; + } + + if ( kronaElement.getAttribute('key') != undefined ) + { + showKeys = kronaElement.getAttribute('key') == 'true'; + } + + for + ( + var element = getFirstChild(kronaElement); + element; + element = getNextSibling(element) + ) + { + switch ( element.tagName.toLowerCase() ) + { + case 'attributes': + magnitudeName = element.getAttribute('magnitude'); + // + for + ( + var attributeElement = getFirstChild(element); + attributeElement; + attributeElement = getNextSibling(attributeElement) + ) + { + var tag = attributeElement.tagName.toLowerCase(); + + if ( tag == 'attribute' ) + { + var attribute = new Attribute(); + attribute.name = attributeElement.firstChild.nodeValue.toLowerCase(); + attribute.displayName = attributeElement.getAttribute('display'); + + if ( attributeElement.getAttribute('hrefBase') ) + { + attribute.hrefBase = attributeElement.getAttribute('hrefBase'); + } + + if ( attributeElement.getAttribute('target') ) + { + attribute.target = attributeElement.getAttribute('target'); + } + + if ( attribute.name == magnitudeName ) + { + magnitudeIndex = attributes.length; + } + + if ( attributeElement.getAttribute('listAll') ) + { + attribute.listAll = attributeElement.getAttribute('listAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('listNode') ) + { + attribute.listNode = attributeElement.getAttribute('listNode').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataAll') ) + { + attribute.dataAll = attributeElement.getAttribute('dataAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataNode') ) + { + attribute.dataNode = attributeElement.getAttribute('dataNode').toLowerCase(); + } + + if ( attributeElement.getAttribute('postUrl') ) + { + attribute.postUrl = attributeElement.getAttribute('postUrl'); + } + + if ( attributeElement.getAttribute('postVar') ) + { + attribute.postVar = attributeElement.getAttribute('postVar'); + } + + if ( attributeElement.getAttribute('mono') ) + { + attribute.mono = true; + } + + attributes.push(attribute); + } + else if ( tag == 'list' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.list = true; + attributes.push(attribute); + } + else if ( tag == 'data' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.data = true; + attributes.push(attribute); + + var enableScript = document.createElement('script'); + var date = new Date(); + enableScript.src = + attributeElement.getAttribute('enable') + '?' + + date.getTime(); + document.body.appendChild(enableScript); + } + } + break; + + case 'color': + hueName = element.getAttribute('attribute'); + hueStart = Number(element.getAttribute('hueStart')) / 360; + hueEnd = Number(element.getAttribute('hueEnd')) / 360; + valueStart = Number(element.getAttribute('valueStart')); + valueEnd = Number(element.getAttribute('valueEnd')); + // + interpolateHue(hueStart, hueEnd, valueStart, valueEnd); + // + if ( element.getAttribute('default') == 'true' ) + { + hueDefault = true; + } + break; + + case 'datasets': + datasetNames = new Array(); + // + for ( j = getFirstChild(element); j; j = getNextSibling(j) ) + { + datasetNames.push(j.firstChild.nodeValue); + } + datasets = datasetNames.length; + break; + + case 'node': + head = loadTreeDOM + ( + element, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + break; + } + } + + // get GET options + // + var urlHalves = String(document.location).split('?'); + var datasetDefault = 0; + var maxDepthDefault; + var nodeDefault = 0; + // + if ( urlHalves[1] ) + { + var vars = urlHalves[1].split('&'); + + for ( i = 0; i < vars.length; i++ ) + { + var pair = vars[i].split('='); + + switch ( pair[0] ) + { + case 'collapse': + collapse = pair[1] == 'true'; + break; + + case 'color': + hueDefault = pair[1] == 'true'; + break; + + case 'dataset': + datasetDefault = Number(pair[1]); + break; + + case 'depth': + maxDepthDefault = Number(pair[1]) + 1; + break; + + case 'key': + showKeys = pair[1] == 'true'; + break; + + case 'font': + fontSize = Number(pair[1]); + break; + + case 'node': + nodeDefault = Number(pair[1]); + break; + + default: + getVariables.push(pair[0] + '=' + pair[1]); + break; + } + } + } + + addOptionElements(hueName, hueDefault); + setCallBacks(); + + head.sort(); + maxAbsoluteDepth = 0; + selectDataset(datasetDefault); + + if ( maxDepthDefault && maxDepthDefault < head.maxDepth ) + { + maxAbsoluteDepth = maxDepthDefault; + } + else + { + maxAbsoluteDepth = head.maxDepth; + } + + selectNode(nodes[nodeDefault]); + + setInterval(update, 20); + + window.onresize = handleResize; + updateMaxAbsoluteDepth(); + updateViewNeeded = true; +} + +function loadTreeDOM +( + domNode, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd +) +{ + var newNode = new Node(); + + newNode.name = domNode.getAttribute('name'); + + if ( domNode.getAttribute('href') ) + { + newNode.href = domNode.getAttribute('href'); + } + + if ( hueName ) + { + newNode.hues = new Array(); + } + + for ( var i = getFirstChild(domNode); i; i = getNextSibling(i) ) + { + switch ( i.tagName.toLowerCase() ) + { + case 'node': + var newChild = loadTreeDOM + ( + i, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + newChild.parent = newNode; + newNode.children.push(newChild); + break; + + default: + var attributeName = i.tagName.toLowerCase(); + var index = attributeIndex(attributeName); + // + newNode.attributes[index] = new Array(); + // + for ( var j = getFirstChild(i); j; j = getNextSibling(j) ) + { + if ( attributes[index] == undefined ) + { + var x = 5; + } + if ( attributes[index].list ) + { + newNode.attributes[index].push(new Array()); + + for ( var k = getFirstChild(j); k; k = getNextSibling(k) ) + { + newNode.attributes[index][newNode.attributes[index].length - 1].push(k.firstChild.nodeValue); + } + } + else + { + var value = j.firstChild ? j.firstChild.nodeValue : ''; + + if ( j.getAttribute('href') ) + { + var target; + + if ( attributes[index].target ) + { + target = ' target="' + attributes[index].target + '"'; + } + + value = '<a href="' + attributes[index].hrefBase + j.getAttribute('href') + '"' + target + '>' + value + '</a>'; + } + + newNode.attributes[index].push(value); + } + } + // + if ( attributeName == magnitudeName || attributeName == hueName ) + { + for ( j = 0; j < datasets; j++ ) + { + var value = newNode.attributes[index][j] == undefined ? 0 : Number(newNode.attributes[index][j]); + + newNode.attributes[index][j] = value; + + if ( attributeName == hueName ) + { + var hue = lerp + ( + value, + valueStart, + valueEnd, + hueStart, + hueEnd + ); + + if ( hue < hueStart == hueStart < hueEnd ) + { + hue = hueStart; + } + else if ( hue > hueEnd == hueStart < hueEnd ) + { + hue = hueEnd; + } + + newNode.hues[j] = hue; + } + } + + if ( attributeName == hueName ) + { + newNode.hue = new Tween(newNode.hues[0], newNode.hues[0]); + } + } + break; + } + } + + return newNode; +} + +function maxAbsoluteDepthDecrease() +{ + if ( maxAbsoluteDepth > 2 ) + { + maxAbsoluteDepth--; + head.setMaxDepths(); + handleResize(); + } +} + +function maxAbsoluteDepthIncrease() +{ + if ( maxAbsoluteDepth < head.maxDepth ) + { + maxAbsoluteDepth++; + head.setMaxDepths(); + handleResize(); + } +} + +function measureText(text, bold) +{ + context.font = bold ? fontBold : fontNormal; + var dim = context.measureText(text); + return dim.width; +} + +function min(a, b) +{ + return a < b ? a : b; +} + +function minWidth() +{ + // Min wedge width (at center) for displaying a node (or for displaying a + // label if it's at the highest level being viewed, multiplied by 2 to make + // further calculations simpler + + return (fontSize * 2.3); +} + +function mouseMove(e) +{ + mouseX = e.pageX; + mouseY = e.pageY - headerHeight; + mouseXRel = (mouseX - centerX) * backingScale() + mouseYRel = (mouseY - centerY) * backingScale() + + if ( head && ! quickLook ) + { + checkHighlight(); + } +} + +function mouseClick(e) +{ + if ( highlightedNode == focusNode && focusNode != selectedNode || selectedNode.hasParent(highlightedNode) ) + { + if ( highlightedNode.hasChildren() ) + { + expand(highlightedNode); + } + } + else if ( progress == 1 )//( highlightedNode != selectedNode ) + { + setFocus(highlightedNode); +// document.body.style.cursor='ew-resize'; + draw(); + checkHighlight(); + var date = new Date(); + mouseDownTime = date.getTime(); + mouseDown = true; + } +} + +function mouseUp(e) +{ + if ( quickLook ) + { + navigateBack(); + quickLook = false; + } + + mouseDown = false; +} + +function navigateBack() +{ + if ( nodeHistoryPosition > 0 ) + { + nodeHistory[nodeHistoryPosition] = selectedNode; + nodeHistoryPosition--; + + if ( nodeHistory[nodeHistoryPosition].collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + setSelectedNode(nodeHistory[nodeHistoryPosition]); + updateDatasetButtons(); + updateView(); + } +} + +function navigateUp() +{ + if ( selectedNode.getParent() ) + { + selectNode(selectedNode.getParent()); + updateView(); + } +} + +function navigateForward() +{ + if ( nodeHistoryPosition < nodeHistory.length - 1 ) + { + nodeHistoryPosition++; + var newNode = nodeHistory[nodeHistoryPosition]; + + if ( newNode.collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + if ( nodeHistoryPosition == nodeHistory.length - 1 ) + { + // this will ensure the forward button is disabled + + nodeHistory.length = nodeHistoryPosition; + } + + setSelectedNode(newNode); + updateDatasetButtons(); + updateView(); + } +} + +function nextDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == datasets - 1 ) + { + newDataset = 0; + } + else + { + newDataset++; + } + } + while ( datasetDropDown.options[newDataset].disabled ) + + selectDataset(newDataset); +} + +function onDatasetChange() +{ + selectDataset(datasetDropDown.selectedIndex); +} + +function onKeyDown(event) +{ + if + ( + event.keyCode == 37 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateBack(); + event.preventDefault(); + } + else if + ( + event.keyCode == 39 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateForward(); + event.preventDefault(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { + prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { + nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 9 && datasets > 1 ) + { + selectLastDataset(); + event.preventDefault(); + } + else if ( event.keyCode == 83 ) + { + progress += .2; + } + else if ( event.keyCode == 66 ) + { + progress -= .2; + } + else if ( event.keyCode == 70 ) + { + progress = 1; + } +} + +function onKeyPress(event) +{ + if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onKeyUp(event) +{ + if ( event.keyCode == 27 && document.activeElement.id == 'search' ) + { + search.value = ''; + onSearchChange(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onSearchChange() +{ + nSearchResults = 0; + head.search(); + + if ( search.value == '' ) + { + searchResults.innerHTML = ''; + } + else + { + searchResults.innerHTML = nSearchResults + ' results'; + } + + setFocus(selectedNode); + draw(); +} + +function post(url, variable, value, postWindow) +{ + var form = document.createElement('form'); + var input = document.createElement('input'); + var inputDataset = document.createElement('input'); + + form.appendChild(input); + form.appendChild(inputDataset); + + form.method = "POST"; + form.action = url; + + if ( postWindow == undefined ) + { + form.target = '_blank'; + postWindow = window; + } + + input.type = 'hidden'; + input.name = variable; + input.value = value; + + inputDataset.type = 'hidden'; + inputDataset.name = 'dataset'; + inputDataset.value = currentDataset; + + postWindow.document.body.appendChild(form); + form.submit(); +} + +function prevDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == 0 ) + { + newDataset = datasets - 1; + } + else + { + newDataset--; + } + } + while ( datasetDropDown.options[newDataset].disabled ); + + selectDataset(newDataset); +} + +function radiusDecrease() +{ + if ( bufferFactor < .309 ) + { + bufferFactor += .03; + updateViewNeeded = true; + } +} + +function radiusIncrease() +{ + if ( bufferFactor > .041 ) + { + bufferFactor -= .03; + updateViewNeeded = true; + } +} + +function resetKeyOffset() +{ + currentKey = 1; + keyMinTextLeft = centerX + gRadius + buffer - buffer / (keys + 1) / 2 + fontSize / 2; + keyMinAngle = 0; +} + +function rgbText(r, g, b) +{ + var rgbArray = + [ + "rgb(", + Math.floor(r), + ",", + Math.floor(g), + ",", + Math.floor(b), + ")" + ]; + + return rgbArray.join(''); +} + +function round(number) +{ + if ( number >= 1 || number <= -1 ) + { + return number.toFixed(0); + } + else + { + return number.toPrecision(1); + } +} + +function roundedRectangle(x, y, width, height, radius) +{ + if ( radius * 2 > width ) + { + radius = width / 2; + } + + if ( radius * 2 > height ) + { + radius = height / 2; + } + + context.beginPath(); + context.arc(x + radius, y + radius, radius, Math.PI, Math.PI * 3 / 2, false); + context.lineTo(x + width - radius, y); + context.arc(x + width - radius, y + radius, radius, Math.PI * 3 / 2, Math.PI * 2, false); + context.lineTo(x + width, y + height - radius); + context.arc(x + width - radius, y + height - radius, radius, 0, Math.PI / 2, false); + context.lineTo(x + radius, y + height); + context.arc(x + radius, y + height - radius, radius, Math.PI / 2, Math.PI, false); + context.lineTo(x, y + radius); +} + +function passClick(e) +{ + mouseClick(e); +} + +function searchResultString(results) +{ + var searchResults = this.searchResults; + + if ( this.isSearchResult ) + { + // don't count ourselves + searchResults--; + } + + return ' - ' + results + (results > 1 ? ' results' : ' result'); +} + +function setCallBacks() +{ + canvas.onselectstart = function(){return false;} // prevent unwanted highlighting + options.onselectstart = function(){return false;} // prevent unwanted highlighting + document.onmousemove = mouseMove; + window.onblur = focusLost; + window.onmouseout = focusLost; + document.onkeyup = onKeyUp; + document.onkeydown = onKeyDown; + canvas.onmousedown = mouseClick; + document.onmouseup = mouseUp; + keyControl.onclick = toggleKeys; + collapseCheckBox = document.getElementById('collapse'); + collapseCheckBox.checked = collapse; + collapseCheckBox.onclick = handleResize; + collapseCheckBox.onmousedown = suppressEvent; + maxAbsoluteDepthText = document.getElementById('maxAbsoluteDepth'); + maxAbsoluteDepthButtonDecrease = document.getElementById('maxAbsoluteDepthDecrease'); + maxAbsoluteDepthButtonIncrease = document.getElementById('maxAbsoluteDepthIncrease'); + maxAbsoluteDepthButtonDecrease.onclick = maxAbsoluteDepthDecrease; + maxAbsoluteDepthButtonIncrease.onclick = maxAbsoluteDepthIncrease; + maxAbsoluteDepthButtonDecrease.onmousedown = suppressEvent; + maxAbsoluteDepthButtonIncrease.onmousedown = suppressEvent; + fontSizeText = document.getElementById('fontSize'); + fontSizeButtonDecrease = document.getElementById('fontSizeDecrease'); + fontSizeButtonIncrease = document.getElementById('fontSizeIncrease'); + fontSizeButtonDecrease.onclick = fontSizeDecrease; + fontSizeButtonIncrease.onclick = fontSizeIncrease; + fontSizeButtonDecrease.onmousedown = suppressEvent; + fontSizeButtonIncrease.onmousedown = suppressEvent; + radiusButtonDecrease = document.getElementById('radiusDecrease'); + radiusButtonIncrease = document.getElementById('radiusIncrease'); + radiusButtonDecrease.onclick = radiusDecrease; + radiusButtonIncrease.onclick = radiusIncrease; + radiusButtonDecrease.onmousedown = suppressEvent; + radiusButtonIncrease.onmousedown = suppressEvent; + maxAbsoluteDepth = 0; + backButton = document.getElementById('back'); + backButton.onclick = navigateBack; + backButton.onmousedown = suppressEvent; + forwardButton = document.getElementById('forward'); + forwardButton.onclick = navigateForward; + forwardButton.onmousedown = suppressEvent; + snapshotButton = document.getElementById('snapshot'); + snapshotButton.onclick = snapshot; + snapshotButton.onmousedown = suppressEvent; + detailsName = document.getElementById('detailsName'); + detailsExpand = document.getElementById('detailsExpand'); + detailsInfo = document.getElementById('detailsInfo'); + search = document.getElementById('search'); + search.onkeyup = onSearchChange; + search.onmousedown = suppressEvent; + searchResults = document.getElementById('searchResults'); + useHueDiv = document.getElementById('useHueDiv'); + linkButton = document.getElementById('linkButton'); + linkButton.onclick = showLink; + linkButton.onmousedown = suppressEvent; + linkText = document.getElementById('linkText'); + linkText.onblur = hideLink; + linkText.onmousedown = suppressEvent; + hide(linkText); + var helpButton = document.getElementById('help'); + helpButton.onmousedown = suppressEvent; + var searchClear = document.getElementById('searchClear'); + searchClear.onmousedown = suppressEvent; + if ( datasets > 1 ) + { + datasetDropDown.onmousedown = suppressEvent; + var prevDatasetButton = document.getElementById('prevDataset'); + prevDatasetButton.onmousedown = suppressEvent; + var nextDatasetButton = document.getElementById('nextDataset'); + nextDatasetButton.onmousedown = suppressEvent; + var lastDatasetButton = document.getElementById('lastDataset'); + lastDatasetButton.onmousedown = suppressEvent; + } + + image = document.getElementById('hiddenImage'); + image.onload = function() + { + hiddenPattern = context.createPattern(image, 'repeat'); + } + + var loadingImageElement = document.getElementById('loadingImage'); + + if ( loadingImageElement ) + { + loadingImage = loadingImageElement.src; + } +} + +function selectDataset(newDataset) +{ + lastDataset = currentDataset; + currentDataset = newDataset + if ( datasets > 1 ) + { + datasetDropDown.selectedIndex = currentDataset; + updateDatasetButtons(); + datasetAlpha.start = 1.5; + datasetChanged = true; + } + head.setMagnitudes(0); + head.setDepth(1, 1); + head.setMaxDepths(); + handleResize(); +} + +function selectLastDataset() +{ + selectDataset(lastDataset); + handleResize(); +} + +function selectNode(newNode) +{ + if ( selectedNode != newNode ) + { + // truncate history at current location to create a new branch + // + nodeHistory.length = nodeHistoryPosition; + + if ( selectedNode != 0 ) + { + nodeHistory.push(selectedNode); + nodeHistoryPosition++; + } + + setSelectedNode(newNode); + //updateView(); + } + + updateDatasetButtons(); +} + +function setFocus(node) +{ + if ( node == focusNode ) + { +// return; + } + + focusNode = node; + + if ( node.href ) + { + detailsName.innerHTML = + '<a target="_blank" href="' + node.href + '">' + node.name + '</a>'; + } + else + { + detailsName.innerHTML = node.name; + } + + var table = '<table>'; + //TODO: use CSS margins instead of an additional column + table += '<tr><td></td><td></td></tr>'; + + for ( var i = 0; i < node.attributes.length; i++ ) + { + if ( attributes[i].displayName && node.attributes[i] != undefined ) + { + var index = node.attributes[i].length == 1 && attributes[i].mono ? 0 : currentDataset; + + if ( typeof node.attributes[i][currentDataset] == 'number' || node.attributes[i][index] != undefined && node.attributes[i][currentDataset] != '' ) + { + var value = node.attributes[i][index]; + + if ( attributes[i].listNode != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listNode) + ',' + i + + ',false);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].listAll != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listAll) + ',' + i + + ',true);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].dataNode != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataNode) + ',' + i + + ',false);return false;" title="Show data">' + + value + '</a>'; + } + else if ( attributes[i].dataAll != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataAll) + ',' + i + + ',true);return false;" title="Show data">' + + value + '</a>'; + } + + table += + '<tr><td><strong>' + attributes[i].displayName + ':</strong></td><td>' + + value + '</td></tr>'; + } + } + } + + table += '</table>'; + detailsInfo.innerHTML = table; + + detailsExpand.disabled = !focusNode.hasChildren() || focusNode == selectedNode; +} + +function setSelectedNode(newNode) +{ + if ( selectedNode && selectedNode.hasParent(newNode) ) + { + zoomOut = true; + } + else + { + zoomOut = false; + } + + selectedNodeLast = selectedNode; + selectedNode = newNode; + + //if ( focusNode != selectedNode ) + { + setFocus(selectedNode); + } +} + +function waitForData(dataWindow, target, title, time, postUrl, postVar) +{ + if ( nodeData.length == target ) + { + if ( postUrl != undefined ) + { + for ( var i = 0; i < nodeData.length; i++ ) + { + nodeData[i] = nodeData[i].replace(/\n/g, ','); + } + + var postString = nodeData.join(''); + postString = postString.slice(0, -1); + + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + + post(postUrl, postVar, postString, dataWindow); + } + else + { + //dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + //document.body.removeChild(document.getElementById('data')); + + dataWindow.document.open(); + dataWindow.document.write('<pre>' + nodeData.join('') + '</pre>'); + dataWindow.document.close(); + } + + dataWindow.document.title = title; // replace after document.write() + } + else + { + var date = new Date(); + + if ( date.getTime() - time > 10000 ) + { + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + dataWindow.document.body.innerHTML = + 'Timed out loading supplemental files for:<br/>' + document.location; + } + else + { + setTimeout(function() {waitForData(dataWindow, target, title, time, postUrl, postVar);}, 100); + } + } +} + +function data(newData) +{ + nodeData.push(newData); +} + +function enableData() +{ + dataEnabled = true; +} + +function showData(indexData, indexAttribute, summary) +{ + var dataWindow = window.open('', '_blank'); + var title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + dataWindow.document.title = title; + + nodeData = new Array(); + + if ( dataWindow && dataWindow.document && dataWindow.document.body != null ) + { + //var loadImage = document.createElement('img'); + //loadImage.src = "file://localhost/Users/ondovb/Krona/KronaTools/img/loading.gif"; + //loadImage.id = "loading"; + //loadImage.alt = "Loading..."; + //dataWindow.document.body.appendChild(loadImage); + dataWindow.document.body.innerHTML = + '<img id="loading" src="' + loadingImage + '" alt="Loading..."></img>'; + } + + var scripts = document.createElement('div'); + scripts.id = 'data'; + document.body.appendChild(scripts); + + var files = focusNode.getData(indexData, summary); + + var date = new Date(); + var time = date.getTime(); + + for ( var i = 0; i < files.length; i++ ) + { + var script = document.createElement('script'); + script.src = files[i] + '?' + time; + scripts.appendChild(script); + } + + waitForData(dataWindow, files.length, title, time, attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar); + + return false; +} + +function showList(indexList, indexAttribute, summary) +{ + var list = focusNode.getList(indexList, summary); + + if ( attributes[indexAttribute].postUrl != undefined ) + { + post(attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar, list.join(',')); + } + else + { + var dataWindow = window.open('', '_blank'); + + if ( true || navigator.appName == 'Microsoft Internet Explorer' ) // :( + { + dataWindow.document.open(); + dataWindow.document.write('<pre>' + list.join('\n') + '</pre>'); + dataWindow.document.close(); + } + else + { + var pre = document.createElement('pre'); + dataWindow.document.body.appendChild(pre); + pre.innerHTML = list; + } + + dataWindow.document.title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + } +} + +function snapshot() +{ + svg = svgHeader(); + + resetKeyOffset(); + + snapshotMode = true; + + selectedNode.draw(false, true); + selectedNode.draw(true, true); + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + } + + if ( hueDisplayName && useHue() ) + { + drawLegendSVG(); + } + + snapshotMode = false; + + svg += svgFooter(); + + var snapshotWindow = window.open('', '_blank', '', 'replace=false'); + snapshotWindow.document.write('<html><body><a href="data:image/svg+xml,' + encodeURIComponent(svg) + '" download="snapshot.svg">Download Snapshot</a></html></body>'); + snapshotWindow.document.write(svg); +} + +function save() +{ + alert(document.body.innerHTML); +} + +function spacer() +{ + if ( snapshotMode ) + { + return '   '; + } + else + { + return ' '; + } +} + +function suppressEvent(e) +{ + e.cancelBubble = true; + if (e.stopPropagation) e.stopPropagation(); +} + +function svgFooter() +{ + return '</svg>'; +} + +function svgHeader() +{ + var patternWidth = fontSize * .6;//radius / 50; + + return '\ +<?xml version="1.0" standalone="no"?>\ +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" \ + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\ +<svg width="' + imageWidth + '" height="' + imageHeight + '" version="1.1"\ + xmlns="http://www.w3.org/2000/svg">\ +<title>Krona (snapshot) - ' + +(datasets > 1 ? datasetNames[currentDataset] + ' - ' : '') + selectedNode.name + +'</title>\ +<defs>\ + <style type="text/css">\ + text {font-size: ' + fontSize + 'px; font-family: ' + fontFamily + '; dominant-baseline:central}\ + path {stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + path.wedge {stroke:none}\ + path.line {fill:none;stroke:black;}\ + line {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + line.tick {stroke-width:' + thinLineWidth * fontSize / 6 + ';}\ + line.pattern {stroke-width:' + thinLineWidth * fontSize / 18 + ';}\ + circle {fill:none;stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + rect {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + .highlight {stroke:black;stroke-width:'+ highlightLineWidth * fontSize / 12 + ';}\ + .searchHighlight {fill:rgb(255, 255, 100);stroke:none;}\ + </style>\ +<pattern id="hiddenPattern" patternUnits="userSpaceOnUse" \ +x="0" y="0" width="' + patternWidth + '" height="' + patternWidth + '">\ +<line class="pattern" x1="0" y1="0" x2="' + patternWidth / 2 + '" y2="' + patternWidth / 2 + '"/>\ +<line class="pattern" x1="' + patternWidth / 2 + '" y1="' + patternWidth + +'" x2="' + patternWidth + '" y2="' + patternWidth / 2 + '"/>\ +</pattern>\ +</defs>\ +'; +} + +function svgText(text, x, y, anchor, bold, color) +{ + if ( typeof(anchor) == 'undefined' ) + { + anchor = 'start'; + } + + if ( color == undefined ) + { + color = 'black'; + } + + return '<text x="' + x + '" y="' + y + + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" text-anchor="' + anchor + '">' + text + '</text>'; +} + +function toggleKeys() +{ + if ( showKeys ) + { + keyControl.value = '…'; + showKeys = false; + } + else + { + keyControl.value = 'x'; + showKeys = true; + } + + updateKeyControl(); + + if ( progress == 1 ) + { + draw(); + } +} + +function update() +{ + if ( ! head ) + { + return; + } + + if ( mouseDown && focusNode != selectedNode ) + { + var date = new Date(); + + if ( date.getTime() - mouseDownTime > quickLookHoldLength ) + { + if ( focusNode.hasChildren() ) + { + expand(focusNode); + quickLook = true; + } + } + } + + if ( updateViewNeeded ) + { + resize(); + mouseX = -1; + mouseY = -1; + + collapse = collapseCheckBox.checked; + compress = true;//compressCheckBox.checked; + shorten = true;//shortenCheckBox.checked; + + checkSelectedCollapse(); + updateMaxAbsoluteDepth(); + + if ( focusNode.getCollapse() || focusNode.depth > maxAbsoluteDepth ) + { + setFocus(selectedNode); + } + else + { + setFocus(focusNode); + } + + updateView(); + + updateViewNeeded = false; + } + + var date = new Date(); + progress = (date.getTime() - tweenStartTime) / tweenLength; +// progress += .01; + + if ( progress >= 1 ) + { + progress = 1; + } + + if ( progress != progressLast ) + { + tweenFactor =// progress; + (1 / (1 + Math.exp(-tweenCurvature * (progress - .5))) - .5) / + (tweenMax - .5) / 2 + .5; + + if ( progress == 1 ) + { + snapshotButton.disabled = false; + zoomOut = false; + + //updateKeyControl(); + + if ( ! quickLook ) + { + //checkHighlight(); + } + + + if ( fpsDisplay ) + { + fpsDisplay.innerHTML = 'fps: ' + Math.round(tweenFrames * 1000 / tweenLength); + } + } + + draw(); + } + + progressLast = progress; +} + +function updateDatasetButtons() +{ + if ( datasets == 1 ) + { + return; + } + + var node = selectedNode ? selectedNode : head; + + datasetButtonLast.disabled = + node.attributes[magnitudeIndex][lastDataset] == 0; + + datasetButtonPrev.disabled = true; + datasetButtonNext.disabled = true; + + for ( var i = 0; i < datasets; i++ ) + { + var disable = node.attributes[magnitudeIndex][i] == 0; + + datasetDropDown.options[i].disabled = disable; + + if ( ! disable ) + { + if ( i != currentDataset ) + { + datasetButtonPrev.disabled = false; + datasetButtonNext.disabled = false; + } + } + } +} + +function updateDatasetWidths() +{ + if ( datasets > 1 ) + { + for ( var i = 0; i < datasets; i++ ) + { + context.font = fontBold; + var dim = context.measureText(datasetNames[i]); + datasetWidths[i] = dim.width; + } + } +} + +function updateKeyControl() +{ + if ( keys == 0 )//|| progress != 1 ) + { + keyControl.style.visibility = 'hidden'; + } + else + { + keyControl.style.visibility = 'visible'; + keyControl.style.right = margin + 'px'; + + if ( showKeys ) + { + keyControl.style.top = + imageHeight - + ( + keys * (keySize + keyBuffer) - + keyBuffer + + margin + + keyControl.clientHeight * 1.5 + ) + 'px'; + } + else + { + keyControl.style.top = + (imageHeight - margin - keyControl.clientHeight) + 'px'; + } + } +} + +function updateView() +{ + if ( selectedNode.depth > maxAbsoluteDepth - 1 ) + { + maxAbsoluteDepth = selectedNode.depth + 1; + } + + highlightedNode = selectedNode; + + angleFactor = 2 * Math.PI / (selectedNode.magnitude); + + maxPossibleDepth = Math.floor(gRadius / (fontSize * minRingWidthFactor)); + + if ( maxPossibleDepth < 4 ) + { + maxPossibleDepth = 4; + } + + var minRadiusInner = fontSize * 8 / gRadius; + var minRadiusFirst = fontSize * 6 / gRadius; + var minRadiusOuter = fontSize * 5 / gRadius; + + if ( .25 < minRadiusInner ) + { + minRadiusInner = .25; + } + + if ( .15 < minRadiusFirst ) + { + minRadiusFirst = .15; + } + + if ( .15 < minRadiusOuter ) + { + minRadiusOuter = .15; + } + + // visibility of nodes depends on the depth they are displayed at, + // so we need to set the max depth assuming they can all be displayed + // and iterate it down based on the deepest child node we can display + // + var maxDepth; + var newMaxDepth = selectedNode.getMaxDepth() - selectedNode.getDepth() + 1; + // + do + { + maxDepth = newMaxDepth; + + if ( ! compress && maxDepth > maxPossibleDepth ) + { + maxDepth = maxPossibleDepth; + } + + if ( compress ) + { + compressedRadii = new Array(maxDepth); + + compressedRadii[0] = minRadiusInner; + + var offset = 0; + + while + ( + lerp + ( + Math.atan(offset + 2), + Math.atan(offset + 1), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) - minRadiusInner > minRadiusFirst && + offset < 10 + ) + { + offset++; + } + + offset--; + + for ( var i = 1; i < maxDepth; i++ ) + { + compressedRadii[i] = lerp + ( + Math.atan(i + offset), + Math.atan(offset), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) + } + } + else + { + nodeRadius = 1 / maxDepth; + } + + newMaxDepth = selectedNode.maxVisibleDepth(maxDepth); + + if ( compress ) + { + if ( newMaxDepth <= maxPossibleDepth ) + { +// compress + } + } + else + { + if ( newMaxDepth > maxPossibleDepth ) + { + newMaxDepth = maxPossibleDepth; + } + } + } + while ( newMaxDepth < maxDepth ); + + maxDisplayDepth = maxDepth; + + lightnessFactor = (lightnessMax - lightnessBase) / (maxDepth > 8 ? 8 : maxDepth); + keys = 0; + + nLabelOffsets = new Array(maxDisplayDepth - 1); + labelOffsets = new Array(maxDisplayDepth - 1); + labelLastNodes = new Array(maxDisplayDepth - 1); + labelFirstNodes = new Array(maxDisplayDepth - 1); + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + if ( compress ) + { + if ( i == maxDisplayDepth - 1 ) + { + nLabelOffsets[i] = 0; + } + else + { + var width = + (compressedRadii[i + 1] - compressedRadii[i]) * + gRadius; + + nLabelOffsets[i] = Math.floor(width / fontSize / 1.2); + + if ( nLabelOffsets[i] > 2 ) + { + nLabelOffsets[i] = min + ( + Math.floor(width / fontSize / 1.75), + 5 + ); + } + } + } + else + { + nLabelOffsets[i] = Math.max + ( + Math.floor(Math.sqrt((nodeRadius * gRadius / fontSize)) * 1.5), + 3 + ); + } + + labelOffsets[i] = Math.floor((nLabelOffsets[i] - 1) / 2); + labelLastNodes[i] = new Array(nLabelOffsets[i] + 1); + labelFirstNodes[i] = new Array(nLabelOffsets[i] + 1); + + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + // these arrays will allow nodes with neighboring labels to link to + // each other to determine max label length + + labelLastNodes[i][j] = 0; + labelFirstNodes[i][j] = 0; + } + } + + fontSizeText.innerHTML = fontSize; + fontNormal = fontSize + 'px ' + fontFamily; + context.font = fontNormal; + fontBold = 'bold ' + fontSize + 'px ' + fontFamily; + tickLength = fontSize * .7; + + head.setTargets(0); + + keySize = ((imageHeight - margin * 3) * 1 / 2) / keys * 3 / 4; + + if ( keySize > fontSize * maxKeySizeFactor ) + { + keySize = fontSize * maxKeySizeFactor; + } + + keyBuffer = keySize / 3; + + fontSizeLast = fontSize; + + if ( datasetChanged ) + { + datasetChanged = false; + } + else + { + datasetAlpha.start = 0; + } + + var date = new Date(); + tweenStartTime = date.getTime(); + progress = 0; + tweenFrames = 0; + + updateKeyControl(); + updateDatasetWidths(); + + document.title = 'Krona - ' + selectedNode.name; + updateNavigationButtons(); + snapshotButton.disabled = true; + + maxAbsoluteDepthText.innerHTML = maxAbsoluteDepth - 1; + + maxAbsoluteDepthButtonDecrease.disabled = (maxAbsoluteDepth == 2); + maxAbsoluteDepthButtonIncrease.disabled = (maxAbsoluteDepth == head.maxDepth); + + if ( collapse != collapseLast && search.value != '' ) + { + onSearchChange(); + collapseLast = collapse; + } +} + +function updateMaxAbsoluteDepth() +{ + while ( maxAbsoluteDepth > 1 && selectedNode.depth > maxAbsoluteDepth - 1 ) + { + selectedNode = selectedNode.getParent(); + } +} + +function updateNavigationButtons() +{ + backButton.disabled = (nodeHistoryPosition == 0); +// upButton.disabled = (selectedNode.getParent() == 0); + forwardButton.disabled = (nodeHistoryPosition == nodeHistory.length); +} + +function useHue() +{ + return useHueCheckBox && useHueCheckBox.checked; +} +/* +function zoomOut() +{ + return ( + selectedNodeLast != 0 && + selectedNodeLast.getDepth() < selectedNode.getDepth()); +} +*/ + </script> +</head> +<body> +<img id="hiddenImage" src="data:image/png;base64,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" style="display:none"/> +<img id="loadingImage" 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style="display:none"/> +<noscript>Javascript must be enabled to view this page.</noscript> +<div style="display:none"> + <krona collapse="true" key="true"> + <attributes magnitude="magnitude"> + <attribute display="Total">magnitude</attribute> + </attributes> + <datasets> + <dataset>kt</dataset> + </datasets> + +<node name="all"><magnitude><val>46</val></magnitude><node name="unclassified"><magnitude><val>1</val></magnitude></node><node name="root"><magnitude><val>45</val></magnitude><node name="cellular organisms"><magnitude><val>45</val></magnitude><node name="Bacteria"><magnitude><val>45</val></magnitude><node name="Pseudomonadota"><magnitude><val>45</val></magnitude><node name="Gammaproteobacteria"><magnitude><val>45</val></magnitude><node name="Enterobacterales"><magnitude><val>24</val></magnitude><node name="Enterobacteriaceae"><magnitude><val>24</val></magnitude><node name="Escherichia"><magnitude><val>14</val></magnitude><node name="Escherichia coli"><magnitude><val>14</val></magnitude><node name="Escherichia coli K-12"><magnitude><val>14</val></magnitude><node name="Escherichia coli str. K-12 substr. MG1655"><magnitude><val>14</val></magnitude></node></node></node></node><node name="Salmonella"><magnitude><val>10</val></magnitude><node name="Salmonella enterica"><magnitude><val>10</val></magnitude><node name="Salmonella enterica subsp. enterica"><magnitude><val>10</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium"><magnitude><val>10</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"><magnitude><val>10</val></magnitude></node></node></node></node></node></node></node><node name="Pseudomonadales"><magnitude><val>21</val></magnitude><node name="Pseudomonadaceae"><magnitude><val>21</val></magnitude><node name="Pseudomonas"><magnitude><val>21</val></magnitude><node name="Pseudomonas aeruginosa group"><magnitude><val>21</val></magnitude><node name="Pseudomonas aeruginosa"><magnitude><val>21</val></magnitude><node name="Pseudomonas aeruginosa PAO1"><magnitude><val>21</val></magnitude></node></node></node></node></node></node></node></node></node></node></node></node></krona></div></body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,23 @@ +2.1739 1 1 no rank 0 unclassified +97.8261 45 0 no rank 1 root +97.8261 45 0 no rank 131567 cellular organisms +97.8261 45 0 superkingdom 2 Bacteria +97.8261 45 0 phylum 1224 Pseudomonadota +97.8261 45 0 class 1236 Gammaproteobacteria +52.1739 24 0 order 91347 Enterobacterales +52.1739 24 0 family 543 Enterobacteriaceae +30.4348 14 0 genus 561 Escherichia +30.4348 14 0 species 562 Escherichia coli +30.4348 14 0 strain 83333 Escherichia coli K-12 +30.4348 14 14 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +21.7391 10 0 genus 590 Salmonella +21.7391 10 0 species 28901 Salmonella enterica +21.7391 10 0 subspecies 59201 Salmonella enterica subsp. enterica +21.7391 10 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +21.7391 10 10 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +45.6522 21 0 order 72274 Pseudomonadales +45.6522 21 0 family 135621 Pseudomonadaceae +45.6522 21 0 genus 286 Pseudomonas +45.6522 21 0 species group 136841 Pseudomonas aeruginosa group +45.6522 21 0 species 287 Pseudomonas aeruginosa +45.6522 21 21 strain 208964 Pseudomonas aeruginosa PAO1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/pb.hifi_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,40 @@ +1 46ac816b-5257-0939-9707-d4e402ca7f66 208964 14073 0.624991 strain 208964:2034 +1 2834ee47-67d1-b9b9-a644-8d48b51ef5f0 208964 603 0.399668 strain 208964:57 +1 58130cac-3fbb-69e0-cd73-f584cea7dc94 511145 27102 0.135414 no rank 511145:866 +1 c28e35a1-5a3f-a437-6fa6-c6aca123fb7a 511145 22071 0.615559 no rank 511145:3054 +1 b1c42de6-1927-4fb4-931c-26ea9c1a125b 511145 207 0.195652 no rank 511145:9 +1 e112e5b5-4746-3cba-e53e-a16d32986d7a 208964 1020 0.731373 strain 208964:190 +1 a48e104f-ed2a-15ad-9e16-087e18062131 99287 27687 0.286037 strain 99287:1785 +1 dffb75c8-0f85-de32-360e-01c88e7519c0 99287 40410 0.524709 strain 99287:4655 +1 8c854602-9d71-7f71-0b9e-2103e53eb1f3 99287 933 0.726688 strain 99287:157 +1 88acfcc8-6092-3d67-24ff-08a0c729d292 208964 28608 0.587633 strain 208964:3750 +1 fb77e180-7d01-f781-776f-bdfcad00fbc8 99287 17943 0.475701 strain 99287:1842 +1 f71a9e94-d34a-e077-178a-d48b07507070 511145 53712 0.869238 no rank 511145:11950 +1 f964749a-6d47-6c21-e7f2-4d0835a35a3b 99287 642 0.573209 strain 99287:94 +1 406338db-9f37-0eb6-5d10-e6316ca896ea 99287 9255 0.616099 strain 99287:1302 +1 8867579d-91e4-3751-d245-1d9296fc390f 99287 28203 0.660267 strain 99287:4314 +1 aac5d808-4179-375e-edc4-fd089b7b53f8 99287 20985 0.174696 strain 99287:820 +1 f3c24ded-b4ee-3006-07b6-4859e87146e3 208964 12954 0.71503 strain 208964:2241 +1 1edb2cdb-1289-1f2a-abc6-08338f372923 208964 15972 0.31383 strain 208964:1153 +1 6345023a-4846-edaf-e9dd-a41f3dc48f53 511145 4962 0.592201 no rank 511145:694 +1 a8577a53-a35a-c6ed-4f2d-51f4e1750b93 99287 864 0.0763889 strain 99287:32 +1 bd619d24-26bc-4dfe-75b9-052f241cbf49 511145 31755 0.341553 no rank 511145:2331 +1 d61026de-c088-fac5-cf67-b76d8cf481ab 208964 4428 0.78907 strain 208964:845 +1 294128de-cb85-4061-2c9a-0d7f7248eccf 208964 4134 0.45658 strain 208964:410 +1 753335d5-a752-bde7-5a4c-13ab429f472d 208964 15255 0.0832842 strain 208964:322 +1 c1989402-f62f-21e0-e827-5c44c4d7562e 511145 32733 0.695552 no rank 511145:5320 +1 8a7703b3-9d44-ade2-1746-bb6c0bd3cc24 208964 3357 0.605302 strain 208964:437 +1 410a70bf-df52-5535-e301-822750188972 99287 7602 0.438569 strain 99287:725 +1 0b66b503-69ec-2798-2442-ebee9a26ca47 208964 22935 0.6753 strain 208964:3642 +1 b4d8e5b9-1597-48a3-f2db-5e7e37578597 208964 6225 0.356466 strain 208964:474 +1 c514c133-303c-ceaf-cfdc-b70536c26e32 99287 9018 0.478598 strain 99287:913 +1 518f3cec-ce4a-3a0f-d6bf-03a4433c7612 208964 33669 0.67531 strain 208964:5315 +1 7c871d7a-5122-b779-a6fe-24b3417b0d4d 511145 10275 0.341655 no rank 511145:759 +1 de93f009-2707-a131-b038-108e8373cea7 99287 19668 0.577435 strain 99287:2579 +1 3a62aec2-7254-e342-ea17-e43f2e3c933a 99287 25908 0.259476 strain 99287:1501 +1 0b62d3c8-5482-b549-457a-ffeca8907812 511145 10296 0.316191 no rank 511145:686 +1 8323893b-d729-09be-770b-c0697f571c28 511145 3924 0.771789 no rank 511145:707 +1 a4d8d18d-afde-b01a-d552-476bc9831614 208964 5094 0.736455 strain 208964:931 +1 2bc1c4e3-a780-9ba8-dbbf-66336e0c1b9a 511145 1944 0.343621 no rank 511145:117 +0 cbebaff1-ab59-f0cd-9854-fca99cb223e7 0 13575 0 no rank +1 3b93efb1-3066-00d4-566f-64c1fecc6951 511145 18780 0.464457 no rank 511145:2020
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+ <script id="notfound">window.onload=function(){document.body.innerHTML=""}</script> + <script language="javascript" type="text/javascript"> +{//----------------------------------------------------------------------------- +// +// PURPOSE +// +// Krona is a flexible tool for exploring the relative proportions of +// hierarchical data, such as metagenomic classifications, using a +// radial, space-filling display. It is implemented using HTML5 and +// JavaScript, allowing charts to be explored locally or served over the +// Internet, requiring only a current version of any major web +// browser. Krona charts can be created using an Excel template or from +// common bioinformatic formats using the provided conversion scripts. +// +// +// COPYRIGHT LICENSE +// +// Copyright (c) 2011, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and +// Adam Phillippy +// +// This Software was prepared for the Department of Homeland Security +// (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as +// part of contract HSHQDC-07-C-00020 to manage and operate the National +// Biodefense Analysis and Countermeasures Center (NBACC), a Federally +// Funded Research and Development Center. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// * Neither the name of the Battelle National Biodefense Institute nor +// the names of its contributors may be used to endorse or promote +// products derived from this software without specific prior written +// permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// +// TRADEMARK LICENSE +// +// KRONA(TM) is a trademark of the Department of Homeland Security, and use +// of the trademark is subject to the following conditions: +// +// * Distribution of the unchanged, official code/software using the +// KRONA(TM) mark is hereby permitted by the Department of Homeland +// Security, provided that the software is distributed without charge +// and modification. +// +// * Distribution of altered source code/software using the KRONA(TM) mark +// is not permitted unless written permission has been granted by the +// Department of Homeland Security. +// +// +// FOR MORE INFORMATION VISIT +// +// https://github.com/marbl/Krona/wiki/ +// +//----------------------------------------------------------------------------- +} + + +var canvas; +var context; +var svg; // for snapshot mode +var collapse = true; +var collapseCheckBox; +var collapseLast; +var compress; +var compressCheckBox; +var maxAbsoluteDepthText; +var maxAbsoluteDepthButtonDecrease; +var maxAbsoluteDepthButtonIncrease; +var fontSize = 11; +var fontSizeText; +var fontSizeButtonDecrease; +var fontSizeButtonIncrease; +var fontSizeLast; +var radiusButtonDecrease; +var radiusButtonIncrease; +var shorten; +var shortenCheckBox; +var maxAbsoluteDepth; +var backButton; +var upButton; +var forwardButton; +var snapshotButton; +var snapshotMode = false; +var details; +var detailsName; +var search; +var searchResults; +var nSearchResults; +var useHueCheckBox; +var useHueDiv; +var datasetDropDown; +var datasetButtonLast; +var datasetButtonPrev; +var datasetButtonNext; +var keyControl; +var showKeys = true; +var linkButton; +var linkText; +var frame; + +// Node references. Note that the meanings of 'selected' and 'focused' are +// swapped in the docs. +// +var head; // the root of the entire tree +var selectedNode = 0; // the root of the current view +var focusNode = 0; // a node chosen for more info (single-click) +var highlightedNode = 0; // mouse hover node +var highlightingHidden = false; +var nodes = new Array(); +var currentNodeID = 0; // to iterate while loading + +var nodeHistory = new Array(); +var nodeHistoryPosition = 0; + +var dataEnabled = false; // true when supplemental files are present + +// store non-Krona GET variables so they can be passed on to links +// +var getVariables = new Array(); + +// selectedNodeLast is separate from the history, since we need to check +// properties of the last node viewed when browsing through the history +// +var selectedNodeLast = 0; +var zoomOut = false; + +// temporary zoom-in while holding the mouse button on a wedge +// +var quickLook = false; // true when in quick look state +var mouseDown = false; +var mouseDownTime; // to detect mouse button hold +var quickLookHoldLength = 200; + +var imageWidth; +var imageHeight; +var centerX; +var centerY; +var gRadius; +var updateViewNeeded = false; + +// Determines the angle that the pie chart starts at. 90 degrees makes the +// center label consistent with the children. +// +var rotationOffset = Math.PI / 2; + +var buffer; +var bufferFactor = .1; + +// The maps are the small pie charts showing the current slice being viewed. +// +var mapBuffer = 10; +var mapRadius = 0; +var maxMapRadius = 25; +var mapWidth = 150; +var maxLabelOverhang = Math.PI * 4.18; + +// Keys are the labeled boxes for slices in the highest level that are too thin +// to label. +// +var maxKeySizeFactor = 2; // will be multiplied by font size +var keySize; +var keys; +var keyBuffer = 10; +var currentKey; +var keyMinTextLeft; +var keyMinAngle; + +var minRingWidthFactor = 5; // will be multiplied by font size +var maxPossibleDepth; // the theoretical max that can be displayed +var maxDisplayDepth; // the actual depth that will be displayed +var headerHeight = 0;//document.getElementById('options').clientHeight; +var historySpacingFactor = 1.6; // will be multiplied by font size +var historyAlphaDelta = .25; + +// appearance +// +var lineOpacity = 0.3; +var saturation = 0.5; +var lightnessBase = 0.6; +var lightnessMax = .8; +var thinLineWidth = .3; +var highlightLineWidth = 1.5; +var labelBoxBuffer = 6; +var labelBoxRounding = 15; +var labelWidthFudge = 1.05; // The width of unshortened labels are set slightly + // longer than the name width so the animation + // finishes faster. +var fontNormal; +var fontBold; +var fontFamily = 'sans-serif'; +//var fontFaceBold = 'bold Arial'; +var nodeRadius; +var angleFactor; +var tickLength; +var compressedRadii; + +// colors +// +var highlightFill = 'rgba(255, 255, 255, .3)'; +var colorUnclassified = 'rgb(220,220,220)'; + +// label staggering +// +var labelOffsets; // will store the current offset at each depth +// +// This will store pointers to the last node that had a label in each offset (or "track") of a +// each depth. These will be used to shorten neighboring labels that would overlap. +// The [nLabelNodes] index will store the last node with a radial label. +// labelFirstNodes is the same, but to check for going all the way around and +// overlapping the first labels. +// +var labelLastNodes; +var labelFirstNodes; +// +var nLabelOffsets = 3; // the number of offsets to use + +var mouseX = -1; +var mouseY = -1; +var mouseXRel = -1; +var mouseYRel = -1; + +// tweening +// +var progress = 0; // for tweening; goes from 0 to 1. +var progressLast = 0; +var tweenFactor = 0; // progress converted by a curve for a smoother effect. +var tweenLength = 850; // in ms +var tweenCurvature = 13; +// +// tweenMax is used to scale the sigmoid function so its range is [0,1] for the +// domain [0,1] +// +var tweenMax = 1 / (1 + Math.exp(-tweenCurvature / 2)); +// +var tweenStartTime; + +// for framerate debug +// +var tweenFrames = 0; +var fpsDisplay = document.getElementById('frameRate'); + +// Arrays to translate xml attribute names into displayable attribute names +// +var attributes = new Array(); +// +var magnitudeIndex; // the index of attribute arrays used for magnitude +var membersAssignedIndex; +var membersSummaryIndex; + +// For defining gradients +// +var hueDisplayName; +var hueStopPositions; +var hueStopHues; +var hueStopText; + +// multiple datasets +// +var currentDataset = 0; +var lastDataset = 0; +var datasets = 1; +var datasetNames; +var datasetSelectSize = 30; +var datasetAlpha = new Tween(0, 0); +var datasetWidths = new Array(); +var datasetChanged; +var datasetSelectWidth = 50; + +window.onload = load; + +var image; +var hiddenPattern; +var loadingImage; +var logoImage; + +function backingScale() +{ + if ('devicePixelRatio' in window) + { + if (window.devicePixelRatio > 1) + { + return window.devicePixelRatio; + } + } + + return 1; +} + +function resize() +{ + imageWidth = window.innerWidth; + imageHeight = window.innerHeight; + + if ( ! snapshotMode ) + { + context.canvas.width = imageWidth * backingScale(); + context.canvas.height = imageHeight * backingScale(); + context.canvas.style.width = imageWidth + "px" + context.canvas.style.height = imageHeight + "px" + context.scale(backingScale(), backingScale()); + } + + if ( datasetDropDown ) + { + var ratio = + (datasetDropDown.offsetTop + datasetDropDown.clientHeight) * 2 / + imageHeight; + + if ( ratio > 1 ) + { + ratio = 1; + } + + ratio = Math.sqrt(ratio); + + datasetSelectWidth = + (datasetDropDown.offsetLeft + datasetDropDown.clientWidth) * ratio; + } + var leftMargin = datasets > 1 ? datasetSelectWidth + 30 : 0; + var minDimension = imageWidth - mapWidth - leftMargin > imageHeight ? + imageHeight : + imageWidth - mapWidth - leftMargin; + + maxMapRadius = minDimension * .03; + buffer = minDimension * bufferFactor; + margin = minDimension * .015; + centerX = (imageWidth - mapWidth - leftMargin) / 2 + leftMargin; + centerY = imageHeight / 2; + gRadius = minDimension / 2 - buffer; + //context.font = '11px sans-serif'; +} + +function handleResize() +{ + updateViewNeeded = true; +} + +function Attribute() +{ +} + +function Tween(start, end) +{ + this.start = start; + this.end = end; + this.current = this.start; + + this.current = function() + { + if ( progress == 1 || this.start == this.end ) + { + return this.end; + } + else + { + return this.start + tweenFactor * (this.end - this.start); + } + }; + + this.setTarget = function(target) + { + this.start = this.current(); + this.end = target; + } +} + +function Node() +{ + this.id = currentNodeID; + currentNodeID++; + nodes[this.id] = this; + + this.angleStart = new Tween(Math.PI, 0); + this.angleEnd = new Tween(Math.PI, 0); + this.radiusInner = new Tween(1, 1); + this.labelRadius = new Tween(1, 1); + this.labelWidth = new Tween(0, 0); + this.scale = new Tween(1, 1); // TEMP + this.radiusOuter = new Tween(1, 1); + + this.r = new Tween(255, 255); + this.g = new Tween(255, 255); + this.b = new Tween(255, 255); + + this.alphaLabel = new Tween(0, 1); + this.alphaLine = new Tween(0, 1); + this.alphaArc = new Tween(0, 0); + this.alphaWedge = new Tween(0, 1); + this.alphaOther = new Tween(0, 1); + this.alphaPattern = new Tween(0, 0); + this.children = Array(); + this.parent = 0; + + this.attributes = new Array(attributes.length); + + this.addChild = function(child) + { + this.children.push(child); + }; + + this.addLabelNode = function(depth, labelOffset) + { + if ( labelHeadNodes[depth][labelOffset] == 0 ) + { + // this will become the head node for this list + + labelHeadNodes[depth][labelOffset] = this; + this.labelPrev = this; + } + + var head = labelHeadNodes[depth][labelOffset]; + + this.labelNext = head; + this.labelPrev = head.labelPrev; + head.labelPrev.labelNext = this; + head.labelPrev = this; + } + + this.canDisplayDepth = function() + { + // whether this node is at a depth that can be displayed, according + // to the max absolute depth + + return this.depth <= maxAbsoluteDepth; + } + + this.canDisplayHistory = function() + { + var radiusInner; + + if ( compress ) + { + radiusInner = compressedRadii[0]; + } + else + { + radiusInner = nodeRadius; + } + + return ( + -this.labelRadius.end * gRadius + + historySpacingFactor * fontSize / 2 < + radiusInner * gRadius + ); + } + + this.canDisplayLabelCurrent = function() + { + return ( + (this.angleEnd.current() - this.angleStart.current()) * + (this.radiusInner.current() * gRadius + gRadius) >= + minWidth()); + } + + this.checkHighlight = function() + { + if ( this.children.length == 0 && this == focusNode ) + { + //return false; + } + + if ( this.hide ) + { + return false; + } + + if ( this.radiusInner.end == 1 ) + { + // compressed to the outside; don't check + + return false; + } + + var highlighted = false; + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + for ( var i = 0; i < this.children.length; i++ ) + { + highlighted = this.children[i].checkHighlight(); + + if ( highlighted ) + { + return true; + } + } + + if ( this.radial ) + { + var angleText = (angleStartCurrent + angleEndCurrent) / 2; + var radiusText = (gRadius + radiusInner) / 2; + + context.rotate(angleText); + context.beginPath(); + context.moveTo(radiusText, -fontSize); + context.lineTo(radiusText, fontSize); + context.lineTo(radiusText + centerX, fontSize); + context.lineTo(radiusText + centerX, -fontSize); + context.closePath(); + context.rotate(-angleText); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(this.getPercentage()) + '%' + ' ' + this.name; + + if ( this.searchResultChildren() ) + { + label += searchResultString(this.searchResultChildren()); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + radiusText + measureText(label) + ) + { + highlighted = true; + } + } + } + else + { + for ( var i = 0; i < this.hiddenLabels.length; i++ ) + { + var hiddenLabel = this.hiddenLabels[i]; + + context.rotate(hiddenLabel.angle); + context.beginPath(); + context.moveTo(gRadius, -fontSize); + context.lineTo(gRadius, fontSize); + context.lineTo(gRadius + centerX, fontSize); + context.lineTo(gRadius + centerX, -fontSize); + context.closePath(); + context.rotate(-hiddenLabel.angle); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(hiddenLabel.value) + ' more'; + + if ( hiddenLabel.search ) + { + label += searchResultString(hiddenLabel.search); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + gRadius + fontSize + measureText(label) + ) + { + highlighted = true; + break; + } + } + } + } + + if ( ! highlighted && this != selectedNode && ! this.getCollapse() ) + { + context.beginPath(); + context.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false); + context.arc(0, 0, gRadius, angleEndCurrent, angleStartCurrent, true); + context.closePath(); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + highlighted = true; + } + + if + ( + ! highlighted && + (angleEndCurrent - angleStartCurrent) * + (radiusInner + gRadius) < + minWidth() && + this.getDepth() == selectedNode.getDepth() + 1 + ) + { + if ( showKeys && this.checkHighlightKey() ) + { + highlighted = true; + } + } + } + + if ( highlighted ) + { + if ( this != highlightedNode ) + { + // document.body.style.cursor='pointer'; + } + + highlightedNode = this; + } + + return highlighted; + } + + this.checkHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + var cx = centerX; + var cy = centerY - this.labelRadius.end * gRadius; + //var dim = context.measureText(this.name); + + var width = this.nameWidth; + + if ( this.searchResultChildren() ) + { + var results = searchResultString(this.searchResultChildren()); + var dim = context.measureText(results); + width += dim.width; + } + + if + ( + mouseX > cx - width / 2 && + mouseX < cx + width / 2 && + mouseY > cy - historySpacingFactor * fontSize / 2 && + mouseY < cy + historySpacingFactor * fontSize / 2 + ) + { + highlightedNode = this; + return; + } + + if ( this.getParent() ) + { + this.getParent().checkHighlightCenter(); + } + } + + this.checkHighlightKey = function() + { + var offset = keyOffset(); + + var xMin = imageWidth - keySize - margin - this.keyNameWidth - keyBuffer; + var xMax = imageWidth - margin; + var yMin = offset; + var yMax = offset + keySize; + + currentKey++; + + return ( + mouseX > xMin && + mouseX < xMax && + mouseY > yMin && + mouseY < yMax); + } + + this.checkHighlightMap = function() + { + if ( this.parent ) + { + this.parent.checkHighlightMap(); + } + + if ( this.getCollapse() || this == focusNode ) + { + return; + } + + var box = this.getMapPosition(); + + if + ( + mouseX > box.x - mapRadius && + mouseX < box.x + mapRadius && + mouseY > box.y - mapRadius && + mouseY < box.y + mapRadius + ) + { + highlightedNode = this; + } + } + +/* this.collapse = function() + { + for (var i = 0; i < this.children.length; i++ ) + { + this.children[i] = this.children[i].collapse(); + } + + if + ( + this.children.length == 1 && + this.children[0].magnitude == this.magnitude + ) + { + this.children[0].parent = this.parent; + this.children[0].getDepth() = this.parent.getDepth() + 1; + return this.children[0]; + } + else + { + return this; + } + } +*/ + this.draw = function(labelMode, selected, searchHighlighted) + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; +// var hidden = false; + + if ( selectedNode == this ) + { + selected = true; + } + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + var canDisplayLabelCurrent = this.canDisplayLabelCurrent(); + var hiddenSearchResults = false; + +/* if ( ! this.hide ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.children[i].hide && this.children[i].searchResults ) + { + hiddenSearchResults = true; + } + } + } +*/ + var drawChildren = + ( ! this.hide || ! this.hidePrev && progress < 1 ) && + ( ! this.hideAlone || ! this.hideAlonePrev && progress < 1 ); + +// if ( this.alphaWedge.current() > 0 || this.alphaLabel.current() > 0 ) + { + var lastChildAngleEnd = angleStartCurrent; + + if ( this.hasChildren() )//canDisplayChildren ) + { + lastChildAngleEnd = + this.children[this.children.length - 1].angleEnd.current() + + rotationOffset; + } + + if ( labelMode ) + { + var drawRadial = + !( + this.parent && + this.parent != selectedNode && + angleEndCurrent == this.parent.angleEnd.current() + rotationOffset + ); + + //if ( angleStartCurrent != angleEndCurrent ) + { + this.drawLines(angleStartCurrent, angleEndCurrent, radiusInner, drawRadial, selected); + } + + var alphaOtherCurrent = this.alphaOther.current(); + var childRadiusInner; + + if ( this == selectedNode || alphaOtherCurrent ) + { + childRadiusInner = + this.children.length ? + this.children[this.children.length - 1].radiusInner.current() * gRadius + : radiusInner + } + + if ( this == selectedNode ) + { + this.drawReferenceRings(childRadiusInner); + } + + if + ( + selected && + ! searchHighlighted && + this != selectedNode && + ( + this.isSearchResult || + this.hideAlone && this.searchResultChildren() || + false +// this.hide && +// this.containsSearchResult + ) + ) + { + context.globalAlpha = this.alphaWedge.current(); + + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + + if + ( + this.keyed && + ! showKeys && + this.searchResults && + ! searchHighlighted && + this != highlightedNode && + this != focusNode + ) + { + var angle = (angleEndCurrent + angleStartCurrent) / 2; + this.drawLabel(angle, true, false, true, true); + } + + //this.drawHighlight(false); + searchHighlighted = true; + } + + if + ( + this == selectedNode || +// true + //(canDisplayLabelCurrent) && + this != highlightedNode && + this != focusNode + ) + { + if ( this.radial != this.radialPrev && this.alphaLabel.end == 1 ) + { + context.globalAlpha = tweenFactor; + } + else + { + context.globalAlpha = this.alphaLabel.current(); + } + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + this.hideAlone && this.searchResultChildren() || + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNode && ! this.radial, + selected, + this.radial + ); + + if ( this.radial != this.radialPrev && this.alphaLabel.start == 1 && progress < 1 ) + { + context.globalAlpha = 1 - tweenFactor; + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNodeLast && ! this.radialPrev, + selected, + this.radialPrev + ); + } + } + + if + ( + alphaOtherCurrent && + lastChildAngleEnd != null + ) + { + if + ( + (angleEndCurrent - lastChildAngleEnd) * + (childRadiusInner + gRadius) >= + minWidth() + ) + { + //context.font = fontNormal; + context.globalAlpha = this.alphaOther.current(); + + drawTextPolar + ( + this.getUnclassifiedText(), + this.getUnclassifiedPercentage(), + (lastChildAngleEnd + angleEndCurrent) / 2, + (childRadiusInner + gRadius) / 2, + true, + false, + false, + 0, + 0 + ); + } + } + + if ( this == selectedNode && this.keyUnclassified && showKeys ) + { + this.drawKey + ( + (lastChildAngleEnd + angleEndCurrent) / 2, + false, + false + ); + } + } + else + { + var alphaWedgeCurrent = this.alphaWedge.current(); + + if ( alphaWedgeCurrent || this.alphaOther.current() ) + { + var currentR = this.r.current(); + var currentG = this.g.current(); + var currentB = this.b.current(); + + var fill = rgbText(currentR, currentG, currentB); + + var radiusOuter; + var lastChildAngle; + var truncateWedge = + ( + (this.hasChildren() || this == selectedNode ) && + ! this.keyed && + (compress || depth < maxDisplayDepth) && + drawChildren + ); + + if ( truncateWedge ) + { + radiusOuter = this.children.length ? this.children[0].radiusInner.current() * gRadius : radiusInner; + } + else + { + radiusOuter = gRadius; + } + /* + if ( this.hasChildren() ) + { + radiusOuter = this.children[0].getUncollapsed().radiusInner.current() * gRadius + 1; + } + else + { // TEMP + radiusOuter = radiusInner + nodeRadius * gRadius; + + if ( radiusOuter > gRadius ) + { + radiusOuter = gRadius; + } + } + */ + context.globalAlpha = alphaWedgeCurrent; + + if ( radiusInner != radiusOuter || truncateWedge ) + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + radiusOuter,//this.radiusOuter.current() * gRadius, + //'rgba(0, 200, 0, .1)', + fill, + this.alphaPattern.current() + ); + + if ( truncateWedge ) + { + // fill in the extra space if the sum of our childrens' + // magnitudes is less than ours + + if ( lastChildAngleEnd < angleEndCurrent )//&& false) // TEMP + { + if ( radiusOuter > 1 ) + { + // overlap slightly to hide the seam + + // radiusOuter -= 1; + } + + if ( alphaWedgeCurrent < 1 ) + { + context.globalAlpha = this.alphaOther.current(); + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius, + colorUnclassified, + 0 + ); + context.globalAlpha = alphaWedgeCurrent; + } + + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius,//this.radiusOuter.current() * gRadius, + //'rgba(200, 0, 0, .1)', + fill, + this.alphaPattern.current() + ); + } + } + + if ( radiusOuter < gRadius ) + { + // patch up the seam + // + context.beginPath(); + context.arc(0, 0, radiusOuter, angleStartCurrent/*lastChildAngleEnd*/, angleEndCurrent, false); + context.strokeStyle = fill; + context.lineWidth = 1; + context.stroke(); + } + } + + if ( this.keyed && selected && showKeys )//&& progress == 1 ) + { + this.drawKey + ( + (angleStartCurrent + angleEndCurrent) / 2, + ( + this == highlightedNode || + this == focusNode || + this.searchResults + ), + this == highlightedNode || this == focusNode + ); + } + } + } + } + + this.hiddenLabels = Array(); + + if ( drawChildren ) + { + // draw children + // + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.drawHiddenChildren(i, selected, labelMode, searchHighlighted) ) + { + i = this.children[i].hiddenEnd; + } + else + { + this.children[i].draw(labelMode, selected, searchHighlighted); + } + } + } + }; + + this.drawHiddenChildren = function + ( + firstHiddenChild, + selected, + labelMode, + searchHighlighted + ) + { + var firstChild = this.children[firstHiddenChild]; + + if ( firstChild.hiddenEnd == null || firstChild.radiusInner.current() == 1 ) + { + return false; + } + + for ( var i = firstHiddenChild; i < firstChild.hiddenEnd; i++ ) + { + if ( ! this.children[i].hide || ! this.children[i].hidePrev && progress < 1 ) + { + return false; + } + } + + var angleStart = firstChild.angleStart.current() + rotationOffset; + var lastChild = this.children[firstChild.hiddenEnd]; + var angleEnd = lastChild.angleEnd.current() + rotationOffset; + var radiusInner = gRadius * firstChild.radiusInner.current(); + var hiddenChildren = firstChild.hiddenEnd - firstHiddenChild + 1; + + if ( labelMode ) + { + var hiddenSearchResults = 0; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + hiddenSearchResults += this.children[i].searchResults; + + if ( this.children[i].magnitude == 0 ) + { + hiddenChildren--; + } + } + + if + ( + selected && + (angleEnd - angleStart) * + (gRadius + gRadius) >= + minWidth() || + this == highlightedNode && + hiddenChildren || + hiddenSearchResults + ) + { + context.globalAlpha = this.alphaWedge.current(); + + this.drawHiddenLabel + ( + angleStart, + angleEnd, + hiddenChildren, + hiddenSearchResults + ); + } + } + + var drawWedges = true; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + // all hidden children must be completely hidden to draw together + + if ( this.children[i].alphaPattern.current() != this.children[i].alphaWedge.current() ) + { + drawWedges = false; + break; + } + } + + if ( labelMode ) + { + if ( drawWedges ) + { + var drawRadial = (angleEnd < this.angleEnd.current() + rotationOffset); + this.drawLines(angleStart, angleEnd, radiusInner, drawRadial); + } + + if ( hiddenSearchResults && ! searchHighlighted ) + { + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + highlightFill, + 0, + true + ); + } + } + else if ( drawWedges ) + { + context.globalAlpha = this.alphaWedge.current(); + + var fill = rgbText + ( + firstChild.r.current(), + firstChild.g.current(), + firstChild.b.current() + ); + + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + fill, + context.globalAlpha, + false + ); + } + + return drawWedges; + } + + this.drawHiddenLabel = function(angleStart, angleEnd, value, hiddenSearchResults) + { + var textAngle = (angleStart + angleEnd) / 2; + var labelRadius = gRadius + fontSize;//(radiusInner + radius) / 2; + + var hiddenLabel = Array(); + + hiddenLabel.value = value; + hiddenLabel.angle = textAngle; + hiddenLabel.search = hiddenSearchResults; + + this.hiddenLabels.push(hiddenLabel); + + drawTick(gRadius - fontSize * .75, fontSize * 1.5, textAngle); + drawTextPolar + ( + value.toString() + ' more', + 0, // inner text + textAngle, + labelRadius, + true, // radial + hiddenSearchResults, // bubble + this == highlightedNode || this == focusNode, // bold + false, + hiddenSearchResults + ); + } + + this.drawHighlight = function(bold) + { + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + //this.setHighlightStyle(); + + if ( this == focusNode && this == highlightedNode && this.hasChildren() ) + { +// context.fillStyle = "rgba(255, 255, 255, .3)"; + arrow + ( + angleStartCurrent, + angleEndCurrent, + radiusInner + ); + } + else + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + } + + // check if hidden children should be highlighted + // + for ( var i = 0; i < this.children.length; i++ ) + { + if + ( + this.children[i].getDepth() - selectedNode.getDepth() + 1 <= + maxDisplayDepth && + this.children[i].hiddenEnd != null + ) + { + var firstChild = this.children[i]; + var lastChild = this.children[firstChild.hiddenEnd]; + var hiddenAngleStart = firstChild.angleStart.current() + rotationOffset; + var hiddenAngleEnd = lastChild.angleEnd.current() + rotationOffset; + var hiddenRadiusInner = gRadius * firstChild.radiusInner.current(); + + drawWedge + ( + hiddenAngleStart, + hiddenAngleEnd, + hiddenRadiusInner, + gRadius, + 'rgba(255, 255, 255, .3)', + 0, + true + ); + + if ( false && ! this.searchResults ) + { + this.drawHiddenLabel + ( + hiddenAngleStart, + hiddenAngleEnd, + firstChild.hiddenEnd - i + 1 + ); + } + + i = firstChild.hiddenEnd; + } + } + +// context.strokeStyle = 'black'; + context.fillStyle = 'black'; + + var highlight = ! ( progress < 1 && zoomOut && this == selectedNodeLast ); + + var angle = (angleEndCurrent + angleStartCurrent) / 2; + + if ( ! (this.keyed && showKeys) ) + { + this.drawLabel(angle, true, bold, true, this.radial); + } + } + + this.drawHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + context.lineWidth = highlightLineWidth; + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .6)"; + + context.fillStyle = 'black'; + this.drawLabel(3 * Math.PI / 2, true, true, false); + context.font = fontNormal; + } + + this.drawKey = function(angle, highlight, bold) + { + var offset = keyOffset(); + var color; + var colorText = this.magnitude == 0 ? 'gray' : 'black'; + var patternAlpha = this.alphaPattern.end; + var boxLeft = imageWidth - keySize - margin; + var textY = offset + keySize / 2; + + var label; + var keyNameWidth; + + if ( this == selectedNode ) + { + color = colorUnclassified; + label = + this.getUnclassifiedText() + + ' ' + + this.getUnclassifiedPercentage(); + keyNameWidth = measureText(label, false); + } + else + { + label = this.keyLabel; + color = rgbText(this.r.end, this.g.end, this.b.end); + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + label = label + searchResultString(this.searchResultChildren()); + } + + keyNameWidth = measureText(label, bold); + } + else + { + keyNameWidth = this.keyNameWidth; + } + } + + var textLeft = boxLeft - keyBuffer - keyNameWidth - fontSize / 2; + var labelLeft = textLeft; + + if ( labelLeft > keyMinTextLeft - fontSize / 2 ) + { + keyMinTextLeft -= fontSize / 2; + + if ( keyMinTextLeft < centerX - gRadius + fontSize / 2 ) + { + keyMinTextLeft = centerX - gRadius + fontSize / 2; + } + + labelLeft = keyMinTextLeft; + } + + var lineX = new Array(); + var lineY = new Array(); + + var bendRadius; + var keyAngle = Math.atan((textY - centerY) / (labelLeft - centerX)); + var arcAngle; + + if ( keyAngle < 0 ) + { + keyAngle += Math.PI; + } + + if ( keyMinAngle == 0 || angle < keyMinAngle ) + { + keyMinAngle = angle; + } + + if ( angle > Math.PI && keyMinAngle > Math.PI ) + { + // allow lines to come underneath the chart + + angle -= Math.PI * 2; + } + + lineX.push(Math.cos(angle) * gRadius); + lineY.push(Math.sin(angle) * gRadius); + + if ( angle < keyAngle && textY > centerY + Math.sin(angle) * (gRadius + buffer * (currentKey - 1) / (keys + 1) / 2 + buffer / 2) ) + { + bendRadius = gRadius + buffer - buffer * currentKey / (keys + 1) / 2; + } + else + { + bendRadius = gRadius + buffer * currentKey / (keys + 1) / 2 + buffer / 2; + } + + var outside = + Math.sqrt + ( + Math.pow(labelLeft - centerX, 2) + + Math.pow(textY - centerY, 2) + ) > bendRadius; + + if ( ! outside ) + { + arcAngle = Math.asin((textY - centerY) / bendRadius); + + keyMinTextLeft = min(keyMinTextLeft, centerX + bendRadius * Math.cos(arcAngle) - fontSize / 2); + + if ( labelLeft < textLeft && textLeft > centerX + bendRadius * Math.cos(arcAngle) ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + else + { + keyMinTextLeft = min(keyMinTextLeft, labelLeft - fontSize / 2); + + if ( angle < keyAngle ) + { + // flip everything over y = x + // + arcAngle = Math.PI / 2 - keyLineAngle + ( + Math.PI / 2 - angle, + Math.PI / 2 - keyAngle, + bendRadius, + textY - centerY, + labelLeft - centerX, + lineY, + lineX + ); + + } + else + { + arcAngle = keyLineAngle + ( + angle, + keyAngle, + bendRadius, + labelLeft - centerX, + textY - centerY, + lineX, + lineY + ); + } + } + + if ( labelLeft > centerX + bendRadius * Math.cos(arcAngle) || + textY > centerY + bendRadius * Math.sin(arcAngle) + .01) +// if ( outside || ) + { + lineX.push(labelLeft - centerX); + lineY.push(textY - centerY); + + if ( textLeft != labelLeft ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + + context.globalAlpha = this.alphaWedge.current(); + + if ( snapshotMode ) + { + var labelSVG; + + if ( this == selectedNode ) + { + labelSVG = + this.getUnclassifiedText() + + spacer() + + this.getUnclassifiedPercentage(); + } + else + { + labelSVG = this.name + spacer() + this.getPercentage() + '%'; + } + + svg += + '<rect fill="' + color + '" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + + if ( patternAlpha ) + { + svg += + '<rect fill="url(#hiddenPattern)" style="stroke:none" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + } + + svg += + '<path class="line' + + (highlight ? ' highlight' : '') + + '" d="M ' + (lineX[0] + centerX) + ',' + + (lineY[0] + centerY); + + if ( angle != arcAngle ) + { + svg += + ' L ' + (centerX + bendRadius * Math.cos(angle)) + ',' + + (centerY + bendRadius * Math.sin(angle)) + + ' A ' + bendRadius + ',' + bendRadius + ' 0 ' + + '0,' + (angle > arcAngle ? '0' : '1') + ' ' + + (centerX + bendRadius * Math.cos(arcAngle)) + ',' + + (centerY + bendRadius * Math.sin(arcAngle)); + } + + for ( var i = 1; i < lineX.length; i++ ) + { + svg += + ' L ' + (centerX + lineX[i]) + ',' + + (centerY + lineY[i]); + } + + svg += '"/>'; + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + labelSVG = labelSVG + searchResultString(this.searchResultChildren()); + } + + drawBubbleSVG + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + svg += svgText(labelSVG, boxLeft - keyBuffer, textY, 'end', bold, colorText); + } + else + { + context.fillStyle = color; + context.translate(-centerX, -centerY); + context.strokeStyle = 'black'; + context.globalAlpha = 1;//this.alphaWedge.current(); + + context.fillRect(boxLeft, offset, keySize, keySize); + + if ( patternAlpha ) + { + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + + // make clipping box for Firefox performance + context.beginPath(); + context.moveTo(boxLeft, offset); + context.lineTo(boxLeft + keySize, offset); + context.lineTo(boxLeft + keySize, offset + keySize); + context.lineTo(boxLeft, offset + keySize); + context.closePath(); + context.save(); + context.clip(); + + context.fillRect(boxLeft, offset, keySize, keySize); + context.fillRect(boxLeft, offset, keySize, keySize); + + context.restore(); // remove clipping region + } + + if ( highlight ) + { + this.setHighlightStyle(); + context.fillRect(boxLeft, offset, keySize, keySize); + } + else + { + context.lineWidth = thinLineWidth; + } + + context.strokeRect(boxLeft, offset, keySize, keySize); + + if ( lineX.length ) + { + context.beginPath(); + context.moveTo(lineX[0] + centerX, lineY[0] + centerY); + + context.arc(centerX, centerY, bendRadius, angle, arcAngle, angle > arcAngle); + + for ( var i = 1; i < lineX.length; i++ ) + { + context.lineTo(lineX[i] + centerX, lineY[i] + centerY); + } + + context.globalAlpha = this == selectedNode ? + this.children[0].alphaWedge.current() : + this.alphaWedge.current(); + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.stroke(); + context.globalAlpha = 1; + } + + if ( highlight ) + { + drawBubbleCanvas + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + drawText(label, boxLeft - keyBuffer, offset + keySize / 2, 0, 'end', bold, colorText); + + context.translate(centerX, centerY); + } + + currentKey++; + } + + this.drawLabel = function(angle, bubble, bold, selected, radial) + { + if ( context.globalAlpha == 0 ) + { + return; + } + + var innerText; + var label; + var radius; + + if ( radial ) + { + radius = (this.radiusInner.current() + 1) * gRadius / 2; + } + else + { + radius = this.labelRadius.current() * gRadius; + } + + if ( radial && (selected || bubble ) ) + { + var percentage = this.getPercentage(); + innerText = percentage + '%'; + } + + if + ( + ! radial && + this != selectedNode && + ! bubble && + ( !zoomOut || this != selectedNodeLast) + ) + { + label = this.shortenLabel(); + } + else + { + label = this.name; + } + + var flipped = drawTextPolar + ( + label, + innerText, + angle, + radius, + radial, + bubble, + bold, +// this.isSearchResult && this.shouldAddSearchResultsString() && (!selected || this == selectedNode || highlight), + this.isSearchResult && (!selected || this == selectedNode || bubble), + (this.hideAlone || !selected || this == selectedNode ) ? this.searchResultChildren() : 0 + ); + + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + if + ( + ! radial && + ! bubble && + this != selectedNode && + this.angleEnd.end != this.angleStart.end && + nLabelOffsets[depth - 2] > 2 && + this.labelWidth.current() > (this.angleEnd.end - this.angleStart.end) * Math.abs(radius) && + ! ( zoomOut && this == selectedNodeLast ) && + this.labelRadius.end > 0 + ) + { + // name extends beyond wedge; draw tick mark towards the central + // radius for easier identification + + var radiusCenter = compress ? + (compressedRadii[depth - 1] + compressedRadii[depth - 2]) / 2 : + (depth - .5) * nodeRadius; + + if ( this.labelRadius.end > radiusCenter ) + { + if ( flipped ) + { + drawTick(radius - tickLength * 1.4 , tickLength, angle); + } + else + { + drawTick(radius - tickLength * 1.7, tickLength, angle); + } + } + else + { + if ( flipped ) + { + drawTick(radius + tickLength * .7, tickLength, angle); + } + else + { + drawTick(radius + tickLength * .4, tickLength, angle); + } + } + } + } + + this.drawLines = function(angleStart, angleEnd, radiusInner, drawRadial, selected) + { + if ( snapshotMode ) + { + if ( this != selectedNode) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + if ( this.alphaArc.end ) + { + var dArray = + [ + " M ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, + " 0 ", x1, ",", y1 + ]; + + svg += '<path class="line" d="' + dArray.join('') + '"/>'; + } + + if ( drawRadial && this.alphaLine.end ) + { + svg += '<line x1="' + x3 + '" y1="' + y3 + '" x2="' + x4 + '" y2="' + y4 + '"/>'; + } + } + } + else + { + context.lineWidth = thinLineWidth; + context.strokeStyle = 'black'; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.globalAlpha = this.alphaArc.current(); + context.stroke(); + + if ( drawRadial ) + { + var x1 = radiusInner * Math.cos(angleEnd); + var y1 = radiusInner * Math.sin(angleEnd); + var x2 = gRadius * Math.cos(angleEnd); + var y2 = gRadius * Math.sin(angleEnd); + + context.beginPath(); + context.moveTo(x1, y1); + context.lineTo(x2, y2); + +// if ( this.getCollapse() )//( selected && this != selectedNode ) + { + context.globalAlpha = this.alphaLine.current(); + } + + context.stroke(); + } + } + } + + this.drawMap = function(child) + { + if ( this.parent ) + { + this.parent.drawMap(child); + } + + if ( this.getCollapse() && this != child || this == focusNode ) + { + return; + } + + var angleStart = + (child.baseMagnitude - this.baseMagnitude) / this.magnitude * Math.PI * 2 + + rotationOffset; + var angleEnd = + (child.baseMagnitude - this.baseMagnitude + child.magnitude) / + this.magnitude * Math.PI * 2 + + rotationOffset; + + var box = this.getMapPosition(); + + context.save(); + context.fillStyle = 'black'; + context.textAlign = 'end'; + context.textBaseline = 'middle'; + + var textX = box.x - mapRadius - mapBuffer; + var percentage = getPercentage(child.magnitude / this.magnitude); + + var highlight = this == selectedNode || this == highlightedNode; + + if ( highlight ) + { + context.font = fontBold; + } + else + { + context.font = fontNormal; + } + + context.fillText(percentage + '% of', textX, box.y - mapRadius / 3); + context.fillText(this.name, textX, box.y + mapRadius / 3); + + if ( highlight ) + { + context.font = fontNormal; + } + + if ( this == highlightedNode && this != selectedNode ) + { + context.fillStyle = 'rgb(245, 245, 245)'; +// context.fillStyle = 'rgb(200, 200, 200)'; + } + else + { + context.fillStyle = 'rgb(255, 255, 255)'; + } + + context.beginPath(); + context.arc(box.x, box.y, mapRadius, 0, Math.PI * 2, true); + context.closePath(); + context.fill(); + + if ( this == selectedNode ) + { + context.lineWidth = 1; + context.fillStyle = 'rgb(100, 100, 100)'; + } + else + { + if ( this == highlightedNode ) + { + context.lineWidth = .2; + context.fillStyle = 'rgb(190, 190, 190)'; + } + else + { + context.lineWidth = .2; + context.fillStyle = 'rgb(200, 200, 200)'; + } + } + + var maxDepth = this.getMaxDepth(); + + if ( ! compress && maxDepth > maxPossibleDepth + this.getDepth() - 1 ) + { + maxDepth = maxPossibleDepth + this.getDepth() - 1; + } + + if ( this.getDepth() < selectedNode.getDepth() ) + { + if ( child.getDepth() - 1 >= maxDepth ) + { + maxDepth = child.getDepth(); + } + } + + var radiusInner; + + if ( compress ) + { + radiusInner = 0; +// Math.atan(child.getDepth() - this.getDepth()) / +// Math.PI * 2 * .9; + } + else + { + radiusInner = + (child.getDepth() - this.getDepth()) / + (maxDepth - this.getDepth() + 1); + } + + context.stroke(); + context.beginPath(); + + if ( radiusInner == 0 ) + { + context.moveTo(box.x, box.y); + } + else + { + context.arc(box.x, box.y, mapRadius * radiusInner, angleEnd, angleStart, true); + } + + context.arc(box.x, box.y, mapRadius, angleStart, angleEnd, false); + context.closePath(); + context.fill(); + + if ( this == highlightedNode && this != selectedNode ) + { + context.lineWidth = 1; + context.stroke(); + } + + context.restore(); + } + + this.drawReferenceRings = function(childRadiusInner) + { + if ( snapshotMode ) + { + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + childRadiusInner + '"/>'; + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + gRadius + '"/>'; + } + else + { + context.globalAlpha = 1 - this.alphaLine.current();//this.getUncollapsed().alphaLine.current(); + context.beginPath(); + context.arc(0, 0, childRadiusInner, 0, Math.PI * 2, false); + context.stroke(); + context.beginPath(); + context.arc(0, 0, gRadius, 0, Math.PI * 2, false); + context.stroke(); + } + } + + this.getCollapse = function() + { + return ( + collapse && + this.collapse && + this.depth != maxAbsoluteDepth + ); + } + + this.getDepth = function() + { + if ( collapse ) + { + return this.depthCollapsed; + } + else + { + return this.depth; + } + } + + this.getMagnitude = function() + { + return this.attributes[magnitudeIndex][currentDataset]; + } + + this.getMapPosition = function() + { + return { + x : (details.offsetLeft + details.clientWidth - mapRadius), + y : ((focusNode.getDepth() - this.getDepth()) * + (mapBuffer + mapRadius * 2) - mapRadius) + + details.clientHeight + details.offsetTop + }; + } + + this.getMaxDepth = function(limit) + { + var max; + + if ( collapse ) + { + return this.maxDepthCollapsed; + } + else + { + if ( this.maxDepth > maxAbsoluteDepth ) + { + return maxAbsoluteDepth; + } + else + { + return this.maxDepth; + } + } + } + + this.getData = function(index, summary) + { + var files = new Array(); + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null && + this.attributes[index][currentDataset] != '' + ) + { + files.push + ( + document.location + + '.files/' + + this.attributes[index][currentDataset] + ); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + files = files.concat(this.children[i].getData(index, true)); + } + } + + return files; + } + + this.getList = function(index, summary) + { + var list; + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null + ) + { + list = this.attributes[index][currentDataset]; + } + else + { + list = new Array(); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + list = list.concat(this.children[i].getList(index, true)); + } + } + + return list; + } + + this.getParent = function() + { + // returns parent, accounting for collapsing or 0 if doesn't exist + + var parent = this.parent; + + while ( parent != 0 && parent.getCollapse() ) + { + parent = parent.parent; + } + + return parent; + } + + this.getPercentage = function() + { + return getPercentage(this.magnitude / selectedNode.magnitude); + } + + this.getUnclassifiedPercentage = function() + { + if ( this.children.length ) + { + var lastChild = this.children[this.children.length - 1]; + + return getPercentage + ( + ( + this.baseMagnitude + + this.magnitude - + lastChild.magnitude - + lastChild.baseMagnitude + ) / this.magnitude + ) + '%'; + } + else + { + return '100%'; + } + } + + this.getUnclassifiedText = function() + { + return '[other '+ this.name + ']'; + } + + this.getUncollapsed = function() + { + // recurse through collapsed children until uncollapsed node is found + + if ( this.getCollapse() ) + { + return this.children[0].getUncollapsed(); + } + else + { + return this; + } + } + + this.hasChildren = function() + { + return this.children.length && this.depth < maxAbsoluteDepth && this.magnitude; + } + + this.hasParent = function(parent) + { + if ( this.parent ) + { + if ( this.parent == parent ) + { + return true; + } + else + { + return this.parent.hasParent(parent); + } + } + else + { + return false; + } + } + + this.maxVisibleDepth = function(maxDepth) + { + var childInnerRadius; + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var currentMaxDepth = depth; + + if ( this.hasChildren() && depth < maxDepth) + { + var lastChild = this.children[this.children.length - 1]; + + if ( this.name == 'Pseudomonadaceae' ) + { + var x = 3; + } + + if + ( + lastChild.baseMagnitude + lastChild.magnitude < + this.baseMagnitude + this.magnitude + ) + { + currentMaxDepth++; + } + + if ( compress ) + { + childInnerRadius = compressedRadii[depth - 1]; + } + else + { + childInnerRadius = (depth) / maxDepth; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + if + (//true || + this.children[i].magnitude * + angleFactor * + (childInnerRadius + 1) * + gRadius >= + minWidth() + ) + { + var childMaxDepth = this.children[i].maxVisibleDepth(maxDepth); + + if ( childMaxDepth > currentMaxDepth ) + { + currentMaxDepth = childMaxDepth; + } + } + } + } + + return currentMaxDepth; + } + + this.resetLabelWidth = function() + { + var nameWidthOld = this.nameWidth; + + if ( true || ! this.radial )//&& fontSize != fontSizeLast ) + { + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + } + + if ( fontSize != fontSizeLast && this.labelWidth.end == nameWidthOld * labelWidthFudge ) + { + // font size changed; adjust start of tween to match + + this.labelWidth.start = this.nameWidth * labelWidthFudge; + } + else + { + this.labelWidth.start = this.labelWidth.current(); + } + + this.labelWidth.end = this.nameWidth * labelWidthFudge; + } + + this.restrictLabelWidth = function(width) + { + if ( width < this.labelWidth.end ) + { + this.labelWidth.end = width; + } + } + + this.search = function() + { + this.isSearchResult = false; + this.searchResults = 0; + + if + ( + ! this.getCollapse() && + search.value != '' && + this.name.toLowerCase().indexOf(search.value.toLowerCase()) != -1 + ) + { + this.isSearchResult = true; + this.searchResults = 1; + nSearchResults++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.searchResults += this.children[i].search(); + } + + return this.searchResults; + } + + this.searchResultChildren = function() + { + if ( this.isSearchResult ) + { + return this.searchResults - 1; + } + else + { + return this.searchResults; + } + } + + this.setDepth = function(depth, depthCollapsed) + { + this.depth = depth; + this.depthCollapsed = depthCollapsed; + + if + ( + this.children.length == 1 && +// this.magnitude > 0 && + this.children[0].magnitude == this.magnitude && + ( head.children.length > 1 || this.children[0].children.length ) + ) + { + this.collapse = true; + } + else + { + this.collapse = false; + depthCollapsed++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setDepth(depth + 1, depthCollapsed); + } + } + + this.setHighlightStyle = function() + { + context.lineWidth = highlightLineWidth; + + if ( this.hasChildren() || this != focusNode || this != highlightedNode ) + { + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .3)"; + } + else + { + context.strokeStyle = 'rgb(90,90,90)'; + context.fillStyle = "rgba(155, 155, 155, .3)"; + } + } + + this.setLabelWidth = function(node) + { + if ( ! shorten || this.radial ) + { + return; // don't need to set width + } + + if ( node.hide ) + { + alert('wtf'); + return; + } + + var angle = (this.angleStart.end + this.angleEnd.end) / 2; + var a; // angle difference + + if ( node == selectedNode ) + { + a = Math.abs(angle - node.angleOther); + } + else + { + a = Math.abs(angle - (node.angleStart.end + node.angleEnd.end) / 2); + } + + if ( a == 0 ) + { + return; + } + + if ( a > Math.PI ) + { + a = 2 * Math.PI - a; + } + + if ( node.radial || node == selectedNode ) + { + var nodeLabelRadius; + + if ( node == selectedNode ) + { + // radial 'other' label + + nodeLabelRadius = (node.children[0].radiusInner.end + 1) / 2; + } + else + { + nodeLabelRadius = (node.radiusInner.end + 1) / 2; + } + + if ( a < Math.PI / 2 ) + { + var r = this.labelRadius.end * gRadius + .5 * fontSize + var hypotenuse = r / Math.cos(a); + var opposite = r * Math.tan(a); + var fontRadius = .8 * fontSize; + + if + ( + nodeLabelRadius * gRadius < hypotenuse && + this.labelWidth.end / 2 + fontRadius > opposite + ) + { + this.labelWidth.end = 2 * (opposite - fontRadius); + } + } + } + else if + ( + this.labelRadius.end == node.labelRadius.end && + a < Math.PI / 4 + ) + { + // same radius with small angle; use circumferential approximation + + var dist = a * this.labelRadius.end * gRadius - fontSize * (1 - a * 4 / Math.PI) * 1.3; + + if ( this.labelWidth.end < dist ) + { + node.restrictLabelWidth((dist - this.labelWidth.end / 2) * 2); + } + else if ( node.labelWidth.end < dist ) + { + this.restrictLabelWidth((dist - node.labelWidth.end / 2) * 2); + } + else + { + // both labels reach halfway point; restrict both + + this.labelWidth.end = dist; + node.labelWidth.end = dist + } + } + else + { + var r1 = this.labelRadius.end * gRadius; + var r2 = node.labelRadius.end * gRadius; + + // first adjust the radii to account for the height of the font by shifting them + // toward each other + // + var fontFudge = .35 * fontSize; + // + if ( this.labelRadius.end < node.labelRadius.end ) + { + r1 += fontFudge; + r2 -= fontFudge; + } + else if ( this.labelRadius.end > node.labelRadius.end ) + { + r1 -= fontFudge; + r2 += fontFudge; + } + else + { + r1 -= fontFudge; + r2 -= fontFudge; + } + + var r1s = r1 * r1; + var r2s = r2 * r2; + + // distance between the centers of the two labels + // + var dist = Math.sqrt(r1s + r2s - 2 * r1 * r2 * Math.cos(a)); + + // angle at our label center between our radius and the line to the other label center + // + var b = Math.acos((r1s + dist * dist - r2s) / (2 * r1 * dist)); + + // distance from our label center to the intersection of the two tangents + // + var l1 = Math.sin(a + b - Math.PI / 2) * dist / Math.sin(Math.PI - a); + + // distance from other label center the the intersection of the two tangents + // + var l2 = Math.sin(Math.PI / 2 - b) * dist / Math.sin(Math.PI - a); + + l1 = Math.abs(l1) - .4 * fontSize; + l2 = Math.abs(l2) - .4 * fontSize; +/* + // amount to shorten the distances because of the height of the font + // + var l3 = 0; + var fontRadius = fontSize * .55; + // + if ( l1 < 0 || l2 < 0 ) + { + var l4 = fontRadius / Math.tan(a); + l1 = Math.abs(l1); + l2 = Math.abs(l2); + + l1 -= l4; + l2 -= l4; + } + else + { + var c = Math.PI - a; + + l3 = fontRadius * Math.tan(c / 2); + } +*/ + if ( this.labelWidth.end / 2 > l1 && node.labelWidth.end / 2 > l2 ) + { + // shorten the farthest one from the intersection + + if ( l1 > l2 ) + { + this.restrictLabelWidth(2 * (l1));// - l3 - fontRadius)); + } + else + { + node.restrictLabelWidth(2 * (l2));// - l3 - fontRadius)); + } + }/* + else if ( this.labelWidth.end / 2 > l1 + l3 && node.labelWidth.end / 2 > l2 - l3 ) + { + node.restrictLabelWidth(2 * (l2 - l3)); + } + else if ( this.labelWidth.end / 2 > l1 - l3 && node.labelWidth.end / 2 > l2 + l3 ) + { + this.restrictLabelWidth(2 * (l1 - l3)); + }*/ + } + } + + this.setMagnitudes = function(baseMagnitude) + { + this.magnitude = this.getMagnitude(); + this.baseMagnitude = baseMagnitude; + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setMagnitudes(baseMagnitude); + baseMagnitude += this.children[i].magnitude; + } + + this.maxChildMagnitude = baseMagnitude; + } + + this.setMaxDepths = function() + { + this.maxDepth = this.depth; + this.maxDepthCollapsed = this.depthCollapsed; + + for ( i in this.children ) + { + var child = this.children[i]; + + child.setMaxDepths(); + + if ( child.maxDepth > this.maxDepth ) + { + this.maxDepth = child.maxDepth; + } + + if + ( + child.maxDepthCollapsed > this.maxDepthCollapsed && + (child.depth <= maxAbsoluteDepth || maxAbsoluteDepth == 0) + ) + { + this.maxDepthCollapsed = child.maxDepthCollapsed; + } + } + } + + this.setTargetLabelRadius = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var index = depth - 2; + var labelOffset = labelOffsets[index]; + + if ( this.radial ) + { + //this.labelRadius.setTarget((this.radiusInner.end + 1) / 2); + var max = + depth == maxDisplayDepth ? + 1 : + compressedRadii[index + 1]; + + this.labelRadius.setTarget((compressedRadii[index] + max) / 2); + } + else + { + var radiusCenter; + var width; + + if ( compress ) + { + if ( nLabelOffsets[index] > 1 ) + { + this.labelRadius.setTarget + ( + lerp + ( + labelOffset + .75, + 0, + nLabelOffsets[index] + .5, + compressedRadii[index], + compressedRadii[index + 1] + ) + ); + } + else + { + this.labelRadius.setTarget((compressedRadii[index] + compressedRadii[index + 1]) / 2); + } + } + else + { + radiusCenter = + nodeRadius * (depth - 1) + + nodeRadius / 2; + width = nodeRadius; + + this.labelRadius.setTarget + ( + radiusCenter + width * ((labelOffset + 1) / (nLabelOffsets[index] + 1) - .5) + ); + } + } + + if ( ! this.hide && ! this.keyed && nLabelOffsets[index] ) + { + // check last and first labels in each track for overlap + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + var last = labelLastNodes[i][j]; + var first = labelFirstNodes[i][j]; + + if ( last ) + { + if ( j == nLabelOffsets[i] ) + { + // last is radial + this.setLabelWidth(last); + } + else + { + last.setLabelWidth(this); + } + } + + if ( first ) + { + if ( j == nLabelOffsets[i] ) + { + this.setLabelWidth(first); + } + else + { + first.setLabelWidth(this); + } + } + } + } + + if ( selectedNode.canDisplayLabelOther ) + { + this.setLabelWidth(selectedNode); // in case there is an 'other' label + } + + if ( this.radial ) + { + // use the last 'track' of this depth for radial + + labelLastNodes[index][nLabelOffsets[index]] = this; + + if ( labelFirstNodes[index][nLabelOffsets[index]] == 0 ) + { + labelFirstNodes[index][nLabelOffsets[index]] = this; + } + } + else + { + labelLastNodes[index][labelOffset] = this; + + // update offset + + labelOffsets[index] += 1; + + if ( labelOffsets[index] > nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]--; + } + } + else if ( labelOffsets[index] == nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( false && !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]++; + } + } + + if ( labelFirstNodes[index][labelOffset] == 0 ) + { + labelFirstNodes[index][labelOffset] = this; + } + } + } + else if ( this.hide ) + { + this.labelWidth.end = 0; + } + } + + this.setTargets = function() + { + if ( this == selectedNode ) + { + this.setTargetsSelected + ( + 0, + 1, + lightnessBase, + false, + false + ); + return; + } + + var depthRelative = this.getDepth() - selectedNode.getDepth(); + + var parentOfSelected = selectedNode.hasParent(this); +/* ( +// ! this.getCollapse() && + this.baseMagnitude <= selectedNode.baseMagnitude && + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ); +*/ + if ( parentOfSelected ) + { + this.resetLabelWidth(); + } + else + { + //context.font = fontNormal; + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + //this.labelWidth.setTarget(this.labelWidth.end); + this.labelWidth.setTarget(0); + } + + // set angles + // + if ( this.baseMagnitude <= selectedNode.baseMagnitude ) + { + this.angleStart.setTarget(0); + } + else + { + this.angleStart.setTarget(Math.PI * 2); + } + // + if + ( + parentOfSelected || + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ) + { + this.angleEnd.setTarget(Math.PI * 2); + } + else + { + this.angleEnd.setTarget(0); + } + + // children + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargets(); + } + + if ( this.getDepth() <= selectedNode.getDepth() ) + { + // collapse in + + this.radiusInner.setTarget(0); + + if ( parentOfSelected ) + { + this.labelRadius.setTarget + ( + (depthRelative) * + historySpacingFactor * fontSize / gRadius + ); + //this.scale.setTarget(1 - (selectedNode.getDepth() - this.getDepth()) / 18); // TEMP + } + else + { + this.labelRadius.setTarget(0); + //this.scale.setTarget(1); // TEMP + } + } + else if ( depthRelative + 1 > maxDisplayDepth ) + { + // collapse out + + this.radiusInner.setTarget(1); + this.labelRadius.setTarget(1); + //this.scale.setTarget(1); // TEMP + } + else + { + // don't collapse + + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depthRelative - 1]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depthRelative)); + } + + //this.scale.setTarget(1); // TEMP + + if ( this == selectedNode ) + { + this.labelRadius.setTarget(0); + } + else + { + if ( compress ) + { + this.labelRadius.setTarget + ( + (compressedRadii[depthRelative - 1] + compressedRadii[depthRelative]) / 2 + ); + } + else + { + this.labelRadius.setTarget(nodeRadius * (depthRelative) + nodeRadius / 2); + } + } + } + +// this.r.start = this.r.end; +// this.g.start = this.g.end; +// this.b.start = this.b.end; + + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + + this.alphaLine.setTarget(0); + this.alphaArc.setTarget(0); + this.alphaWedge.setTarget(0); + this.alphaPattern.setTarget(0); + this.alphaOther.setTarget(0); + + if ( parentOfSelected && ! this.getCollapse() ) + { + var alpha = + ( + 1 - + (selectedNode.getDepth() - this.getDepth()) / + (Math.floor((compress ? compressedRadii[0] : nodeRadius) * gRadius / (historySpacingFactor * fontSize) - .5) + 1) + ); + + if ( alpha < 0 ) + { + alpha = 0; + } + + this.alphaLabel.setTarget(alpha); + this.radial = false; + } + else + { + this.alphaLabel.setTarget(0); + } + + this.hideAlonePrev = this.hideAlone; + this.hidePrev = this.hide; + + if ( parentOfSelected ) + { + this.hideAlone = false; + this.hide = false; + } + + if ( this.getParent() == selectedNode.getParent() ) + { + this.hiddenEnd = null; + } + + this.radialPrev = this.radial; + } + + this.setTargetsSelected = function(hueMin, hueMax, lightness, hide, nextSiblingHidden) + { + var collapse = this.getCollapse(); + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var canDisplayChildLabels = false; + var lastChild; + + if ( this.hasChildren() )//&& ! hide ) + { + lastChild = this.children[this.children.length - 1]; + this.hideAlone = true; + } + else + { + this.hideAlone = false; + } + + // set child wedges + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargetWedge(); + + if + ( + ! this.children[i].hide && + ( collapse || depth < maxDisplayDepth ) && + this.depth < maxAbsoluteDepth + ) + { + canDisplayChildLabels = true; + this.hideAlone = false; + } + } + + if ( this == selectedNode || lastChild && lastChild.angleEnd.end < this.angleEnd.end - .01) + { + this.hideAlone = false; + } + + if ( this.hideAlonePrev == undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + if ( this == selectedNode ) + { + var otherArc = + this.children.length ? + angleFactor * + ( + this.baseMagnitude + this.magnitude - + lastChild.baseMagnitude - lastChild.magnitude + ) + : this.baseMagnitude + this.magnitude; + this.canDisplayLabelOther = + this.children.length ? + otherArc * + (this.children[0].radiusInner.end + 1) * gRadius >= + minWidth() + : true; + + this.keyUnclassified = false; + + if ( this.canDisplayLabelOther ) + { + this.angleOther = Math.PI * 2 - otherArc / 2; + } + else if ( otherArc > 0.0000000001 ) + { + this.keyUnclassified = true; + keys++; + } + + this.angleStart.setTarget(0); + this.angleEnd.setTarget(Math.PI * 2); + + if ( this.children.length ) + { + this.radiusInner.setTarget(0); + } + else + { + this.radiusInner.setTarget(compressedRadii[0]); + } + + this.hidePrev = this.hide; + this.hide = false; + this.hideAlonePrev = this.hideAlone; + this.hideAlone = false; + this.keyed = false; + } + + if ( hueMax - hueMin > 1 / 12 ) + { + hueMax = hueMin + 1 / 12; + } + + // set lightness + // + if ( ! ( hide || this.hideAlone ) ) + { + if ( useHue() ) + { + lightness = (lightnessBase + lightnessMax) / 2; + } + else + { + lightness = lightnessBase + (depth - 1) * lightnessFactor; + + if ( lightness > lightnessMax ) + { + lightness = lightnessMax; + } + } + } + + if ( hide ) + { + this.hide = true; + } + + if ( this.hidePrev == undefined ) + { + this.hidePrev = this.hide; + } + + var hiddenStart = -1; + var hiddenHueNumer = 0; + var hiddenHueDenom = 0; + var i = 0; + + if ( ! this.hide ) + { + this.hiddenEnd = null; + } + + while ( true ) + { + if ( ! this.hideAlone && ! hide && ( i == this.children.length || ! this.children[i].hide ) ) + { + // reached a non-hidden child or the end; set targets for + // previous group of hidden children (if any) using their + // average hue + + if ( hiddenStart != -1 ) + { + var hiddenHue = hiddenHueDenom ? hiddenHueNumer / hiddenHueDenom : hueMin; + + for ( var j = hiddenStart; j < i; j++ ) + { + this.children[j].setTargetsSelected + ( + hiddenHue, + null, + lightness, + false, + j < i - 1 + ); + + this.children[j].hiddenEnd = null; + } + + this.children[hiddenStart].hiddenEnd = i - 1; + } + } + + if ( i == this.children.length ) + { + break; + } + + var child = this.children[i]; + var childHueMin; + var childHueMax; + + if ( this.magnitude > 0 && ! this.hide && ! this.hideAlone ) + { + if ( useHue() ) + { + childHueMin = child.hues[currentDataset]; + } + else if ( this == selectedNode ) + { + var min = 0.0; + var max = 1.0; + + if ( this.children.length > 6 ) + { + childHueMin = lerp((1 - Math.pow(1 - i / this.children.length, 1.4)) * .95, 0, 1, min, max); + childHueMax = lerp((1 - Math.pow(1 - (i + .55) / this.children.length, 1.4)) * .95, 0, 1, min, max); + } + else + { + childHueMin = lerp(i / this.children.length, 0, 1, min, max); + childHueMax = lerp((i + .55) / this.children.length, 0, 1, min, max); + } + } + else + { + childHueMin = lerp + ( + child.baseMagnitude, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + childHueMax = lerp + ( + child.baseMagnitude + child.magnitude * .99, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + } + } + else + { + childHueMin = hueMin; + childHueMax = hueMax; + } + + if ( ! this.hideAlone && ! hide && ! this.hide && child.hide ) + { + if ( hiddenStart == -1 ) + { + hiddenStart = i; + } + + if ( useHue() ) + { + hiddenHueNumer += childHueMin * child.magnitude; + hiddenHueDenom += child.magnitude; + } + else + { + hiddenHueNumer += childHueMin; + hiddenHueDenom++; + } + } + else + { + hiddenStart = -1; + + this.children[i].setTargetsSelected + ( + childHueMin, + childHueMax, + lightness, + hide || this.keyed || this.hideAlone || this.hide && ! collapse, + false + ); + } + + i++; + } + + if ( this.hue && this.magnitude ) + { + this.hue.setTarget(this.hues[currentDataset]); + + if ( this.attributes[magnitudeIndex][lastDataset] == 0 ) + { + this.hue.start = this.hue.end; + } + } + + this.radialPrev = this.radial; + + if ( this == selectedNode ) + { + this.resetLabelWidth(); + this.labelWidth.setTarget(this.nameWidth * labelWidthFudge); + this.alphaWedge.setTarget(0); + this.alphaLabel.setTarget(1); + this.alphaOther.setTarget(1); + this.alphaArc.setTarget(0); + this.alphaLine.setTarget(0); + this.alphaPattern.setTarget(0); + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + this.radial = false; + this.labelRadius.setTarget(0); + } + else + { + var rgb = hslToRgb + ( + hueMin, + saturation, + lightness + ); + + this.r.setTarget(rgb.r); + this.g.setTarget(rgb.g); + this.b.setTarget(rgb.b); + this.alphaOther.setTarget(0); + + this.alphaWedge.setTarget(1); + + if ( this.hide || this.hideAlone ) + { + this.alphaPattern.setTarget(1); + } + else + { + this.alphaPattern.setTarget(0); + } + + // set radial + // + if ( ! ( hide || this.hide ) )//&& ! this.keyed ) + { + if ( this.hideAlone ) + { + this.radial = true; + } + else if ( false && canDisplayChildLabels ) + { + this.radial = false; + } + else + { + this.radial = true; + + if ( this.hasChildren() && depth < maxDisplayDepth ) + { + var lastChild = this.children[this.children.length - 1]; + + if + ( + lastChild.angleEnd.end == this.angleEnd.end || + ( + (this.angleStart.end + this.angleEnd.end) / 2 - + lastChild.angleEnd.end + ) * (this.radiusInner.end + 1) * gRadius * 2 < + minWidth() + ) + { + this.radial = false; + } + } + } + } + + // set alphaLabel + // + if + ( + collapse || + hide || + this.hide || + this.keyed || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLabel.setTarget(0); + } + else + { + if + ( + (this.radial || nLabelOffsets[depth - 2]) + ) + { + this.alphaLabel.setTarget(1); + } + else + { + this.alphaLabel.setTarget(0); + + if ( this.radialPrev ) + { + this.alphaLabel.start = 0; + } + } + } + + // set alphaArc + // + if + ( + collapse || + hide || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaArc.setTarget(0); + } + else + { + this.alphaArc.setTarget(1); + } + + // set alphaLine + // + if + ( + hide || + this.hide && nextSiblingHidden || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLine.setTarget(0); + } + else + { + this.alphaLine.setTarget(1); + } + + //if ( ! this.radial ) + { + this.resetLabelWidth(); + } + + // set labelRadius target + // + if ( collapse ) + { + this.labelRadius.setTarget(this.radiusInner.end); + } + else + { + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.labelRadius.setTarget(1); + } + else + { + this.setTargetLabelRadius(); + } + } + } + } + + this.setTargetWedge = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + // set angles + // + var baseMagnitudeRelative = this.baseMagnitude - selectedNode.baseMagnitude; + // + this.angleStart.setTarget(baseMagnitudeRelative * angleFactor); + this.angleEnd.setTarget((baseMagnitudeRelative + this.magnitude) * angleFactor); + + // set radiusInner + // + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.radiusInner.setTarget(1); + } + else + { + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depth - 2]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depth - 1)); + } + } + + if ( this.hide != undefined ) + { + this.hidePrev = this.hide; + } + + if ( this.hideAlone != undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + // set hide + // + if + ( + (this.angleEnd.end - this.angleStart.end) * + (this.radiusInner.end * gRadius + gRadius) < + minWidth() + ) + { + if ( depth == 2 && ! this.getCollapse() && this.depth <= maxAbsoluteDepth ) + { + this.keyed = true; + keys++; + this.hide = false; + + var percentage = this.getPercentage(); + this.keyLabel = this.name + ' ' + percentage + '%'; + var dim = context.measureText(this.keyLabel); + this.keyNameWidth = dim.width; + } + else + { + this.keyed = false; + this.hide = depth > 2; + } + } + else + { + this.keyed = false; + this.hide = false; + } + } + + this.shortenLabel = function() + { + var label = this.name; + + var labelWidth = this.nameWidth; + var maxWidth = this.labelWidth.current(); + var minEndLength = 0; + + if ( labelWidth > maxWidth && label.length > minEndLength * 2 ) + { + var endLength = + Math.floor((label.length - 1) * maxWidth / labelWidth / 2); + + if ( endLength < minEndLength ) + { + endLength = minEndLength; + } + + return ( + label.substring(0, endLength) + + '...' + + label.substring(label.length - endLength)); + } + else + { + return label; + } + } + +/* this.shouldAddSearchResultsString = function() + { + if ( this.isSearchResult ) + { + return this.searchResults > 1; + } + else + { + return this.searchResults > 0; + } + } +*/ + this.sort = function() + { + this.children.sort(function(a, b){return b.getMagnitude() - a.getMagnitude()}); + + for (var i = 0; i < this.children.length; i++) + { + this.children[i].sort(); + } + } +} + +var options; + +function addOptionElement(position, innerHTML, title) +{ + var div = document.createElement("div"); +// div.style.position = 'absolute'; +// div.style.top = position + 'px'; + div.innerHTML = innerHTML; +// div.style.display = 'block'; + div.style.padding = '2px'; + + if ( title ) + { + div.title = title; + } + + options.appendChild(div); + var height = 0;//div.clientHeight; + return position + height; +} + +function addOptionElements(hueName, hueDefault) +{ + options = document.createElement('div'); + options.style.position = 'absolute'; + options.style.top = '0px'; + options.addEventListener('mousedown', function(e) {mouseClick(e)}, false); +// options.onmouseup = function(e) {mouseUp(e)} + document.body.appendChild(options); + + document.body.style.font = '11px sans-serif'; + var position = 5; + + details = document.createElement('div'); + details.style.position = 'absolute'; + details.style.top = '1%'; + details.style.right = '2%'; + details.style.textAlign = 'right'; + document.body.insertBefore(details, canvas); +// <div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"> + + details.innerHTML = '\ +<span id="detailsName" style="font-weight:bold"></span> \ +<input type="button" id="detailsExpand" onclick="expand(focusNode);"\ +value="↔" title="Expand this wedge to become the new focus of the chart"/><br/>\ +<div id="detailsInfo" style="float:right"></div>'; + + keyControl = document.createElement('input'); + keyControl.type = 'button'; + keyControl.value = showKeys ? 'x' : '…'; + keyControl.style.position = ''; + keyControl.style.position = 'fixed'; + keyControl.style.visibility = 'hidden'; + + document.body.insertBefore(keyControl, canvas); + + var logoElement = document.getElementById('logo'); + + if ( logoElement ) + { + logoImage = logoElement.src; + } + else + { + logoImage = 'http://marbl.github.io/Krona/img/logo-med.png'; + } + +// document.getElementById('options').style.fontSize = '9pt'; + position = addOptionElement + ( + position, +'<a style="margin:2px" target="_blank" href="https://github.com/marbl/Krona/wiki"><img style="vertical-align:middle;width:108px;height:30px;" src="' + logoImage + '" alt="Logo of Krona"/></a><input type="button" id="back" value="←" title="Go back (Shortcut: ←)"/>\ +<input type="button" id="forward" value="→" title="Go forward (Shortcut: →)"/> \ + Search: <input type="text" id="search"/>\ +<input id="searchClear" type="button" value="x" onclick="clearSearch()"/> \ +<span id="searchResults"></span>' + ); + + if ( datasets > 1 ) + { + var size = datasets < datasetSelectSize ? datasets : datasetSelectSize; + + var select = + '<table style="border-collapse:collapse;padding:0px"><tr><td style="padding:0px">' + + '<select id="datasets" style="min-width:100px" size="' + size + '" onchange="onDatasetChange()">'; + + for ( var i = 0; i < datasetNames.length; i++ ) + { + select += '<option>' + datasetNames[i] + '</option>'; + } + + select += + '</select></td><td style="vertical-align:top;padding:1px;">' + + '<input style="display:block" title="Previous dataset (Shortcut: ↑)" id="prevDataset" type="button" value="↑" onclick="prevDataset()" disabled="true"/>' + + '<input title="Next dataset (Shortcut: ↓)" id="nextDataset" type="button" value="↓" onclick="nextDataset()"/><br/></td>' + + '<td style="padding-top:1px;vertical-align:top"><input title="Switch to the last dataset that was viewed (Shortcut: TAB)" id="lastDataset" type="button" style="font:11px Times new roman" value="last" onclick="selectLastDataset()"/></td></tr></table>'; + + position = addOptionElement(position + 5, select); + + datasetDropDown = document.getElementById('datasets'); + datasetButtonLast = document.getElementById('lastDataset'); + datasetButtonPrev = document.getElementById('prevDataset'); + datasetButtonNext = document.getElementById('nextDataset'); + + position += datasetDropDown.clientHeight; + } + + position = addOptionElement + ( + position + 5, +'<input type="button" id="maxAbsoluteDepthDecrease" value="-"/>\ +<span id="maxAbsoluteDepth"></span>\ + <input type="button" id="maxAbsoluteDepthIncrease" value="+"/> Max depth', +'Maximum depth to display, counted from the top level \ +and including collapsed wedges.' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="fontSizeDecrease" value="-"/>\ +<span id="fontSize"></span>\ + <input type="button" id="fontSizeIncrease" value="+"/> Font size' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="radiusDecrease" value="-"/>\ +<input type="button" id="radiusIncrease" value="+"/> Chart size' + ); + + if ( hueName ) + { + hueDisplayName = attributes[attributeIndex(hueName)].displayName; + + position = addOptionElement + ( + position + 5, + '<input type="checkbox" id="useHue" style="float:left" ' + + '/><div>Color by<br/>' + hueDisplayName + + '</div>' + ); + + useHueCheckBox = document.getElementById('useHue'); + useHueCheckBox.checked = hueDefault; + useHueCheckBox.onclick = handleResize; + useHueCheckBox.onmousedown = suppressEvent; + } + /* + position = addOptionElement + ( + position + 5, + ' <input type="checkbox" id="shorten" checked="checked" />Shorten labels</div>', + 'Prevent labels from overlapping by shortening them' + ); + + position = addOptionElement + ( + position, + ' <input type="checkbox" id="compress" checked="checked" />Compress', + 'Compress wedges if needed to show the entire depth' + ); + */ + position = addOptionElement + ( + position, + '<input type="checkbox" id="collapse" checked="checked" />Collapse', + 'Collapse wedges that are redundant (entirely composed of another wedge)' + ); + + position = addOptionElement + ( + position + 5, + '<input type="button" id="snapshot" value="Snapshot"/>', +'Render the current view as SVG (Scalable Vector Graphics), a publication-\ +quality format that can be printed and saved (see Help for browser compatibility)' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="linkButton" value="Link"/>\ +<input type="text" size="30" id="linkText"/>', +'Show a link to this view that can be copied for bookmarking or sharing' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="help" value="?"\ +onclick="window.open(\'https://github.com/marbl/Krona/wiki/Browsing%20Krona%20charts\', \'help\')"/>', +'Help' + ); +} + +function arrow(angleStart, angleEnd, radiusInner) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + var angleCenter = (angleStart + angleEnd) / 2; + var radiusArrowInner = radiusInner - gRadius / 10;//nodeRadius * gRadius; + var radiusArrowOuter = gRadius * 1.1;//(1 + nodeRadius); + var radiusArrowCenter = (radiusArrowInner + radiusArrowOuter) / 2; + var pointLength = (radiusArrowOuter - radiusArrowInner) / 5; + + context.fillStyle = highlightFill; + context.lineWidth = highlightLineWidth; + + // First, mask out the first half of the arrow. This will prevent the tips + // from superimposing if the arrow goes most of the way around the circle. + // Masking is done by setting the clipping region to the inverse of the + // half-arrow, which is defined by cutting the half-arrow out of a large + // rectangle + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter, true); + context.closePath(); + context.moveTo(-imageWidth, -imageHeight); + context.lineTo(imageWidth, -imageHeight); + context.lineTo(imageWidth, imageHeight); + context.lineTo(-imageWidth, imageHeight); + context.closePath(); + context.save(); + context.clip(); + + // Next, draw the other half-arrow with the first half masked out + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleStart, true); + context.lineTo + ( + radiusArrowInner * Math.cos(angleStart), + radiusArrowInner * Math.sin(angleStart) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleStart) + pointLength * Math.sin(angleStart), + radiusArrowCenter * Math.sin(angleStart) - pointLength * Math.cos(angleStart) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleStart), + radiusArrowOuter * Math.sin(angleStart) + ); + context.arc(0, 0, gRadius, angleStart, angleCenter, false); + context.fill(); + context.stroke(); + + // Finally, remove the clipping region and draw the first half-arrow. This + // half is extended slightly to fill the seam. + // + context.restore(); + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter - 2 / (2 * Math.PI * radiusInner), angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter - 2 / (2 * Math.PI * gRadius), true); + context.fill(); + context.stroke(); +} + +function attributeIndex(aname) +{ + for ( var i = 0 ; i < attributes.length; i++ ) + { + if ( aname == attributes[i].name ) + { + return i; + } + } + + return null; +} + +function checkHighlight() +{ + var lastHighlightedNode = highlightedNode; + var lastHighlightingHidden = highlightingHidden; + + highlightedNode = selectedNode; + resetKeyOffset(); + + if ( progress == 1 ) + { + selectedNode.checkHighlight(); + if ( selectedNode.getParent() ) + { + selectedNode.getParent().checkHighlightCenter(); + } + + focusNode.checkHighlightMap(); + } + + if ( highlightedNode != selectedNode ) + { + if ( highlightedNode == focusNode ) + { +// canvas.style.display='none'; +// window.resizeBy(1,0); +// canvas.style.cursor='ew-resize'; +// window.resizeBy(-1,0); +// canvas.style.display='inline'; + } + else + { +// canvas.style.cursor='pointer'; + } + } + else + { +// canvas.style.cursor='auto'; + } + + if + ( + ( + true || + highlightedNode != lastHighlightedNode || + highlightingHidden != highlightingHiddenLast + ) && + progress == 1 + ) + { + draw(); // TODO: handle in update() + } +} + +function checkSelectedCollapse() +{ + var newNode = selectedNode; + + while ( newNode.getCollapse() ) + { + newNode = newNode.children[0]; + } + + if ( newNode.children.length == 0 && newNode.getParent() ) + { + newNode = newNode.getParent(); + } + + if ( newNode != selectedNode ) + { + selectNode(newNode); + } +} + +function clearSearch() +{ + if ( search.value != '' ) + { + search.value = ''; + onSearchChange(); + } +} + +function createSVG() +{ + svgNS = "http://www.w3.org/2000/svg"; + var SVG = {}; + SVG.xlinkns = "http://www.w3.org/1999/xlink"; + + var newSVG = document.createElementNS(svgNS, "svg:svg"); + + newSVG.setAttribute("id", "canvas"); + // How big is the canvas in pixels + newSVG.setAttribute("width", '100%'); + newSVG.setAttribute("height", '100%'); + // Set the coordinates used by drawings in the canvas +// newSVG.setAttribute("viewBox", "0 0 " + imageWidth + " " + imageHeight); + // Define the XLink namespace that SVG uses + newSVG.setAttributeNS + ( + "http://www.w3.org/2000/xmlns/", + "xmlns:xlink", + SVG.xlinkns + ); + + return newSVG; +} + +function degrees(radians) +{ + return radians * 180 / Math.PI; +} + +function draw() +{ + tweenFrames++; + //resize(); +// context.fillRect(0, 0, imageWidth, imageHeight); + context.clearRect(0, 0, imageWidth, imageHeight); + + context.font = fontNormal; + context.textBaseline = 'middle'; + + //context.strokeStyle = 'rgba(0, 0, 0, 0.3)'; + context.translate(centerX, centerY); + + resetKeyOffset(); + + head.draw(false, false); // draw pie slices + head.draw(true, false); // draw labels + + var pathRoot = selectedNode; + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + pathRoot = focusNode; + } + + if + ( + highlightedNode && + highlightedNode.getDepth() >= selectedNode.getDepth() && + highlightedNode != focusNode + ) + { + if + ( + progress == 1 && + highlightedNode != selectedNode && + ( + highlightedNode != focusNode || + focusNode.children.length > 0 + ) + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlight(true); + } + + //pathRoot = highlightedNode; + } + else if + ( + progress == 1 && + highlightedNode.getDepth() < selectedNode.getDepth() + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlightCenter(); + } + + if ( quickLook && false) // TEMP + { + context.globalAlpha = 1 - progress / 2; + selectedNode.drawHighlight(true); + } + else if ( progress < 1 )//&& zoomOut() ) + { + if ( !zoomOut)//() ) + { + context.globalAlpha = selectedNode.alphaLine.current(); + selectedNode.drawHighlight(true); + } + else if ( selectedNodeLast ) + { + context.globalAlpha = 1 - 4 * Math.pow(progress - .5, 2); + selectedNodeLast.drawHighlight(false); + } + } + + drawDatasetName(); + + //drawHistory(); + + context.translate(-centerX, -centerY); + context.globalAlpha = 1; + + mapRadius = + (imageHeight / 2 - details.clientHeight - details.offsetTop) / + (pathRoot.getDepth() - 1) * 3 / 4 / 2; + + if ( mapRadius > maxMapRadius ) + { + mapRadius = maxMapRadius; + } + + mapBuffer = mapRadius / 2; + + //context.font = fontNormal; + pathRoot.drawMap(pathRoot); + + if ( hueDisplayName && useHue() ) + { + drawLegend(); + } +} + +function drawBubble(angle, radius, width, radial, flip) +{ + var height = fontSize * 2; + var x; + var y; + + width = width + fontSize; + + if ( radial ) + { + y = -fontSize; + + if ( flip ) + { + x = radius - width + fontSize / 2; + } + else + { + x = radius - fontSize / 2; + } + } + else + { + x = -width / 2; + y = -radius - fontSize; + } + + if ( snapshotMode ) + { + drawBubbleSVG(x + centerX, y + centerY, width, height, fontSize, angle); + } + else + { + drawBubbleCanvas(x, y, width, height, fontSize, angle); + } +} + +function drawBubbleCanvas(x, y, width, height, radius, rotation) +{ + context.strokeStyle = 'black'; + context.lineWidth = highlightLineWidth; + context.fillStyle = 'rgba(255, 255, 255, .75)'; + context.rotate(rotation); + roundedRectangle(x, y, width, fontSize * 2, fontSize); + context.fill(); + context.stroke(); + context.rotate(-rotation); +} + +function drawBubbleSVG(x, y, width, height, radius, rotation) +{ + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" fill="rgba(255, 255, 255, .75)' + + '" class="highlight" ' + + 'transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; +} + +function drawDatasetName() +{ + var alpha = datasetAlpha.current(); + + if ( alpha > 0 ) + { + var radius = gRadius * compressedRadii[0] / -2; + + if ( alpha > 1 ) + { + alpha = 1; + } + + context.globalAlpha = alpha; + + drawBubble(0, -radius, datasetWidths[currentDataset], false, false); + drawText(datasetNames[currentDataset], 0, radius, 0, 'center', true); + } +} + +function drawHistory() +{ + var alpha = 1; + context.textAlign = 'center'; + + for ( var i = 0; i < nodeHistoryPosition && alpha > 0; i++ ) + { + + context.globalAlpha = alpha - historyAlphaDelta * tweenFactor; + context.fillText + ( + nodeHistory[nodeHistoryPosition - i - 1].name, + 0, + (i + tweenFactor) * historySpacingFactor * fontSize - 1 + ); + + if ( alpha > 0 ) + { + alpha -= historyAlphaDelta; + } + } + + context.globalAlpha = 1; +} + +function drawLegend() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + context.fillStyle = 'black'; + context.textAlign = 'start'; + context.font = fontNormal; +// context.fillText(valueStartText, textLeft, top + height); +// context.fillText(valueEndText, textLeft, top); + context.fillText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var gradient = context.createLinearGradient(0, top + height, 0, top); + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + gradient.addColorStop(hueStopPositions[i], hueStopHsl[i]); + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + context.fillText(hueStopText[i], textLeft, textY); + } + } + + context.fillStyle = gradient; + context.fillRect(left, top, width, height); + context.lineWidth = thinLineWidth; + context.strokeRect(left, top, width, height); +} + +function drawLegendSVG() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + var text = ''; + + text += svgText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var svgtest = '<linearGradient id="gradient" x1="0%" y1="100%" x2="0%" y2="0%">'; + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + svgtest += + '<stop offset="' + round(hueStopPositions[i] * 100) + + '%" style="stop-color:' + hueStopHsl[i] + '"/>'; + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + text += svgText(hueStopText[i], textLeft, textY); + } + } + + svgtest += '</linearGradient>'; + //alert(svgtest); + svg += svgtest; + svg += + '<rect style="fill:url(#gradient)" x="' + left + '" y="' + top + + '" width="' + width + '" height="' + height + '"/>'; + + svg += text; +} + +function drawSearchHighlights(label, bubbleX, bubbleY, rotation, center) +{ + var index = -1; + var labelLength = label.length; + + bubbleX -= fontSize / 4; + + do + { + index = label.toLowerCase().indexOf(search.value.toLowerCase(), index + 1); + + if ( index != -1 && index < labelLength ) + { + var dim = context.measureText(label.substr(0, index)); + var x = bubbleX + dim.width; + + dim = context.measureText(label.substr(index, search.value.length)); + + var y = bubbleY - fontSize * 3 / 4; + var width = dim.width + fontSize / 2; + var height = fontSize * 3 / 2; + var radius = fontSize / 2; + + if ( snapshotMode ) + { + if ( center ) + { + x += centerX; + y += centerY; + } + + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" class="searchHighlight' + + '" transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.fillStyle = 'rgb(255, 255, 100)'; + context.rotate(rotation); + roundedRectangle(x, y, width, height, radius); + context.fill(); + context.rotate(-rotation); + } + } + } + while ( index != -1 && index < labelLength ); +} + +function drawText(text, x, y, angle, anchor, bold, color) +{ + if ( color == undefined ) + { + color = 'black'; + } + + if ( snapshotMode ) + { + svg += + '<text x="' + (centerX + x) + '" y="' + (centerY + y) + + '" text-anchor="' + anchor + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" transform="rotate(' + degrees(angle) + ',' + centerX + ',' + centerY + ')">' + + text + '</text>'; + } + else + { + context.fillStyle = color; + context.textAlign = anchor; + context.font = bold ? fontBold : fontNormal; + context.rotate(angle); + context.fillText(text, x, y); + context.rotate(-angle); + } +} + +function drawTextPolar +( + text, + innerText, + angle, + radius, + radial, + bubble, + bold, + searchResult, + searchResults +) +{ + var anchor; + var textX; + var textY; + var spacer; + var totalText = text; + var flip; + + if ( snapshotMode ) + { + spacer = '   '; + } + else + { + spacer = ' '; + } + + if ( radial ) + { + flip = angle < 3 * Math.PI / 2; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + anchor = 'end'; + + if ( innerText ) + { + totalText = text + spacer + innerText; + } + } + else + { + anchor = 'start'; + + if ( innerText ) + { + totalText = innerText + spacer + text; + } + } + + textX = radius; + textY = 0; + } + else + { + flip = angle < Math.PI || angle > 2 * Math.PI; + var label; + + anchor = snapshotMode ? 'middle' : 'center'; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + } + + angle += Math.PI / 2; + textX = 0; + textY = -radius; + } + + if ( bubble ) + { + var textActual = totalText; + + if ( innerText && snapshotMode ) + { + if ( flip ) + { + textActual = text + ' ' + innerText; + } + else + { + textActual = innerText + ' ' + text; + } + } + + if ( searchResults ) + { + textActual = textActual + searchResultString(searchResults); + } + + var textWidth = measureText(textActual, bold); + + var x = textX; + + if ( anchor == 'end' ) + { + x -= textWidth; + } + else if ( anchor != 'start' ) + { + // centered + x -= textWidth / 2; + } + + drawBubble(angle, radius, textWidth, radial, flip); + + if ( searchResult ) + { + drawSearchHighlights + ( + textActual, + x, + textY, + angle, + true + ) + } + } + + if ( searchResults ) + { + totalText = totalText + searchResultString(searchResults); + } + + drawText(totalText, textX, textY, angle, anchor, bold); + + return flip; +} + +function drawTick(start, length, angle) +{ + if ( snapshotMode ) + { + svg += + '<line x1="' + (centerX + start) + + '" y1="' + centerY + + '" x2="' + (centerX + start + length) + + '" y2="' + centerY + + '" class="tick" transform="rotate(' + + degrees(angle) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.rotate(angle); + context.beginPath(); + context.moveTo(start, 0); + context.lineTo(start + length, 0); + context.lineWidth = thinLineWidth * 2; + context.stroke(); + context.rotate(-angle); + } +} + +function drawWedge +( + angleStart, + angleEnd, + radiusInner, + radiusOuter, + color, + patternAlpha, + highlight +) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + if ( snapshotMode ) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + var dArray = + [ + " M ", x1, ",", y1, + " L ", x2, ",", y2, + " A ", gRadius, ",", gRadius, " 0 ", longArc, ",1 ", x3, ",", y3, + " L ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, " 0 ", x1, ",", y1, + " Z " + ]; + + svg += + '<path class="'+ (highlight ? 'highlight' : 'wedge') + '" fill="' + color + + '" d="' + dArray.join('') + '"/>'; + + if ( patternAlpha > 0 ) + { + svg += + '<path class="wedge" fill="url(#hiddenPattern)" d="' + + dArray.join('') + '"/>'; + } + } + else + { + // fudge to prevent seams during animation + // + angleEnd += 1 / gRadius; + + context.fillStyle = color; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.arc(0, 0, radiusOuter, angleEnd, angleStart, true); + context.closePath(); + context.fill(); + + if ( patternAlpha > 0 ) + { + context.save(); + context.clip(); + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + context.fill(); + context.restore(); + } + + if ( highlight ) + { + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.strokeStyle = 'black'; + context.stroke(); + } + } +} + +function expand(node) +{ + selectNode(node); + updateView(); +} + +function focusLost() +{ + mouseX = -1; + mouseY = -1; + checkHighlight(); + document.body.style.cursor = 'auto'; +} + +function fontSizeDecrease() +{ + if ( fontSize > 1 ) + { + fontSize--; + updateViewNeeded = true; + } +} + +function fontSizeIncrease() +{ + fontSize++; + updateViewNeeded = true; +} + +function getGetString(name, value, bool) +{ + return name + '=' + (bool ? value ? 'true' : 'false' : value); +} + +function hideLink() +{ + hide(linkText); + show(linkButton); +} + +function show(object) +{ + object.style.display = 'inline'; +} + +function hide(object) +{ + object.style.display = 'none'; +} + +function showLink() +{ + var urlHalves = String(document.location).split('?'); + var newGetVariables = new Array(); + + newGetVariables.push + ( + getGetString('dataset', currentDataset, false), + getGetString('node', selectedNode.id, false), + getGetString('collapse', collapse, true), + getGetString('color', useHue(), true), + getGetString('depth', maxAbsoluteDepth - 1, false), + getGetString('font', fontSize, false), + getGetString('key', showKeys, true) + ); + + hide(linkButton); + show(linkText); + linkText.value = urlHalves[0] + '?' + getVariables.concat(newGetVariables).join('&'); + //linkText.disabled = false; + linkText.focus(); + linkText.select(); + //linkText.disabled = true; +// document.location = urlHalves[0] + '?' + getVariables.join('&'); +} + +function getFirstChild(element) +{ + element = element.firstChild; + + if ( element && element.nodeType != 1 ) + { + element = getNextSibling(element); + } + + return element; +} + +function getNextSibling(element) +{ + do + { + element = element.nextSibling; + } + while ( element && element.nodeType != 1 ); + + return element; +} + +function getPercentage(fraction) +{ + return round(fraction * 100); +} + +function hslText(hue) +{ + if ( 1 || snapshotMode ) + { + // Safari doesn't seem to allow hsl() in SVG + + var rgb = hslToRgb(hue, saturation, (lightnessBase + lightnessMax) / 2); + + return rgbText(rgb.r, rgb.g, rgb.b); + } + else + { + var hslArray = + [ + 'hsl(', + Math.floor(hue * 360), + ',', + Math.floor(saturation * 100), + '%,', + Math.floor((lightnessBase + lightnessMax) * 50), + '%)' + ]; + + return hslArray.join(''); + } +} + +function hslToRgb(h, s, l) +{ + var m1, m2; + var r, g, b; + + if (s == 0) + { + r = g = b = Math.floor((l * 255)); + } + else + { + if (l <= 0.5) + { + m2 = l * (s + 1); + } + else + { + m2 = l + s - l * s; + } + + m1 = l * 2 - m2; + + r = Math.floor(hueToRgb(m1, m2, h + 1 / 3)); + g = Math.floor(hueToRgb(m1, m2, h)); + b = Math.floor(hueToRgb(m1, m2, h - 1/3)); + } + + return {r: r, g: g, b: b}; +} + +function hueToRgb(m1, m2, hue) +{ + var v; + + while (hue < 0) + { + hue += 1; + } + + while (hue > 1) + { + hue -= 1; + } + + if (6 * hue < 1) + v = m1 + (m2 - m1) * hue * 6; + else if (2 * hue < 1) + v = m2; + else if (3 * hue < 2) + v = m1 + (m2 - m1) * (2/3 - hue) * 6; + else + v = m1; + + return 255 * v; +} + +function interpolateHue(hueStart, hueEnd, valueStart, valueEnd) +{ + // since the gradient will be RGB based, we need to add stops to hit all the + // colors in the hue spectrum + + hueStopPositions = new Array(); + hueStopHsl = new Array(); + hueStopText = new Array(); + + hueStopPositions.push(0); + hueStopHsl.push(hslText(hueStart)); + hueStopText.push(round(valueStart)); + + for + ( + var i = (hueStart > hueEnd ? 5 / 6 : 1 / 6); + (hueStart > hueEnd ? i > 0 : i < 1); + i += (hueStart > hueEnd ? -1 : 1) / 6 + ) + { + if + ( + hueStart > hueEnd ? + i > hueEnd && i < hueStart : + i > hueStart && i < hueEnd + ) + { + hueStopPositions.push(lerp(i, hueStart, hueEnd, 0, 1)); + hueStopHsl.push(hslText(i)); + hueStopText.push(round(lerp + ( + i, + hueStart, + hueEnd, + valueStart, + valueEnd + ))); + } + } + + hueStopPositions.push(1); + hueStopHsl.push(hslText(hueEnd)); + hueStopText.push(round(valueEnd)); +} + +function keyLineAngle(angle, keyAngle, bendRadius, keyX, keyY, pointsX, pointsY) +{ + if ( angle < Math.PI / 2 && keyY < bendRadius * Math.sin(angle) + || angle > Math.PI / 2 && keyY < bendRadius) + { + return Math.asin(keyY / bendRadius); + } + else + { + // find the angle of the normal to a tangent line that goes to + // the label + + var textDist = Math.sqrt + ( + Math.pow(keyX, 2) + + Math.pow(keyY, 2) + ); + + var tanAngle = Math.acos(bendRadius / textDist) + keyAngle; + + if ( angle < tanAngle || angle < Math.PI / 2 )//|| labelLeft < centerX ) + { + // angle doesn't reach far enough for tangent; collapse and + // connect directly to label + + if ( keyY / Math.tan(angle) > 0 ) + { + pointsX.push(keyY / Math.tan(angle)); + pointsY.push(keyY); + } + else + { + pointsX.push(bendRadius * Math.cos(angle)); + pointsY.push(bendRadius * Math.sin(angle)); + } + + return angle; + } + else + { + return tanAngle; + } + } +} + +function keyOffset() +{ + return imageHeight - (keys - currentKey + 1) * (keySize + keyBuffer) + keyBuffer - margin; +} + +function lerp(value, fromStart, fromEnd, toStart, toEnd) +{ + return (value - fromStart) * + (toEnd - toStart) / + (fromEnd - fromStart) + + toStart; +} + +function createCanvas() +{ + canvas = document.createElement('canvas'); + document.body.appendChild(canvas); + context = canvas.getContext('2d'); +} + +function load() +{ + document.body.style.overflow = "hidden"; + document.body.style.margin = 0; + + createCanvas(); + + if ( context == undefined ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + if ( typeof context.fillText != 'function' ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 canvas text (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + resize(); + + var kronaElement = document.getElementsByTagName('krona')[0]; + + var magnitudeName; + var hueName; + var hueDefault; + var hueStart; + var hueEnd; + var valueStart; + var valueEnd; + + if ( kronaElement.getAttribute('collapse') != undefined ) + { + collapse = kronaElement.getAttribute('collapse') == 'true'; + } + + if ( kronaElement.getAttribute('key') != undefined ) + { + showKeys = kronaElement.getAttribute('key') == 'true'; + } + + for + ( + var element = getFirstChild(kronaElement); + element; + element = getNextSibling(element) + ) + { + switch ( element.tagName.toLowerCase() ) + { + case 'attributes': + magnitudeName = element.getAttribute('magnitude'); + // + for + ( + var attributeElement = getFirstChild(element); + attributeElement; + attributeElement = getNextSibling(attributeElement) + ) + { + var tag = attributeElement.tagName.toLowerCase(); + + if ( tag == 'attribute' ) + { + var attribute = new Attribute(); + attribute.name = attributeElement.firstChild.nodeValue.toLowerCase(); + attribute.displayName = attributeElement.getAttribute('display'); + + if ( attributeElement.getAttribute('hrefBase') ) + { + attribute.hrefBase = attributeElement.getAttribute('hrefBase'); + } + + if ( attributeElement.getAttribute('target') ) + { + attribute.target = attributeElement.getAttribute('target'); + } + + if ( attribute.name == magnitudeName ) + { + magnitudeIndex = attributes.length; + } + + if ( attributeElement.getAttribute('listAll') ) + { + attribute.listAll = attributeElement.getAttribute('listAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('listNode') ) + { + attribute.listNode = attributeElement.getAttribute('listNode').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataAll') ) + { + attribute.dataAll = attributeElement.getAttribute('dataAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataNode') ) + { + attribute.dataNode = attributeElement.getAttribute('dataNode').toLowerCase(); + } + + if ( attributeElement.getAttribute('postUrl') ) + { + attribute.postUrl = attributeElement.getAttribute('postUrl'); + } + + if ( attributeElement.getAttribute('postVar') ) + { + attribute.postVar = attributeElement.getAttribute('postVar'); + } + + if ( attributeElement.getAttribute('mono') ) + { + attribute.mono = true; + } + + attributes.push(attribute); + } + else if ( tag == 'list' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.list = true; + attributes.push(attribute); + } + else if ( tag == 'data' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.data = true; + attributes.push(attribute); + + var enableScript = document.createElement('script'); + var date = new Date(); + enableScript.src = + attributeElement.getAttribute('enable') + '?' + + date.getTime(); + document.body.appendChild(enableScript); + } + } + break; + + case 'color': + hueName = element.getAttribute('attribute'); + hueStart = Number(element.getAttribute('hueStart')) / 360; + hueEnd = Number(element.getAttribute('hueEnd')) / 360; + valueStart = Number(element.getAttribute('valueStart')); + valueEnd = Number(element.getAttribute('valueEnd')); + // + interpolateHue(hueStart, hueEnd, valueStart, valueEnd); + // + if ( element.getAttribute('default') == 'true' ) + { + hueDefault = true; + } + break; + + case 'datasets': + datasetNames = new Array(); + // + for ( j = getFirstChild(element); j; j = getNextSibling(j) ) + { + datasetNames.push(j.firstChild.nodeValue); + } + datasets = datasetNames.length; + break; + + case 'node': + head = loadTreeDOM + ( + element, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + break; + } + } + + // get GET options + // + var urlHalves = String(document.location).split('?'); + var datasetDefault = 0; + var maxDepthDefault; + var nodeDefault = 0; + // + if ( urlHalves[1] ) + { + var vars = urlHalves[1].split('&'); + + for ( i = 0; i < vars.length; i++ ) + { + var pair = vars[i].split('='); + + switch ( pair[0] ) + { + case 'collapse': + collapse = pair[1] == 'true'; + break; + + case 'color': + hueDefault = pair[1] == 'true'; + break; + + case 'dataset': + datasetDefault = Number(pair[1]); + break; + + case 'depth': + maxDepthDefault = Number(pair[1]) + 1; + break; + + case 'key': + showKeys = pair[1] == 'true'; + break; + + case 'font': + fontSize = Number(pair[1]); + break; + + case 'node': + nodeDefault = Number(pair[1]); + break; + + default: + getVariables.push(pair[0] + '=' + pair[1]); + break; + } + } + } + + addOptionElements(hueName, hueDefault); + setCallBacks(); + + head.sort(); + maxAbsoluteDepth = 0; + selectDataset(datasetDefault); + + if ( maxDepthDefault && maxDepthDefault < head.maxDepth ) + { + maxAbsoluteDepth = maxDepthDefault; + } + else + { + maxAbsoluteDepth = head.maxDepth; + } + + selectNode(nodes[nodeDefault]); + + setInterval(update, 20); + + window.onresize = handleResize; + updateMaxAbsoluteDepth(); + updateViewNeeded = true; +} + +function loadTreeDOM +( + domNode, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd +) +{ + var newNode = new Node(); + + newNode.name = domNode.getAttribute('name'); + + if ( domNode.getAttribute('href') ) + { + newNode.href = domNode.getAttribute('href'); + } + + if ( hueName ) + { + newNode.hues = new Array(); + } + + for ( var i = getFirstChild(domNode); i; i = getNextSibling(i) ) + { + switch ( i.tagName.toLowerCase() ) + { + case 'node': + var newChild = loadTreeDOM + ( + i, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + newChild.parent = newNode; + newNode.children.push(newChild); + break; + + default: + var attributeName = i.tagName.toLowerCase(); + var index = attributeIndex(attributeName); + // + newNode.attributes[index] = new Array(); + // + for ( var j = getFirstChild(i); j; j = getNextSibling(j) ) + { + if ( attributes[index] == undefined ) + { + var x = 5; + } + if ( attributes[index].list ) + { + newNode.attributes[index].push(new Array()); + + for ( var k = getFirstChild(j); k; k = getNextSibling(k) ) + { + newNode.attributes[index][newNode.attributes[index].length - 1].push(k.firstChild.nodeValue); + } + } + else + { + var value = j.firstChild ? j.firstChild.nodeValue : ''; + + if ( j.getAttribute('href') ) + { + var target; + + if ( attributes[index].target ) + { + target = ' target="' + attributes[index].target + '"'; + } + + value = '<a href="' + attributes[index].hrefBase + j.getAttribute('href') + '"' + target + '>' + value + '</a>'; + } + + newNode.attributes[index].push(value); + } + } + // + if ( attributeName == magnitudeName || attributeName == hueName ) + { + for ( j = 0; j < datasets; j++ ) + { + var value = newNode.attributes[index][j] == undefined ? 0 : Number(newNode.attributes[index][j]); + + newNode.attributes[index][j] = value; + + if ( attributeName == hueName ) + { + var hue = lerp + ( + value, + valueStart, + valueEnd, + hueStart, + hueEnd + ); + + if ( hue < hueStart == hueStart < hueEnd ) + { + hue = hueStart; + } + else if ( hue > hueEnd == hueStart < hueEnd ) + { + hue = hueEnd; + } + + newNode.hues[j] = hue; + } + } + + if ( attributeName == hueName ) + { + newNode.hue = new Tween(newNode.hues[0], newNode.hues[0]); + } + } + break; + } + } + + return newNode; +} + +function maxAbsoluteDepthDecrease() +{ + if ( maxAbsoluteDepth > 2 ) + { + maxAbsoluteDepth--; + head.setMaxDepths(); + handleResize(); + } +} + +function maxAbsoluteDepthIncrease() +{ + if ( maxAbsoluteDepth < head.maxDepth ) + { + maxAbsoluteDepth++; + head.setMaxDepths(); + handleResize(); + } +} + +function measureText(text, bold) +{ + context.font = bold ? fontBold : fontNormal; + var dim = context.measureText(text); + return dim.width; +} + +function min(a, b) +{ + return a < b ? a : b; +} + +function minWidth() +{ + // Min wedge width (at center) for displaying a node (or for displaying a + // label if it's at the highest level being viewed, multiplied by 2 to make + // further calculations simpler + + return (fontSize * 2.3); +} + +function mouseMove(e) +{ + mouseX = e.pageX; + mouseY = e.pageY - headerHeight; + mouseXRel = (mouseX - centerX) * backingScale() + mouseYRel = (mouseY - centerY) * backingScale() + + if ( head && ! quickLook ) + { + checkHighlight(); + } +} + +function mouseClick(e) +{ + if ( highlightedNode == focusNode && focusNode != selectedNode || selectedNode.hasParent(highlightedNode) ) + { + if ( highlightedNode.hasChildren() ) + { + expand(highlightedNode); + } + } + else if ( progress == 1 )//( highlightedNode != selectedNode ) + { + setFocus(highlightedNode); +// document.body.style.cursor='ew-resize'; + draw(); + checkHighlight(); + var date = new Date(); + mouseDownTime = date.getTime(); + mouseDown = true; + } +} + +function mouseUp(e) +{ + if ( quickLook ) + { + navigateBack(); + quickLook = false; + } + + mouseDown = false; +} + +function navigateBack() +{ + if ( nodeHistoryPosition > 0 ) + { + nodeHistory[nodeHistoryPosition] = selectedNode; + nodeHistoryPosition--; + + if ( nodeHistory[nodeHistoryPosition].collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + setSelectedNode(nodeHistory[nodeHistoryPosition]); + updateDatasetButtons(); + updateView(); + } +} + +function navigateUp() +{ + if ( selectedNode.getParent() ) + { + selectNode(selectedNode.getParent()); + updateView(); + } +} + +function navigateForward() +{ + if ( nodeHistoryPosition < nodeHistory.length - 1 ) + { + nodeHistoryPosition++; + var newNode = nodeHistory[nodeHistoryPosition]; + + if ( newNode.collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + if ( nodeHistoryPosition == nodeHistory.length - 1 ) + { + // this will ensure the forward button is disabled + + nodeHistory.length = nodeHistoryPosition; + } + + setSelectedNode(newNode); + updateDatasetButtons(); + updateView(); + } +} + +function nextDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == datasets - 1 ) + { + newDataset = 0; + } + else + { + newDataset++; + } + } + while ( datasetDropDown.options[newDataset].disabled ) + + selectDataset(newDataset); +} + +function onDatasetChange() +{ + selectDataset(datasetDropDown.selectedIndex); +} + +function onKeyDown(event) +{ + if + ( + event.keyCode == 37 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateBack(); + event.preventDefault(); + } + else if + ( + event.keyCode == 39 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateForward(); + event.preventDefault(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { + prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { + nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 9 && datasets > 1 ) + { + selectLastDataset(); + event.preventDefault(); + } + else if ( event.keyCode == 83 ) + { + progress += .2; + } + else if ( event.keyCode == 66 ) + { + progress -= .2; + } + else if ( event.keyCode == 70 ) + { + progress = 1; + } +} + +function onKeyPress(event) +{ + if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onKeyUp(event) +{ + if ( event.keyCode == 27 && document.activeElement.id == 'search' ) + { + search.value = ''; + onSearchChange(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onSearchChange() +{ + nSearchResults = 0; + head.search(); + + if ( search.value == '' ) + { + searchResults.innerHTML = ''; + } + else + { + searchResults.innerHTML = nSearchResults + ' results'; + } + + setFocus(selectedNode); + draw(); +} + +function post(url, variable, value, postWindow) +{ + var form = document.createElement('form'); + var input = document.createElement('input'); + var inputDataset = document.createElement('input'); + + form.appendChild(input); + form.appendChild(inputDataset); + + form.method = "POST"; + form.action = url; + + if ( postWindow == undefined ) + { + form.target = '_blank'; + postWindow = window; + } + + input.type = 'hidden'; + input.name = variable; + input.value = value; + + inputDataset.type = 'hidden'; + inputDataset.name = 'dataset'; + inputDataset.value = currentDataset; + + postWindow.document.body.appendChild(form); + form.submit(); +} + +function prevDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == 0 ) + { + newDataset = datasets - 1; + } + else + { + newDataset--; + } + } + while ( datasetDropDown.options[newDataset].disabled ); + + selectDataset(newDataset); +} + +function radiusDecrease() +{ + if ( bufferFactor < .309 ) + { + bufferFactor += .03; + updateViewNeeded = true; + } +} + +function radiusIncrease() +{ + if ( bufferFactor > .041 ) + { + bufferFactor -= .03; + updateViewNeeded = true; + } +} + +function resetKeyOffset() +{ + currentKey = 1; + keyMinTextLeft = centerX + gRadius + buffer - buffer / (keys + 1) / 2 + fontSize / 2; + keyMinAngle = 0; +} + +function rgbText(r, g, b) +{ + var rgbArray = + [ + "rgb(", + Math.floor(r), + ",", + Math.floor(g), + ",", + Math.floor(b), + ")" + ]; + + return rgbArray.join(''); +} + +function round(number) +{ + if ( number >= 1 || number <= -1 ) + { + return number.toFixed(0); + } + else + { + return number.toPrecision(1); + } +} + +function roundedRectangle(x, y, width, height, radius) +{ + if ( radius * 2 > width ) + { + radius = width / 2; + } + + if ( radius * 2 > height ) + { + radius = height / 2; + } + + context.beginPath(); + context.arc(x + radius, y + radius, radius, Math.PI, Math.PI * 3 / 2, false); + context.lineTo(x + width - radius, y); + context.arc(x + width - radius, y + radius, radius, Math.PI * 3 / 2, Math.PI * 2, false); + context.lineTo(x + width, y + height - radius); + context.arc(x + width - radius, y + height - radius, radius, 0, Math.PI / 2, false); + context.lineTo(x + radius, y + height); + context.arc(x + radius, y + height - radius, radius, Math.PI / 2, Math.PI, false); + context.lineTo(x, y + radius); +} + +function passClick(e) +{ + mouseClick(e); +} + +function searchResultString(results) +{ + var searchResults = this.searchResults; + + if ( this.isSearchResult ) + { + // don't count ourselves + searchResults--; + } + + return ' - ' + results + (results > 1 ? ' results' : ' result'); +} + +function setCallBacks() +{ + canvas.onselectstart = function(){return false;} // prevent unwanted highlighting + options.onselectstart = function(){return false;} // prevent unwanted highlighting + document.onmousemove = mouseMove; + window.onblur = focusLost; + window.onmouseout = focusLost; + document.onkeyup = onKeyUp; + document.onkeydown = onKeyDown; + canvas.onmousedown = mouseClick; + document.onmouseup = mouseUp; + keyControl.onclick = toggleKeys; + collapseCheckBox = document.getElementById('collapse'); + collapseCheckBox.checked = collapse; + collapseCheckBox.onclick = handleResize; + collapseCheckBox.onmousedown = suppressEvent; + maxAbsoluteDepthText = document.getElementById('maxAbsoluteDepth'); + maxAbsoluteDepthButtonDecrease = document.getElementById('maxAbsoluteDepthDecrease'); + maxAbsoluteDepthButtonIncrease = document.getElementById('maxAbsoluteDepthIncrease'); + maxAbsoluteDepthButtonDecrease.onclick = maxAbsoluteDepthDecrease; + maxAbsoluteDepthButtonIncrease.onclick = maxAbsoluteDepthIncrease; + maxAbsoluteDepthButtonDecrease.onmousedown = suppressEvent; + maxAbsoluteDepthButtonIncrease.onmousedown = suppressEvent; + fontSizeText = document.getElementById('fontSize'); + fontSizeButtonDecrease = document.getElementById('fontSizeDecrease'); + fontSizeButtonIncrease = document.getElementById('fontSizeIncrease'); + fontSizeButtonDecrease.onclick = fontSizeDecrease; + fontSizeButtonIncrease.onclick = fontSizeIncrease; + fontSizeButtonDecrease.onmousedown = suppressEvent; + fontSizeButtonIncrease.onmousedown = suppressEvent; + radiusButtonDecrease = document.getElementById('radiusDecrease'); + radiusButtonIncrease = document.getElementById('radiusIncrease'); + radiusButtonDecrease.onclick = radiusDecrease; + radiusButtonIncrease.onclick = radiusIncrease; + radiusButtonDecrease.onmousedown = suppressEvent; + radiusButtonIncrease.onmousedown = suppressEvent; + maxAbsoluteDepth = 0; + backButton = document.getElementById('back'); + backButton.onclick = navigateBack; + backButton.onmousedown = suppressEvent; + forwardButton = document.getElementById('forward'); + forwardButton.onclick = navigateForward; + forwardButton.onmousedown = suppressEvent; + snapshotButton = document.getElementById('snapshot'); + snapshotButton.onclick = snapshot; + snapshotButton.onmousedown = suppressEvent; + detailsName = document.getElementById('detailsName'); + detailsExpand = document.getElementById('detailsExpand'); + detailsInfo = document.getElementById('detailsInfo'); + search = document.getElementById('search'); + search.onkeyup = onSearchChange; + search.onmousedown = suppressEvent; + searchResults = document.getElementById('searchResults'); + useHueDiv = document.getElementById('useHueDiv'); + linkButton = document.getElementById('linkButton'); + linkButton.onclick = showLink; + linkButton.onmousedown = suppressEvent; + linkText = document.getElementById('linkText'); + linkText.onblur = hideLink; + linkText.onmousedown = suppressEvent; + hide(linkText); + var helpButton = document.getElementById('help'); + helpButton.onmousedown = suppressEvent; + var searchClear = document.getElementById('searchClear'); + searchClear.onmousedown = suppressEvent; + if ( datasets > 1 ) + { + datasetDropDown.onmousedown = suppressEvent; + var prevDatasetButton = document.getElementById('prevDataset'); + prevDatasetButton.onmousedown = suppressEvent; + var nextDatasetButton = document.getElementById('nextDataset'); + nextDatasetButton.onmousedown = suppressEvent; + var lastDatasetButton = document.getElementById('lastDataset'); + lastDatasetButton.onmousedown = suppressEvent; + } + + image = document.getElementById('hiddenImage'); + image.onload = function() + { + hiddenPattern = context.createPattern(image, 'repeat'); + } + + var loadingImageElement = document.getElementById('loadingImage'); + + if ( loadingImageElement ) + { + loadingImage = loadingImageElement.src; + } +} + +function selectDataset(newDataset) +{ + lastDataset = currentDataset; + currentDataset = newDataset + if ( datasets > 1 ) + { + datasetDropDown.selectedIndex = currentDataset; + updateDatasetButtons(); + datasetAlpha.start = 1.5; + datasetChanged = true; + } + head.setMagnitudes(0); + head.setDepth(1, 1); + head.setMaxDepths(); + handleResize(); +} + +function selectLastDataset() +{ + selectDataset(lastDataset); + handleResize(); +} + +function selectNode(newNode) +{ + if ( selectedNode != newNode ) + { + // truncate history at current location to create a new branch + // + nodeHistory.length = nodeHistoryPosition; + + if ( selectedNode != 0 ) + { + nodeHistory.push(selectedNode); + nodeHistoryPosition++; + } + + setSelectedNode(newNode); + //updateView(); + } + + updateDatasetButtons(); +} + +function setFocus(node) +{ + if ( node == focusNode ) + { +// return; + } + + focusNode = node; + + if ( node.href ) + { + detailsName.innerHTML = + '<a target="_blank" href="' + node.href + '">' + node.name + '</a>'; + } + else + { + detailsName.innerHTML = node.name; + } + + var table = '<table>'; + //TODO: use CSS margins instead of an additional column + table += '<tr><td></td><td></td></tr>'; + + for ( var i = 0; i < node.attributes.length; i++ ) + { + if ( attributes[i].displayName && node.attributes[i] != undefined ) + { + var index = node.attributes[i].length == 1 && attributes[i].mono ? 0 : currentDataset; + + if ( typeof node.attributes[i][currentDataset] == 'number' || node.attributes[i][index] != undefined && node.attributes[i][currentDataset] != '' ) + { + var value = node.attributes[i][index]; + + if ( attributes[i].listNode != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listNode) + ',' + i + + ',false);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].listAll != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listAll) + ',' + i + + ',true);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].dataNode != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataNode) + ',' + i + + ',false);return false;" title="Show data">' + + value + '</a>'; + } + else if ( attributes[i].dataAll != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataAll) + ',' + i + + ',true);return false;" title="Show data">' + + value + '</a>'; + } + + table += + '<tr><td><strong>' + attributes[i].displayName + ':</strong></td><td>' + + value + '</td></tr>'; + } + } + } + + table += '</table>'; + detailsInfo.innerHTML = table; + + detailsExpand.disabled = !focusNode.hasChildren() || focusNode == selectedNode; +} + +function setSelectedNode(newNode) +{ + if ( selectedNode && selectedNode.hasParent(newNode) ) + { + zoomOut = true; + } + else + { + zoomOut = false; + } + + selectedNodeLast = selectedNode; + selectedNode = newNode; + + //if ( focusNode != selectedNode ) + { + setFocus(selectedNode); + } +} + +function waitForData(dataWindow, target, title, time, postUrl, postVar) +{ + if ( nodeData.length == target ) + { + if ( postUrl != undefined ) + { + for ( var i = 0; i < nodeData.length; i++ ) + { + nodeData[i] = nodeData[i].replace(/\n/g, ','); + } + + var postString = nodeData.join(''); + postString = postString.slice(0, -1); + + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + + post(postUrl, postVar, postString, dataWindow); + } + else + { + //dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + //document.body.removeChild(document.getElementById('data')); + + dataWindow.document.open(); + dataWindow.document.write('<pre>' + nodeData.join('') + '</pre>'); + dataWindow.document.close(); + } + + dataWindow.document.title = title; // replace after document.write() + } + else + { + var date = new Date(); + + if ( date.getTime() - time > 10000 ) + { + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + dataWindow.document.body.innerHTML = + 'Timed out loading supplemental files for:<br/>' + document.location; + } + else + { + setTimeout(function() {waitForData(dataWindow, target, title, time, postUrl, postVar);}, 100); + } + } +} + +function data(newData) +{ + nodeData.push(newData); +} + +function enableData() +{ + dataEnabled = true; +} + +function showData(indexData, indexAttribute, summary) +{ + var dataWindow = window.open('', '_blank'); + var title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + dataWindow.document.title = title; + + nodeData = new Array(); + + if ( dataWindow && dataWindow.document && dataWindow.document.body != null ) + { + //var loadImage = document.createElement('img'); + //loadImage.src = "file://localhost/Users/ondovb/Krona/KronaTools/img/loading.gif"; + //loadImage.id = "loading"; + //loadImage.alt = "Loading..."; + //dataWindow.document.body.appendChild(loadImage); + dataWindow.document.body.innerHTML = + '<img id="loading" src="' + loadingImage + '" alt="Loading..."></img>'; + } + + var scripts = document.createElement('div'); + scripts.id = 'data'; + document.body.appendChild(scripts); + + var files = focusNode.getData(indexData, summary); + + var date = new Date(); + var time = date.getTime(); + + for ( var i = 0; i < files.length; i++ ) + { + var script = document.createElement('script'); + script.src = files[i] + '?' + time; + scripts.appendChild(script); + } + + waitForData(dataWindow, files.length, title, time, attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar); + + return false; +} + +function showList(indexList, indexAttribute, summary) +{ + var list = focusNode.getList(indexList, summary); + + if ( attributes[indexAttribute].postUrl != undefined ) + { + post(attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar, list.join(',')); + } + else + { + var dataWindow = window.open('', '_blank'); + + if ( true || navigator.appName == 'Microsoft Internet Explorer' ) // :( + { + dataWindow.document.open(); + dataWindow.document.write('<pre>' + list.join('\n') + '</pre>'); + dataWindow.document.close(); + } + else + { + var pre = document.createElement('pre'); + dataWindow.document.body.appendChild(pre); + pre.innerHTML = list; + } + + dataWindow.document.title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + } +} + +function snapshot() +{ + svg = svgHeader(); + + resetKeyOffset(); + + snapshotMode = true; + + selectedNode.draw(false, true); + selectedNode.draw(true, true); + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + } + + if ( hueDisplayName && useHue() ) + { + drawLegendSVG(); + } + + snapshotMode = false; + + svg += svgFooter(); + + var snapshotWindow = window.open('', '_blank', '', 'replace=false'); + snapshotWindow.document.write('<html><body><a href="data:image/svg+xml,' + encodeURIComponent(svg) + '" download="snapshot.svg">Download Snapshot</a></html></body>'); + snapshotWindow.document.write(svg); +} + +function save() +{ + alert(document.body.innerHTML); +} + +function spacer() +{ + if ( snapshotMode ) + { + return '   '; + } + else + { + return ' '; + } +} + +function suppressEvent(e) +{ + e.cancelBubble = true; + if (e.stopPropagation) e.stopPropagation(); +} + +function svgFooter() +{ + return '</svg>'; +} + +function svgHeader() +{ + var patternWidth = fontSize * .6;//radius / 50; + + return '\ +<?xml version="1.0" standalone="no"?>\ +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" \ + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\ +<svg width="' + imageWidth + '" height="' + imageHeight + '" version="1.1"\ + xmlns="http://www.w3.org/2000/svg">\ +<title>Krona (snapshot) - ' + +(datasets > 1 ? datasetNames[currentDataset] + ' - ' : '') + selectedNode.name + +'</title>\ +<defs>\ + <style type="text/css">\ + text {font-size: ' + fontSize + 'px; font-family: ' + fontFamily + '; dominant-baseline:central}\ + path {stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + path.wedge {stroke:none}\ + path.line {fill:none;stroke:black;}\ + line {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + line.tick {stroke-width:' + thinLineWidth * fontSize / 6 + ';}\ + line.pattern {stroke-width:' + thinLineWidth * fontSize / 18 + ';}\ + circle {fill:none;stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + rect {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + .highlight {stroke:black;stroke-width:'+ highlightLineWidth * fontSize / 12 + ';}\ + .searchHighlight {fill:rgb(255, 255, 100);stroke:none;}\ + </style>\ +<pattern id="hiddenPattern" patternUnits="userSpaceOnUse" \ +x="0" y="0" width="' + patternWidth + '" height="' + patternWidth + '">\ +<line class="pattern" x1="0" y1="0" x2="' + patternWidth / 2 + '" y2="' + patternWidth / 2 + '"/>\ +<line class="pattern" x1="' + patternWidth / 2 + '" y1="' + patternWidth + +'" x2="' + patternWidth + '" y2="' + patternWidth / 2 + '"/>\ +</pattern>\ +</defs>\ +'; +} + +function svgText(text, x, y, anchor, bold, color) +{ + if ( typeof(anchor) == 'undefined' ) + { + anchor = 'start'; + } + + if ( color == undefined ) + { + color = 'black'; + } + + return '<text x="' + x + '" y="' + y + + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" text-anchor="' + anchor + '">' + text + '</text>'; +} + +function toggleKeys() +{ + if ( showKeys ) + { + keyControl.value = '…'; + showKeys = false; + } + else + { + keyControl.value = 'x'; + showKeys = true; + } + + updateKeyControl(); + + if ( progress == 1 ) + { + draw(); + } +} + +function update() +{ + if ( ! head ) + { + return; + } + + if ( mouseDown && focusNode != selectedNode ) + { + var date = new Date(); + + if ( date.getTime() - mouseDownTime > quickLookHoldLength ) + { + if ( focusNode.hasChildren() ) + { + expand(focusNode); + quickLook = true; + } + } + } + + if ( updateViewNeeded ) + { + resize(); + mouseX = -1; + mouseY = -1; + + collapse = collapseCheckBox.checked; + compress = true;//compressCheckBox.checked; + shorten = true;//shortenCheckBox.checked; + + checkSelectedCollapse(); + updateMaxAbsoluteDepth(); + + if ( focusNode.getCollapse() || focusNode.depth > maxAbsoluteDepth ) + { + setFocus(selectedNode); + } + else + { + setFocus(focusNode); + } + + updateView(); + + updateViewNeeded = false; + } + + var date = new Date(); + progress = (date.getTime() - tweenStartTime) / tweenLength; +// progress += .01; + + if ( progress >= 1 ) + { + progress = 1; + } + + if ( progress != progressLast ) + { + tweenFactor =// progress; + (1 / (1 + Math.exp(-tweenCurvature * (progress - .5))) - .5) / + (tweenMax - .5) / 2 + .5; + + if ( progress == 1 ) + { + snapshotButton.disabled = false; + zoomOut = false; + + //updateKeyControl(); + + if ( ! quickLook ) + { + //checkHighlight(); + } + + + if ( fpsDisplay ) + { + fpsDisplay.innerHTML = 'fps: ' + Math.round(tweenFrames * 1000 / tweenLength); + } + } + + draw(); + } + + progressLast = progress; +} + +function updateDatasetButtons() +{ + if ( datasets == 1 ) + { + return; + } + + var node = selectedNode ? selectedNode : head; + + datasetButtonLast.disabled = + node.attributes[magnitudeIndex][lastDataset] == 0; + + datasetButtonPrev.disabled = true; + datasetButtonNext.disabled = true; + + for ( var i = 0; i < datasets; i++ ) + { + var disable = node.attributes[magnitudeIndex][i] == 0; + + datasetDropDown.options[i].disabled = disable; + + if ( ! disable ) + { + if ( i != currentDataset ) + { + datasetButtonPrev.disabled = false; + datasetButtonNext.disabled = false; + } + } + } +} + +function updateDatasetWidths() +{ + if ( datasets > 1 ) + { + for ( var i = 0; i < datasets; i++ ) + { + context.font = fontBold; + var dim = context.measureText(datasetNames[i]); + datasetWidths[i] = dim.width; + } + } +} + +function updateKeyControl() +{ + if ( keys == 0 )//|| progress != 1 ) + { + keyControl.style.visibility = 'hidden'; + } + else + { + keyControl.style.visibility = 'visible'; + keyControl.style.right = margin + 'px'; + + if ( showKeys ) + { + keyControl.style.top = + imageHeight - + ( + keys * (keySize + keyBuffer) - + keyBuffer + + margin + + keyControl.clientHeight * 1.5 + ) + 'px'; + } + else + { + keyControl.style.top = + (imageHeight - margin - keyControl.clientHeight) + 'px'; + } + } +} + +function updateView() +{ + if ( selectedNode.depth > maxAbsoluteDepth - 1 ) + { + maxAbsoluteDepth = selectedNode.depth + 1; + } + + highlightedNode = selectedNode; + + angleFactor = 2 * Math.PI / (selectedNode.magnitude); + + maxPossibleDepth = Math.floor(gRadius / (fontSize * minRingWidthFactor)); + + if ( maxPossibleDepth < 4 ) + { + maxPossibleDepth = 4; + } + + var minRadiusInner = fontSize * 8 / gRadius; + var minRadiusFirst = fontSize * 6 / gRadius; + var minRadiusOuter = fontSize * 5 / gRadius; + + if ( .25 < minRadiusInner ) + { + minRadiusInner = .25; + } + + if ( .15 < minRadiusFirst ) + { + minRadiusFirst = .15; + } + + if ( .15 < minRadiusOuter ) + { + minRadiusOuter = .15; + } + + // visibility of nodes depends on the depth they are displayed at, + // so we need to set the max depth assuming they can all be displayed + // and iterate it down based on the deepest child node we can display + // + var maxDepth; + var newMaxDepth = selectedNode.getMaxDepth() - selectedNode.getDepth() + 1; + // + do + { + maxDepth = newMaxDepth; + + if ( ! compress && maxDepth > maxPossibleDepth ) + { + maxDepth = maxPossibleDepth; + } + + if ( compress ) + { + compressedRadii = new Array(maxDepth); + + compressedRadii[0] = minRadiusInner; + + var offset = 0; + + while + ( + lerp + ( + Math.atan(offset + 2), + Math.atan(offset + 1), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) - minRadiusInner > minRadiusFirst && + offset < 10 + ) + { + offset++; + } + + offset--; + + for ( var i = 1; i < maxDepth; i++ ) + { + compressedRadii[i] = lerp + ( + Math.atan(i + offset), + Math.atan(offset), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) + } + } + else + { + nodeRadius = 1 / maxDepth; + } + + newMaxDepth = selectedNode.maxVisibleDepth(maxDepth); + + if ( compress ) + { + if ( newMaxDepth <= maxPossibleDepth ) + { +// compress + } + } + else + { + if ( newMaxDepth > maxPossibleDepth ) + { + newMaxDepth = maxPossibleDepth; + } + } + } + while ( newMaxDepth < maxDepth ); + + maxDisplayDepth = maxDepth; + + lightnessFactor = (lightnessMax - lightnessBase) / (maxDepth > 8 ? 8 : maxDepth); + keys = 0; + + nLabelOffsets = new Array(maxDisplayDepth - 1); + labelOffsets = new Array(maxDisplayDepth - 1); + labelLastNodes = new Array(maxDisplayDepth - 1); + labelFirstNodes = new Array(maxDisplayDepth - 1); + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + if ( compress ) + { + if ( i == maxDisplayDepth - 1 ) + { + nLabelOffsets[i] = 0; + } + else + { + var width = + (compressedRadii[i + 1] - compressedRadii[i]) * + gRadius; + + nLabelOffsets[i] = Math.floor(width / fontSize / 1.2); + + if ( nLabelOffsets[i] > 2 ) + { + nLabelOffsets[i] = min + ( + Math.floor(width / fontSize / 1.75), + 5 + ); + } + } + } + else + { + nLabelOffsets[i] = Math.max + ( + Math.floor(Math.sqrt((nodeRadius * gRadius / fontSize)) * 1.5), + 3 + ); + } + + labelOffsets[i] = Math.floor((nLabelOffsets[i] - 1) / 2); + labelLastNodes[i] = new Array(nLabelOffsets[i] + 1); + labelFirstNodes[i] = new Array(nLabelOffsets[i] + 1); + + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + // these arrays will allow nodes with neighboring labels to link to + // each other to determine max label length + + labelLastNodes[i][j] = 0; + labelFirstNodes[i][j] = 0; + } + } + + fontSizeText.innerHTML = fontSize; + fontNormal = fontSize + 'px ' + fontFamily; + context.font = fontNormal; + fontBold = 'bold ' + fontSize + 'px ' + fontFamily; + tickLength = fontSize * .7; + + head.setTargets(0); + + keySize = ((imageHeight - margin * 3) * 1 / 2) / keys * 3 / 4; + + if ( keySize > fontSize * maxKeySizeFactor ) + { + keySize = fontSize * maxKeySizeFactor; + } + + keyBuffer = keySize / 3; + + fontSizeLast = fontSize; + + if ( datasetChanged ) + { + datasetChanged = false; + } + else + { + datasetAlpha.start = 0; + } + + var date = new Date(); + tweenStartTime = date.getTime(); + progress = 0; + tweenFrames = 0; + + updateKeyControl(); + updateDatasetWidths(); + + document.title = 'Krona - ' + selectedNode.name; + updateNavigationButtons(); + snapshotButton.disabled = true; + + maxAbsoluteDepthText.innerHTML = maxAbsoluteDepth - 1; + + maxAbsoluteDepthButtonDecrease.disabled = (maxAbsoluteDepth == 2); + maxAbsoluteDepthButtonIncrease.disabled = (maxAbsoluteDepth == head.maxDepth); + + if ( collapse != collapseLast && search.value != '' ) + { + onSearchChange(); + collapseLast = collapse; + } +} + +function updateMaxAbsoluteDepth() +{ + while ( maxAbsoluteDepth > 1 && selectedNode.depth > maxAbsoluteDepth - 1 ) + { + selectedNode = selectedNode.getParent(); + } +} + +function updateNavigationButtons() +{ + backButton.disabled = (nodeHistoryPosition == 0); +// upButton.disabled = (selectedNode.getParent() == 0); + forwardButton.disabled = (nodeHistoryPosition == nodeHistory.length); +} + +function useHue() +{ + return useHueCheckBox && useHueCheckBox.checked; +} +/* +function zoomOut() +{ + return ( + selectedNodeLast != 0 && + selectedNodeLast.getDepth() < selectedNode.getDepth()); +} +*/ + </script> +</head> +<body> +<img id="hiddenImage" src="data:image/png;base64,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" style="display:none"/> +<img id="loadingImage" 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style="display:none"/> +<noscript>Javascript must be enabled to view this page.</noscript> +<div style="display:none"> + <krona collapse="true" key="true"> + <attributes magnitude="magnitude"> + <attribute display="Total">magnitude</attribute> + </attributes> + <datasets> + <dataset>kt</dataset> + </datasets> + +<node name="all"><magnitude><val>40</val></magnitude><node name="unclassified"><magnitude><val>1</val></magnitude></node><node name="root"><magnitude><val>39</val></magnitude><node name="cellular organisms"><magnitude><val>39</val></magnitude><node name="Bacteria"><magnitude><val>39</val></magnitude><node name="Pseudomonadota"><magnitude><val>39</val></magnitude><node name="Gammaproteobacteria"><magnitude><val>39</val></magnitude><node name="Enterobacterales"><magnitude><val>25</val></magnitude><node name="Enterobacteriaceae"><magnitude><val>25</val></magnitude><node name="Salmonella"><magnitude><val>13</val></magnitude><node name="Salmonella enterica"><magnitude><val>13</val></magnitude><node name="Salmonella enterica subsp. enterica"><magnitude><val>13</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium"><magnitude><val>13</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"><magnitude><val>13</val></magnitude></node></node></node></node></node><node name="Escherichia"><magnitude><val>12</val></magnitude><node name="Escherichia coli"><magnitude><val>12</val></magnitude><node name="Escherichia coli K-12"><magnitude><val>12</val></magnitude><node name="Escherichia coli str. K-12 substr. MG1655"><magnitude><val>12</val></magnitude></node></node></node></node></node></node><node name="Pseudomonadales"><magnitude><val>14</val></magnitude><node name="Pseudomonadaceae"><magnitude><val>14</val></magnitude><node name="Pseudomonas"><magnitude><val>14</val></magnitude><node name="Pseudomonas aeruginosa group"><magnitude><val>14</val></magnitude><node name="Pseudomonas aeruginosa"><magnitude><val>14</val></magnitude><node name="Pseudomonas aeruginosa PAO1"><magnitude><val>14</val></magnitude></node></node></node></node></node></node></node></node></node></node></node></node></krona></div></body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/pb.hifi_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,23 @@ +2.5000 1 1 no rank 0 unclassified +97.5000 39 0 no rank 1 root +97.5000 39 0 no rank 131567 cellular organisms +97.5000 39 0 superkingdom 2 Bacteria +97.5000 39 0 phylum 1224 Pseudomonadota +97.5000 39 0 class 1236 Gammaproteobacteria +62.5000 25 0 order 91347 Enterobacterales +62.5000 25 0 family 543 Enterobacteriaceae +32.5000 13 0 genus 590 Salmonella +32.5000 13 0 species 28901 Salmonella enterica +32.5000 13 0 subspecies 59201 Salmonella enterica subsp. enterica +32.5000 13 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +32.5000 13 13 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +30.0000 12 0 genus 561 Escherichia +30.0000 12 0 species 562 Escherichia coli +30.0000 12 0 strain 83333 Escherichia coli K-12 +30.0000 12 12 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +35.0000 14 0 order 72274 Pseudomonadales +35.0000 14 0 family 135621 Pseudomonadaceae +35.0000 14 0 genus 286 Pseudomonas +35.0000 14 0 species group 136841 Pseudomonas aeruginosa group +35.0000 14 0 species 287 Pseudomonas aeruginosa +35.0000 14 14 strain 208964 Pseudomonas aeruginosa PAO1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sr_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,1500 @@ +1 AE004091.2_0_0/1 208964 594 0.984848 strain 208964:167 +1 AE004091.2_1_0/1 208964 594 0.89899 strain 208964:150 +1 AE004091.2_2_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_3_0/1 208964 594 0.946128 strain 208964:176 +1 AE004091.2_4_0/1 208964 594 0.95202 strain 208964:161 +1 AE004091.2_5_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_6_0/1 208964 594 0.699495 strain 208964:94 +1 AE004091.2_7_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_8_0/1 208964 594 0.936869 strain 208964:151 +1 AE004091.2_9_0/1 208964 594 0.957071 strain 208964:169 +1 AE004091.2_10_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_11_0/1 208964 594 0.974747 strain 208964:172 +1 AE004091.2_12_0/1 208964 594 0.999158 strain 208964:184 +1 AE004091.2_13_0/1 208964 594 0.936869 strain 208964:166 +1 AE004091.2_14_0/1 208964 594 0.767677 strain 208964:125 +1 AE004091.2_15_0/1 208964 594 0.893939 strain 208964:158 +1 AE004091.2_16_0/1 208964 594 0.881313 strain 208964:133 +1 AE004091.2_17_0/1 208964 594 0.949495 strain 208964:153 +1 AE004091.2_18_0/1 208964 594 0.964646 strain 208964:179 +1 AE004091.2_19_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_20_0/1 208964 594 0.878788 strain 208964:156 +1 AE004091.2_21_0/1 208964 594 0.920034 strain 208964:157 +1 AE004091.2_22_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_23_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_24_0/1 208964 594 0.631313 strain 208964:111 +1 AE004091.2_25_0/1 208964 594 0.846801 strain 208964:142 +1 AE004091.2_26_0/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_27_0/1 208964 594 0.992424 strain 208964:183 +1 AE004091.2_28_0/1 208964 594 0.949495 strain 208964:160 +1 AE004091.2_29_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_30_0/1 208964 594 0.94697 strain 208964:168 +1 AE004091.2_31_0/1 208964 594 0.924242 strain 208964:151 +1 AE004091.2_32_0/1 208964 594 0.944444 strain 208964:160 +1 AE004091.2_33_0/1 208964 594 0.818182 strain 208964:137 +1 AE004091.2_34_0/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_35_0/1 208964 594 0.934343 strain 208964:150 +1 AE004091.2_36_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_37_0/1 208964 594 0.939394 strain 208964:160 +1 AE004091.2_38_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_39_0/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_40_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_41_0/1 208964 594 0.940236 strain 208964:152 +1 AE004091.2_42_0/1 208964 594 0.974747 strain 208964:172 +1 AE004091.2_43_0/1 208964 594 0.987374 strain 208964:169 +1 AE004091.2_44_0/1 208964 594 0.982323 strain 208964:160 +1 AE004091.2_45_0/1 208964 594 0.954545 strain 208964:175 +1 AE004091.2_46_0/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_47_0/1 208964 594 0.974747 strain 208964:159 +1 AE004091.2_48_0/1 208964 594 0.934343 strain 208964:172 +1 AE004091.2_49_0/1 208964 594 0.984848 strain 208964:175 +1 AE004091.2_50_0/1 208964 594 0.978114 strain 208964:152 +1 AE004091.2_51_0/1 208964 594 0.969697 strain 208964:164 +1 AE004091.2_52_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_53_0/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_54_0/1 208964 594 0.90404 strain 208964:151 +1 AE004091.2_55_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_56_0/1 208964 594 0.955387 strain 208964:176 +1 AE004091.2_57_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_58_0/1 208964 594 0.949495 strain 208964:153 +1 AE004091.2_59_0/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_60_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_61_0/1 208964 594 0.761784 strain 208964:134 +1 AE004091.2_62_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_63_0/1 208964 594 0.924242 strain 208964:149 +1 AE004091.2_64_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_65_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_66_0/1 208964 594 0.902357 strain 208964:158 +1 AE004091.2_67_0/1 208964 594 0.941077 strain 208964:152 +1 AE004091.2_68_0/1 208964 594 0.962121 strain 208964:142 +1 AE004091.2_69_0/1 208964 594 0.881313 strain 208964:148 +1 AE004091.2_70_0/1 208964 594 0.881313 strain 208964:148 +1 AE004091.2_71_0/1 208964 594 0.883838 strain 208964:155 +1 AE004091.2_72_0/1 208964 594 0.825758 strain 208964:148 +1 AE004091.2_73_0/1 208964 594 0.968855 strain 208964:162 +1 AE004091.2_74_0/1 208964 594 0.956229 strain 208964:176 +1 AE004091.2_75_0/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_76_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_77_0/1 208964 594 0.89899 strain 208964:151 +1 AE004091.2_78_0/1 208964 594 0.993266 strain 208964:175 +1 AE004091.2_79_0/1 208964 594 0.967172 strain 208964:150 +1 AE004091.2_80_0/1 208964 594 0.988216 strain 208964:175 +1 AE004091.2_81_0/1 208964 594 0.977273 strain 208964:166 +1 AE004091.2_82_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_83_0/1 208964 594 0.972222 strain 208964:172 +1 AE004091.2_84_0/1 208964 594 0.984848 strain 208964:160 +1 AE004091.2_85_0/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_86_0/1 208964 594 0.97138 strain 208964:177 +1 AE004091.2_87_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_88_0/1 208964 594 0.979798 strain 208964:166 +1 AE004091.2_89_0/1 208964 594 0.757576 strain 208964:119 +1 AE004091.2_90_0/1 208964 594 0.967172 strain 208964:171 +1 AE004091.2_91_0/1 208964 594 0.990741 strain 208964:168 +1 AE004091.2_92_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_93_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_94_0/1 208964 594 0.902357 strain 208964:145 +1 AE004091.2_95_0/1 208964 594 0.968013 strain 208964:163 +1 AE004091.2_96_0/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_97_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_98_0/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_99_0/1 208964 594 0.896465 strain 208964:168 +1 AE004091.2_100_0/1 208964 594 0.944444 strain 208964:176 +1 AE004091.2_101_0/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_102_0/1 208964 594 0.883838 strain 208964:161 +1 AE004091.2_103_0/1 208964 594 0.962963 strain 208964:163 +1 AE004091.2_104_0/1 208964 594 0.961279 strain 208964:169 +1 AE004091.2_105_0/1 208964 594 0.957071 strain 208964:148 +1 AE004091.2_106_0/1 208964 594 0.95202 strain 208964:161 +1 AE004091.2_107_0/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_108_0/1 208964 594 0.976431 strain 208964:158 +1 AE004091.2_109_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_110_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_111_0/1 208964 594 0.910774 strain 208964:169 +1 AE004091.2_112_0/1 208964 594 0.878788 strain 208964:153 +1 AE004091.2_113_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_114_0/1 208964 594 0.919192 strain 208964:156 +1 AE004091.2_115_0/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_116_0/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_117_0/1 208964 594 0.957071 strain 208964:169 +1 AE004091.2_118_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_119_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_120_0/1 208964 594 0.991583 strain 208964:182 +1 AE004091.2_121_0/1 208964 594 0.977273 strain 208964:173 +1 AE004091.2_122_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_123_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_124_0/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_125_0/1 208964 594 0.85101 strain 208964:127 +1 AE004091.2_126_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_127_0/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_128_0/1 208964 594 0.959596 strain 208964:177 +1 AE004091.2_129_0/1 208964 594 0.989057 strain 208964:173 +1 AE004091.2_130_0/1 208964 594 0.781987 strain 208964:124 +1 AE004091.2_131_0/1 208964 594 0.990741 strain 208964:168 +1 AE004091.2_132_0/1 208964 594 0.89899 strain 208964:166 +1 AE004091.2_133_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_134_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_135_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_136_0/1 208964 594 0.941919 strain 208964:162 +1 AE004091.2_137_0/1 208964 594 0.894781 strain 208964:152 +1 AE004091.2_138_0/1 208964 594 0.912458 strain 208964:167 +1 AE004091.2_139_0/1 208964 594 0.853535 strain 208964:130 +1 AE004091.2_140_0/1 208964 594 0.772727 strain 208964:137 +1 AE004091.2_141_0/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_142_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_143_0/1 208964 594 0.934343 strain 208964:164 +1 AE004091.2_144_0/1 208964 594 0.863636 strain 208964:149 +1 AE004091.2_145_0/1 208964 594 0.956229 strain 208964:154 +1 AE004091.2_146_0/1 208964 594 0.909091 strain 208964:160 +1 AE004091.2_147_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_148_0/1 208964 594 0.89899 strain 208964:133 +1 AE004091.2_149_0/1 208964 594 0.982323 strain 208964:160 +1 AE004091.2_150_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_151_0/1 208964 594 0.989899 strain 208964:176 +1 AE004091.2_152_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_153_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_154_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_155_0/1 208964 594 0.921717 strain 208964:162 +1 AE004091.2_156_0/1 208964 594 0.919192 strain 208964:171 +1 AE004091.2_157_0/1 208964 594 0.947811 strain 208964:176 +1 AE004091.2_158_0/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_159_0/1 208964 594 0.939394 strain 208964:173 +1 AE004091.2_160_0/1 208964 594 0.833333 strain 208964:127 +1 AE004091.2_161_0/1 208964 594 0.611111 strain 208964:100 +1 AE004091.2_162_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_163_0/1 208964 594 0.959596 strain 208964:169 +1 AE004091.2_164_0/1 208964 594 0.888889 strain 208964:152 +1 AE004091.2_165_0/1 208964 594 0.974747 strain 208964:172 +1 AE004091.2_166_0/1 208964 594 0.930976 strain 208964:172 +1 AE004091.2_167_0/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_168_0/1 208964 594 0.962121 strain 208964:142 +1 AE004091.2_169_0/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_170_0/1 208964 594 0.914141 strain 208964:148 +1 AE004091.2_171_0/1 208964 594 0.929293 strain 208964:163 +1 AE004091.2_172_0/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_173_0/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_174_0/1 208964 594 0.972222 strain 208964:172 +1 AE004091.2_175_0/1 208964 594 0.916667 strain 208964:141 +1 AE004091.2_176_0/1 208964 594 0.948653 strain 208964:160 +1 AE004091.2_177_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_178_0/1 208964 594 0.949495 strain 208964:160 +1 AE004091.2_179_0/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_180_0/1 208964 594 0.922559 strain 208964:165 +1 AE004091.2_181_0/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_182_0/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_183_0/1 208964 594 0.924242 strain 208964:157 +1 AE004091.2_184_0/1 208964 594 0.969697 strain 208964:171 +1 AE004091.2_185_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_186_0/1 208964 594 0.893939 strain 208964:150 +1 AE004091.2_187_0/1 208964 594 0.808081 strain 208964:149 +1 AE004091.2_188_0/1 208964 594 0.989057 strain 208964:176 +1 AE004091.2_189_0/1 208964 594 0.888889 strain 208964:156 +1 AE004091.2_190_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_191_0/1 208964 594 0.95202 strain 208964:175 +1 AE004091.2_192_0/1 208964 594 0.954545 strain 208964:162 +1 AE004091.2_193_0/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_194_0/1 208964 594 0.936027 strain 208964:158 +1 AE004091.2_195_0/1 208964 594 0.967172 strain 208964:171 +1 AE004091.2_196_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_197_0/1 208964 594 0.984848 strain 208964:168 +1 AE004091.2_198_0/1 208964 594 0.883838 strain 208964:119 +1 AE004091.2_199_0/1 208964 594 0.979798 strain 208964:180 +1 AE004091.2_200_0/1 208964 594 0.969697 strain 208964:164 +1 AE004091.2_201_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_202_0/1 208964 594 0.949495 strain 208964:160 +1 AE004091.2_203_0/1 208964 594 0.93266 strain 208964:174 +1 AE004091.2_204_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_205_0/1 208964 594 0.959596 strain 208964:169 +1 AE004091.2_206_0/1 208964 594 0.989057 strain 208964:168 +1 AE004091.2_207_0/1 208964 594 0.964646 strain 208964:170 +1 AE004091.2_208_0/1 208964 594 0.964646 strain 208964:173 +1 AE004091.2_209_0/1 208964 594 0.984848 strain 208964:168 +1 AE004091.2_210_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_211_0/1 208964 594 0.888889 strain 208964:165 +1 AE004091.2_212_0/1 208964 594 0.989899 strain 208964:175 +1 AE004091.2_213_0/1 208964 594 0.982323 strain 208964:160 +1 AE004091.2_214_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_215_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_216_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_217_0/1 208964 594 0.830808 strain 208964:133 +1 AE004091.2_218_0/1 208964 594 0.969697 strain 208964:171 +1 AE004091.2_219_0/1 208964 594 0.991583 strain 208964:175 +1 AE004091.2_220_0/1 208964 594 0.908249 strain 208964:141 +1 AE004091.2_221_0/1 208964 594 0.967172 strain 208964:173 +1 AE004091.2_222_0/1 208964 594 0.926768 strain 208964:135 +1 AE004091.2_223_0/1 208964 594 0.969697 strain 208964:178 +1 AE004091.2_224_0/1 208964 594 0.80303 strain 208964:141 +1 AE004091.2_225_0/1 208964 594 0.949495 strain 208964:153 +1 AE004091.2_226_0/1 208964 594 0.911616 strain 208964:153 +1 AE004091.2_227_0/1 208964 594 0.964646 strain 208964:163 +1 AE004091.2_228_0/1 208964 594 0.924242 strain 208964:171 +1 AE004091.2_229_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_230_0/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_231_0/1 208964 594 0.737374 strain 208964:127 +1 AE004091.2_232_0/1 208964 594 0.611111 strain 208964:108 +1 AE004091.2_233_0/1 208964 594 0.909091 strain 208964:146 +1 AE004091.2_234_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_235_0/1 208964 594 0.888889 strain 208964:149 +1 AE004091.2_236_0/1 208964 594 0.921717 strain 208964:157 +1 AE004091.2_237_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_238_0/1 208964 594 0.957071 strain 208964:176 +1 AE004091.2_239_0/1 208964 594 0.939394 strain 208964:176 +1 AE004091.2_240_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_241_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_242_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_243_0/1 208964 594 0.982323 strain 208964:181 +1 AE004091.2_244_0/1 208964 594 0.977273 strain 208964:168 +1 AE004091.2_245_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_246_0/1 208964 594 0.868687 strain 208964:144 +1 AE004091.2_247_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_248_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_249_0/1 208964 594 0.950337 strain 208964:175 +1 AE004091.2_0_1/1 208964 594 0.988216 strain 208964:175 +1 AE004091.2_1_1/1 208964 594 0.883838 strain 208964:140 +1 AE004091.2_2_1/1 208964 594 0.972222 strain 208964:179 +1 AE004091.2_3_1/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_4_1/1 208964 594 0.876263 strain 208964:156 +1 AE004091.2_5_1/1 208964 594 0.944444 strain 208964:168 +1 AE004091.2_6_1/1 208964 594 0.90404 strain 208964:154 +1 AE004091.2_7_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_8_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_9_1/1 208964 594 0.731481 strain 208964:118 +1 AE004091.2_10_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_11_1/1 208964 594 0.806397 strain 208964:125 +1 AE004091.2_12_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_13_1/1 208964 594 0.93266 strain 208964:164 +1 AE004091.2_14_1/1 208964 594 0.964646 strain 208964:156 +1 AE004091.2_15_1/1 208964 594 0.984848 strain 208964:176 +1 AE004091.2_16_1/1 208964 594 0.972222 strain 208964:151 +1 AE004091.2_17_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_18_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_19_1/1 208964 594 0.944444 strain 208964:160 +1 AE004091.2_20_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_21_1/1 208964 594 0.815657 strain 208964:142 +1 AE004091.2_22_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_23_1/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_24_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_25_1/1 208964 594 0.964646 strain 208964:163 +1 AE004091.2_26_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_27_1/1 208964 594 0.939394 strain 208964:172 +1 AE004091.2_28_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_29_1/1 208964 594 0.964646 strain 208964:158 +1 AE004091.2_30_1/1 208964 594 0.957071 strain 208964:169 +1 AE004091.2_31_1/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_32_1/1 208964 594 0.358586 strain 208964:52 +1 AE004091.2_33_1/1 208964 594 0.969697 strain 208964:172 +1 AE004091.2_34_1/1 208964 594 0.944444 strain 208964:166 +1 AE004091.2_35_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_36_1/1 208964 594 0.977273 strain 208964:173 +1 AE004091.2_37_1/1 208964 594 0.959596 strain 208964:162 +1 AE004091.2_38_1/1 208964 594 0.967172 strain 208964:178 +1 AE004091.2_39_1/1 208964 594 0.962121 strain 208964:163 +1 AE004091.2_40_1/1 208964 594 0.5 strain 208964:92 +1 AE004091.2_41_1/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_42_1/1 208964 594 0.941919 strain 208964:166 +1 AE004091.2_43_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_44_1/1 208964 594 0.981481 strain 208964:166 +1 AE004091.2_45_1/1 208964 594 0.921717 strain 208964:134 +1 AE004091.2_46_1/1 208964 594 0.501683 strain 208964:95 +1 AE004091.2_47_1/1 208964 594 0.93771 strain 208964:158 +1 AE004091.2_48_1/1 208964 594 0.792929 strain 208964:143 +1 AE004091.2_49_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_50_1/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_51_1/1 208964 594 0.941077 strain 208964:168 +1 AE004091.2_52_1/1 208964 594 0.987374 strain 208964:168 +1 AE004091.2_53_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_54_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_55_1/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_56_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_57_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_58_1/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_59_1/1 208964 594 0.976431 strain 208964:165 +1 AE004091.2_60_1/1 208964 594 0.989899 strain 208964:176 +1 AE004091.2_61_1/1 208964 594 0.929293 strain 208964:156 +1 AE004091.2_62_1/1 208964 594 0.901515 strain 208964:137 +1 AE004091.2_63_1/1 208964 594 0.923401 strain 208964:171 +1 AE004091.2_64_1/1 208964 594 0.808081 strain 208964:137 +1 AE004091.2_65_1/1 208964 594 0.878788 strain 208964:149 +1 AE004091.2_66_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_67_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_68_1/1 208964 594 0.909091 strain 208964:152 +1 AE004091.2_69_1/1 208964 594 0.958754 strain 208964:160 +1 AE004091.2_70_1/1 208964 594 0.973906 strain 208964:172 +1 AE004091.2_71_1/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_72_1/1 208964 594 0.949495 strain 208964:168 +1 AE004091.2_73_1/1 208964 594 0.957912 strain 208964:161 +1 AE004091.2_74_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_75_1/1 208964 594 0.979798 strain 208964:180 +1 AE004091.2_76_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_77_1/1 208964 594 0.986532 strain 208964:181 +1 AE004091.2_78_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_79_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_80_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_81_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_82_1/1 208964 594 0.957912 strain 208964:175 +1 AE004091.2_83_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_84_1/1 208964 594 0.957071 strain 208964:176 +1 AE004091.2_85_1/1 208964 594 0.987374 strain 208964:168 +1 AE004091.2_86_1/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_87_1/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_88_1/1 208964 594 0.775253 strain 208964:121 +1 AE004091.2_89_1/1 208964 594 0.914141 strain 208964:170 +1 AE004091.2_90_1/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_91_1/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_92_1/1 208964 594 0.97138 strain 208964:178 +1 AE004091.2_93_1/1 208964 594 0.973064 strain 208964:165 +1 AE004091.2_94_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_95_1/1 208964 594 0.915825 strain 208964:147 +1 AE004091.2_96_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_97_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_98_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_99_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_100_1/1 208964 594 0.888047 strain 208964:156 +1 AE004091.2_101_1/1 208964 594 0.981481 strain 208964:166 +1 AE004091.2_102_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_103_1/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_104_1/1 208964 594 0.64899 strain 208964:110 +1 AE004091.2_105_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_106_1/1 208964 594 0.888889 strain 208964:155 +1 AE004091.2_107_1/1 208964 594 0.934343 strain 208964:176 +1 AE004091.2_108_1/1 208964 594 0.934343 strain 208964:174 +1 AE004091.2_109_1/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_110_1/1 208964 594 0.934343 strain 208964:164 +1 AE004091.2_111_1/1 208964 594 0.804714 strain 208964:135 +1 AE004091.2_112_1/1 208964 594 0.976431 strain 208964:179 +1 AE004091.2_113_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_114_1/1 208964 594 0.957912 strain 208964:169 +1 AE004091.2_115_1/1 208964 594 0.988216 strain 208964:160 +1 AE004091.2_116_1/1 208964 594 0.979798 strain 208964:168 +1 AE004091.2_117_1/1 208964 594 0.782828 strain 208964:127 +1 AE004091.2_118_1/1 208964 594 0.968855 strain 208964:166 +1 AE004091.2_119_1/1 208964 594 0.927609 strain 208964:165 +1 AE004091.2_120_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_121_1/1 208964 594 0.949495 strain 208964:154 +1 AE004091.2_122_1/1 208964 594 0.727273 strain 208964:130 +1 AE004091.2_123_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_124_1/1 208964 594 0.941919 strain 208964:168 +1 AE004091.2_125_1/1 208964 594 0.876263 strain 208964:139 +1 AE004091.2_126_1/1 208964 594 0.984848 strain 208964:168 +1 AE004091.2_127_1/1 208964 594 0.925084 strain 208964:156 +1 AE004091.2_128_1/1 208964 594 0.962121 strain 208964:177 +1 AE004091.2_129_1/1 208964 594 0.924242 strain 208964:169 +1 AE004091.2_130_1/1 208964 594 0.934343 strain 208964:152 +1 AE004091.2_131_1/1 208964 594 0.951178 strain 208964:168 +1 AE004091.2_132_1/1 208964 594 0.989899 strain 208964:175 +1 AE004091.2_133_1/1 208964 594 0.651515 strain 208964:107 +1 AE004091.2_134_1/1 208964 594 0.963805 strain 208964:170 +1 AE004091.2_135_1/1 208964 594 0.934343 strain 208964:164 +1 AE004091.2_136_1/1 208964 594 0.492424 strain 208964:84 +1 AE004091.2_137_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_138_1/1 208964 594 0.848485 strain 208964:141 +1 AE004091.2_139_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_140_1/1 208964 594 0.97138 strain 208964:173 +1 AE004091.2_141_1/1 208964 594 0.926768 strain 208964:156 +1 AE004091.2_142_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_143_1/1 208964 594 0.861111 strain 208964:131 +1 AE004091.2_144_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_145_1/1 208964 594 0.934343 strain 208964:157 +1 AE004091.2_146_1/1 208964 594 0.924242 strain 208964:152 +1 AE004091.2_147_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_148_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_149_1/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_150_1/1 208964 594 0.929293 strain 208964:165 +1 AE004091.2_151_1/1 208964 594 0.989899 strain 208964:182 +1 AE004091.2_152_1/1 208964 594 0.643939 strain 208964:100 +1 AE004091.2_153_1/1 208964 594 0.975589 strain 208964:180 +1 AE004091.2_154_1/1 208964 594 0.820707 strain 208964:139 +1 AE004091.2_155_1/1 208964 594 0.86532 strain 208964:145 +1 AE004091.2_156_1/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_157_1/1 208964 594 0.995791 strain 208964:184 +1 AE004091.2_158_1/1 208964 594 0.949495 strain 208964:175 +1 AE004091.2_159_1/1 208964 594 0.969697 strain 208964:157 +1 AE004091.2_160_1/1 208964 594 0.939394 strain 208964:151 +1 AE004091.2_161_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_162_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_163_1/1 208964 594 0.969697 strain 208964:166 +1 AE004091.2_164_1/1 208964 594 0.909091 strain 208964:161 +1 AE004091.2_165_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_166_1/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_167_1/1 208964 594 0.976431 strain 208964:166 +1 AE004091.2_168_1/1 208964 594 0.868687 strain 208964:148 +1 AE004091.2_169_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_170_1/1 208964 594 0.957912 strain 208964:162 +1 AE004091.2_171_1/1 208964 594 0.97138 strain 208964:164 +1 AE004091.2_172_1/1 208964 594 0.921717 strain 208964:172 +1 AE004091.2_173_1/1 208964 594 0.919192 strain 208964:173 +1 AE004091.2_174_1/1 208964 594 0.934343 strain 208964:157 +1 AE004091.2_175_1/1 208964 594 0.989057 strain 208964:175 +1 AE004091.2_176_1/1 208964 594 0.5 strain 208964:92 +1 AE004091.2_177_1/1 208964 594 0.931818 strain 208964:151 +1 AE004091.2_178_1/1 208964 594 0.953704 strain 208964:168 +1 AE004091.2_179_1/1 208964 594 0.983165 strain 208964:166 +1 AE004091.2_180_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_181_1/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_182_1/1 208964 594 0.984848 strain 208964:160 +1 AE004091.2_183_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_184_1/1 208964 594 0.957912 strain 208964:169 +1 AE004091.2_185_1/1 208964 594 0.86532 strain 208964:134 +1 AE004091.2_186_1/1 208964 594 0.973064 strain 208964:165 +1 AE004091.2_187_1/1 208964 594 0.972222 strain 208964:172 +1 AE004091.2_188_1/1 208964 594 0.939394 strain 208964:172 +1 AE004091.2_189_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_190_1/1 208964 594 0.925084 strain 208964:157 +1 AE004091.2_191_1/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_192_1/1 208964 594 0.979798 strain 208964:168 +1 AE004091.2_193_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_194_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_195_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_196_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_197_1/1 208964 594 0.995791 strain 208964:184 +1 AE004091.2_198_1/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_199_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_200_1/1 208964 594 0.964646 strain 208964:171 +1 AE004091.2_201_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_202_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_203_1/1 208964 594 0.939394 strain 208964:159 +1 AE004091.2_204_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_205_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_206_1/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_207_1/1 208964 594 0.964646 strain 208964:170 +1 AE004091.2_208_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_209_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_210_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_211_1/1 208964 594 0.960438 strain 208964:163 +1 AE004091.2_212_1/1 208964 594 0.987374 strain 208964:182 +1 AE004091.2_213_1/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_214_1/1 208964 594 0.994108 strain 208964:176 +1 AE004091.2_215_1/1 208964 594 0.905724 strain 208964:153 +1 AE004091.2_216_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_217_1/1 208964 594 0.954545 strain 208964:175 +1 AE004091.2_218_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_219_1/1 208964 594 0.926768 strain 208964:165 +1 AE004091.2_220_1/1 208964 594 0.886364 strain 208964:158 +1 AE004091.2_221_1/1 208964 594 0.934343 strain 208964:168 +1 AE004091.2_222_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_223_1/1 208964 594 0.929293 strain 208964:172 +1 AE004091.2_224_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_225_1/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_226_1/1 208964 594 0.914141 strain 208964:153 +1 AE004091.2_227_1/1 208964 594 0.987374 strain 208964:168 +1 AE004091.2_228_1/1 208964 594 0.914141 strain 208964:154 +1 AE004091.2_229_1/1 208964 594 0.939394 strain 208964:158 +1 AE004091.2_230_1/1 208964 594 0.994108 strain 208964:184 +1 AE004091.2_231_1/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_232_1/1 208964 594 0.916667 strain 208964:155 +1 AE004091.2_233_1/1 208964 594 0.676768 strain 208964:120 +1 AE004091.2_234_1/1 208964 594 0.996633 strain 208964:183 +1 AE004091.2_235_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_236_1/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_237_1/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_238_1/1 208964 594 0.941919 strain 208964:152 +1 AE004091.2_239_1/1 208964 594 0.949495 strain 208964:167 +1 AE004091.2_240_1/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_241_1/1 208964 594 0.967172 strain 208964:171 +1 AE004091.2_242_1/1 208964 594 0.924242 strain 208964:162 +1 AE004091.2_243_1/1 208964 594 0.960438 strain 208964:171 +1 AE004091.2_244_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_245_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_246_1/1 208964 594 0.936869 strain 208964:160 +1 AE004091.2_247_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_248_1/1 208964 594 0.973064 strain 208964:158 +1 AE004091.2_249_1/1 208964 594 0.979798 strain 208964:180 +1 NC_000913.3_0_0/1 511145 594 0.974747 no rank 511145:179 +1 NC_000913.3_1_0/1 511145 594 0.826599 no rank 511145:140 +1 NC_000913.3_2_0/1 511145 594 0.939394 no rank 511145:152 +1 NC_000913.3_3_0/1 511145 594 0.954545 no rank 511145:176 +1 NC_000913.3_4_0/1 511145 594 0.979798 no rank 511145:173 +1 NC_000913.3_5_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_6_0/1 511145 594 0.939394 no rank 511145:168 +1 NC_000913.3_7_0/1 511145 594 0.992424 no rank 511145:183 +1 NC_000913.3_8_0/1 511145 594 0.99495 no rank 511145:184 +1 NC_000913.3_9_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_10_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_11_0/1 511145 594 0.618687 no rank 511145:83 +1 NC_000913.3_12_0/1 511145 594 0.989899 no rank 511145:182 +1 NC_000913.3_13_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_14_0/1 511145 594 0.939394 no rank 511145:165 +1 NC_000913.3_15_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_16_0/1 511145 594 0.993266 no rank 511145:168 +1 NC_000913.3_17_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_18_0/1 511145 594 0.969697 no rank 511145:164 +1 NC_000913.3_19_0/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_20_0/1 511145 594 0.979798 no rank 511145:173 +1 NC_000913.3_21_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_22_0/1 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NC_000913.3_72_0/1 511145 594 0.954545 no rank 511145:162 +1 NC_000913.3_73_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_74_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_75_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_76_0/1 511145 594 0.984848 no rank 511145:174 +1 NC_000913.3_77_0/1 511145 594 0.94697 no rank 511145:160 +1 NC_000913.3_78_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_79_0/1 511145 594 0.964646 no rank 511145:177 +1 NC_000913.3_80_0/1 511145 594 0.923401 no rank 511145:156 +1 NC_000913.3_81_0/1 511145 594 0.886364 no rank 511145:142 +1 NC_000913.3_82_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_83_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_84_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_85_0/1 511145 594 0.954545 no rank 511145:161 +1 NC_000913.3_86_0/1 511145 594 0.951178 no rank 511145:168 +1 NC_000913.3_87_0/1 511145 594 0.996633 no rank 511145:176 +1 NC_000913.3_88_0/1 511145 594 0.99495 no 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511145 594 1 no rank 511145:184 +1 NC_000913.3_135_1/1 511145 594 0.96633 no rank 511145:172 +1 NC_000913.3_136_1/1 511145 594 0.99495 no rank 511145:183 +1 NC_000913.3_137_1/1 511145 594 0.993266 no rank 511145:183 +1 NC_000913.3_138_1/1 511145 594 0.93771 no rank 511145:158 +1 NC_000913.3_139_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_140_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_141_1/1 511145 594 0.909091 no rank 511145:167 +1 NC_000913.3_142_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_143_1/1 511145 594 0.974747 no rank 511145:179 +1 NC_000913.3_144_1/1 511145 594 0.833333 no rank 511145:131 +1 NC_000913.3_145_1/1 511145 594 0.994108 no rank 511145:176 +1 NC_000913.3_146_1/1 511145 594 0.973906 no rank 511145:172 +1 NC_000913.3_147_1/1 511145 594 0.989899 no rank 511145:176 +1 NC_000913.3_148_1/1 511145 594 0.972222 no rank 511145:158 +1 NC_000913.3_149_1/1 511145 594 0.974747 no rank 511145:175 +1 NC_000913.3_150_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_151_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_152_1/1 511145 594 0.856061 no rank 511145:129 +1 NC_000913.3_153_1/1 511145 594 0.969697 no rank 511145:164 +1 NC_000913.3_154_1/1 511145 594 0.888889 no rank 511145:136 +1 NC_000913.3_155_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_156_1/1 511145 594 0.974747 no rank 511145:172 +1 NC_000913.3_157_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_158_1/1 511145 594 0.957071 no rank 511145:169 +1 NC_000913.3_159_1/1 511145 594 0.893939 no rank 511145:142 +1 NC_000913.3_160_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_161_1/1 511145 594 0.98569 no rank 511145:175 +1 NC_000913.3_162_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_163_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_164_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_165_1/1 511145 594 0.944444 no rank 511145:168 +1 NC_000913.3_166_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_167_1/1 511145 594 0.955387 no rank 511145:176 +1 NC_000913.3_168_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_169_1/1 511145 594 0.984848 no rank 511145:160 +1 NC_000913.3_170_1/1 511145 594 0.930976 no rank 511145:149 +1 NC_000913.3_171_1/1 511145 594 0.969697 no rank 511145:178 +1 NC_000913.3_172_1/1 511145 594 0.921717 no rank 511145:162 +1 NC_000913.3_173_1/1 511145 594 0.99495 no rank 511145:183 +1 NC_000913.3_174_1/1 511145 594 0.972222 no rank 511145:172 +1 NC_000913.3_175_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_176_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_177_1/1 511145 594 0.991583 no rank 511145:184 +1 NC_000913.3_178_1/1 511145 594 0.916667 no rank 511145:148 +1 NC_000913.3_179_1/1 511145 594 0.896465 no rank 511145:129 +1 NC_000913.3_180_1/1 511145 594 0.982323 no rank 511145:160 +1 NC_000913.3_181_1/1 511145 594 0.974747 no rank 511145:165 +1 NC_000913.3_182_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_183_1/1 511145 594 0.984848 no rank 511145:168 +1 NC_000913.3_184_1/1 511145 594 0.893939 no rank 511145:152 +1 NC_000913.3_185_1/1 511145 594 0.873737 no rank 511145:139 +1 NC_000913.3_186_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_187_1/1 511145 594 0.984848 no rank 511145:167 +1 NC_000913.3_188_1/1 511145 594 0.964646 no rank 511145:170 +1 NC_000913.3_189_1/1 511145 594 0.99495 no rank 511145:183 +1 NC_000913.3_190_1/1 511145 594 0.964646 no rank 511145:163 +1 NC_000913.3_191_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_192_1/1 511145 594 0.996633 no rank 511145:184 +1 NC_000913.3_193_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_194_1/1 511145 594 0.959596 no rank 511145:176 +1 NC_000913.3_195_1/1 511145 594 0.978956 no rank 511145:160 +1 NC_000913.3_196_1/1 511145 594 0.974747 no rank 511145:173 +1 NC_000913.3_197_1/1 511145 594 0.982323 no rank 511145:176 +1 NC_000913.3_198_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_199_1/1 511145 594 0.919192 no rank 511145:150 +1 NC_000913.3_200_1/1 511145 594 0.853535 no rank 511145:151 +1 NC_000913.3_201_1/1 511145 594 0.998317 no rank 511145:176 +1 NC_000913.3_202_1/1 511145 594 0.990741 no rank 511145:176 +1 NC_000913.3_203_1/1 511145 594 0.974747 no rank 511145:172 +1 NC_000913.3_204_1/1 511145 594 0.863636 no rank 511145:130 +1 NC_000913.3_205_1/1 511145 594 0.974747 no rank 511145:172 +1 NC_000913.3_206_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_207_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_208_1/1 511145 594 0.936869 no rank 511145:168 +1 NC_000913.3_209_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_210_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_211_1/1 511145 594 0.988216 no rank 511145:168 +1 NC_000913.3_212_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_213_1/1 511145 594 0.936869 no rank 511145:160 +1 NC_000913.3_214_1/1 511145 594 0.989899 no rank 511145:182 +1 NC_000913.3_215_1/1 511145 594 0.984848 no rank 511145:160 +1 NC_000913.3_216_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_217_1/1 511145 594 0.977273 no rank 511145:173 +1 NC_000913.3_218_1/1 511145 594 0.944444 no rank 511145:173 +1 NC_000913.3_219_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_220_1/1 511145 594 0.988216 no rank 511145:184 +1 NC_000913.3_221_1/1 511145 594 0.978114 no rank 511145:173 +1 NC_000913.3_222_1/1 511145 594 0.977273 no rank 511145:166 +1 NC_000913.3_223_1/1 511145 594 0.986532 no rank 511145:182 +1 NC_000913.3_224_1/1 511145 594 0.944444 no rank 511145:173 +1 NC_000913.3_225_1/1 511145 594 0.967172 no rank 511145:178 +1 NC_000913.3_226_1/1 511145 594 0.987374 no rank 511145:168 +1 NC_000913.3_227_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_228_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_229_1/1 511145 594 0.994108 no rank 511145:176 +1 NC_000913.3_230_1/1 511145 594 0.927609 no rank 511145:150 +1 NC_000913.3_231_1/1 511145 594 0.984848 no rank 511145:176 +1 NC_000913.3_232_1/1 511145 594 0.969697 no rank 511145:178 +1 NC_000913.3_233_1/1 511145 594 0.977273 no rank 511145:173 +1 NC_000913.3_234_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_235_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_236_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_237_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_238_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_239_1/1 511145 594 0.869529 no rank 511145:139 +1 NC_000913.3_240_1/1 511145 594 0.998317 no rank 511145:184 +1 NC_000913.3_241_1/1 511145 594 0.959596 no rank 511145:176 +1 NC_000913.3_242_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_243_1/1 511145 594 0.944444 no rank 511145:163 +1 NC_000913.3_244_1/1 511145 594 0.922559 no rank 511145:169 +1 NC_000913.3_245_1/1 511145 594 0.825758 no rank 511145:139 +1 NC_000913.3_246_1/1 511145 594 0.992424 no rank 511145:184 +1 NC_000913.3_247_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_248_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_249_1/1 511145 594 0.944444 no rank 511145:176 +1 NC_003197.2_0_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_1_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_2_0/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_3_0/1 99287 594 0.969697 strain 99287:171 +1 NC_003197.2_4_0/1 99287 594 0.961279 strain 99287:163 +1 NC_003197.2_5_0/1 99287 594 0.868687 strain 99287:135 +1 NC_003197.2_6_0/1 99287 594 0.929293 strain 99287:172 +1 NC_003197.2_7_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_8_0/1 99287 594 0.871212 strain 99287:147 +1 NC_003197.2_9_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_10_0/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_11_0/1 99287 594 0.96633 strain 99287:178 +1 NC_003197.2_12_0/1 99287 594 0.891414 strain 99287:151 +1 NC_003197.2_13_0/1 99287 594 0.98064 strain 99287:160 +1 NC_003197.2_14_0/1 99287 594 0.919192 strain 99287:162 +1 NC_003197.2_15_0/1 99287 594 0.986532 strain 99287:174 +1 NC_003197.2_16_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_17_0/1 99287 594 0.984848 strain 99287:181 +1 NC_003197.2_18_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_19_0/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_20_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_21_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_22_0/1 99287 594 0.866162 strain 99287:131 +1 NC_003197.2_23_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_24_0/1 99287 594 0.984848 strain 99287:167 +1 NC_003197.2_25_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_26_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_27_0/1 99287 594 0.981481 strain 99287:180 +1 NC_003197.2_28_0/1 99287 594 0.981481 strain 99287:175 +1 NC_003197.2_29_0/1 99287 594 0.936869 strain 99287:166 +1 NC_003197.2_30_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_31_0/1 99287 594 0.873737 strain 99287:147 +1 NC_003197.2_32_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_33_0/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_34_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_35_0/1 99287 594 0.981481 strain 99287:160 +1 NC_003197.2_36_0/1 99287 594 0.962963 strain 99287:176 +1 NC_003197.2_37_0/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_38_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_39_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_40_0/1 99287 594 0.952862 strain 99287:168 +1 NC_003197.2_41_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_42_0/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_43_0/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_44_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_45_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_46_0/1 99287 594 0.995791 strain 99287:184 +1 NC_003197.2_47_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_48_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_49_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_50_0/1 99287 594 0.999158 strain 99287:184 +1 NC_003197.2_51_0/1 99287 594 0.957912 strain 99287:169 +1 NC_003197.2_52_0/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_53_0/1 99287 594 0.99495 strain 99287:183 +1 NC_003197.2_54_0/1 99287 594 0.959596 strain 99287:163 +1 NC_003197.2_55_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_56_0/1 99287 594 0.842593 strain 99287:149 +1 NC_003197.2_57_0/1 99287 594 0.951178 strain 99287:161 +1 NC_003197.2_58_0/1 99287 594 0.979798 strain 99287:159 +1 NC_003197.2_59_0/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_60_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_61_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_62_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_63_0/1 99287 594 0.974747 strain 99287:179 +1 NC_003197.2_64_0/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_65_0/1 99287 594 0.940236 strain 99287:160 +1 NC_003197.2_66_0/1 99287 594 0.936869 strain 99287:158 +1 NC_003197.2_67_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_68_0/1 99287 594 0.994108 strain 99287:176 +1 NC_003197.2_69_0/1 99287 594 0.982323 strain 99287:160 +1 NC_003197.2_70_0/1 99287 594 0.893939 strain 99287:136 +1 NC_003197.2_71_0/1 99287 594 0.996633 strain 99287:181 +1 NC_003197.2_72_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_73_0/1 99287 594 0.973906 strain 99287:172 +1 NC_003197.2_74_0/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_75_0/1 99287 594 0.962121 strain 99287:170 +1 NC_003197.2_76_0/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_77_0/1 99287 594 0.939394 strain 99287:168 +1 NC_003197.2_78_0/1 99287 594 0.893939 strain 99287:152 +1 NC_003197.2_79_0/1 99287 594 0.989899 strain 99287:182 +1 NC_003197.2_80_0/1 99287 594 0.986532 strain 99287:168 +1 NC_003197.2_81_0/1 99287 594 0.944444 strain 99287:173 +1 NC_003197.2_82_0/1 99287 594 0.990741 strain 99287:176 +1 NC_003197.2_83_0/1 99287 594 0.96633 strain 99287:177 +1 NC_003197.2_84_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_85_0/1 99287 594 1 strain 99287:183 +1 NC_003197.2_86_0/1 99287 594 0.898148 strain 99287:160 +1 NC_003197.2_87_0/1 99287 594 0.878788 strain 99287:153 +1 NC_003197.2_88_0/1 99287 594 0.974747 strain 99287:158 +1 NC_003197.2_89_0/1 99287 594 0.990741 strain 99287:183 +1 NC_003197.2_90_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_91_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_92_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_93_0/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_94_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_95_0/1 99287 594 0.967172 strain 99287:172 +1 NC_003197.2_96_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_97_0/1 99287 594 0.982323 strain 99287:160 +1 NC_003197.2_98_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_99_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_100_0/1 99287 594 0.973064 strain 99287:173 +1 NC_003197.2_101_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_102_0/1 99287 594 0.928451 strain 99287:152 +1 NC_003197.2_103_0/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_104_0/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_105_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_106_0/1 99287 594 0.957071 strain 99287:169 +1 NC_003197.2_107_0/1 99287 594 0.98569 strain 99287:168 +1 NC_003197.2_108_0/1 99287 594 0.949495 strain 99287:140 +1 NC_003197.2_109_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_110_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_111_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_112_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_113_0/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_114_0/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_115_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_116_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_117_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_118_0/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_119_0/1 99287 594 0.99495 strain 99287:184 +1 NC_003197.2_120_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_121_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_122_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_123_0/1 99287 594 0.99495 strain 99287:184 +1 NC_003197.2_124_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_125_0/1 99287 594 0.793771 strain 99287:134 +1 NC_003197.2_126_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_127_0/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_128_0/1 99287 594 0.878788 strain 99287:153 +1 NC_003197.2_129_0/1 99287 594 0.909091 strain 99287:162 +1 NC_003197.2_130_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_131_0/1 99287 594 0.957071 strain 99287:162 +1 NC_003197.2_132_0/1 99287 594 0.957071 strain 99287:176 +1 NC_003197.2_133_0/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_134_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_135_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_136_0/1 99287 594 0.968013 strain 99287:165 +1 NC_003197.2_137_0/1 99287 594 0.993266 strain 99287:184 +1 NC_003197.2_138_0/1 99287 594 0.929293 strain 99287:165 +1 NC_003197.2_139_0/1 99287 594 0.96633 strain 99287:170 +1 NC_003197.2_140_0/1 99287 594 0.90404 strain 99287:154 +1 NC_003197.2_141_0/1 99287 594 0.984848 strain 99287:168 +1 NC_003197.2_142_0/1 99287 594 0.974747 strain 99287:172 +1 NC_003197.2_143_0/1 99287 594 0.776094 strain 99287:121 +1 NC_003197.2_144_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_145_0/1 99287 594 0.993266 strain 99287:168 +1 NC_003197.2_146_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_147_0/1 99287 594 0.961279 strain 99287:171 +1 NC_003197.2_148_0/1 99287 594 0.893939 strain 99287:142 +1 NC_003197.2_149_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_150_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_151_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_152_0/1 99287 594 0.964646 strain 99287:163 +1 NC_003197.2_153_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_154_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_155_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_156_0/1 99287 594 0.936869 strain 99287:165 +1 NC_003197.2_157_0/1 99287 594 0.957912 strain 99287:168 +1 NC_003197.2_158_0/1 99287 594 0.969697 strain 99287:171 +1 NC_003197.2_159_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_160_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_161_0/1 99287 594 0.989057 strain 99287:176 +1 NC_003197.2_162_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_163_0/1 99287 594 0.981481 strain 99287:181 +1 NC_003197.2_164_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_165_0/1 99287 594 0.959596 strain 99287:155 +1 NC_003197.2_166_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_167_0/1 99287 594 0.939394 strain 99287:168 +1 NC_003197.2_168_0/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_169_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_170_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_171_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_172_0/1 99287 594 0.979798 strain 99287:174 +1 NC_003197.2_173_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_174_0/1 99287 594 0.934343 strain 99287:176 +1 NC_003197.2_175_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_176_0/1 99287 594 0.963805 strain 99287:164 +1 NC_003197.2_177_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_178_0/1 99287 594 0.998317 strain 99287:183 +1 NC_003197.2_179_0/1 99287 594 0.944444 strain 99287:160 +1 NC_003197.2_180_0/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_181_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_182_0/1 99287 594 0.964646 strain 99287:177 +1 NC_003197.2_183_0/1 99287 594 0.848485 strain 99287:147 +1 NC_003197.2_184_0/1 99287 594 0.979798 strain 99287:173 +1 NC_003197.2_185_0/1 99287 594 0.983165 strain 99287:182 +1 NC_003197.2_186_0/1 99287 594 0.954545 strain 99287:175 +1 NC_003197.2_187_0/1 99287 594 0.96633 strain 99287:170 +1 NC_003197.2_188_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_189_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_190_0/1 99287 594 0.949495 strain 99287:167 +1 NC_003197.2_191_0/1 99287 594 0.962121 strain 99287:177 +1 NC_003197.2_192_0/1 99287 594 0.909091 strain 99287:140 +1 NC_003197.2_193_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_194_0/1 99287 594 0.911616 strain 99287:167 +1 NC_003197.2_195_0/1 99287 594 0.951178 strain 99287:168 +1 NC_003197.2_196_0/1 99287 594 0.957071 strain 99287:149 +1 NC_003197.2_197_0/1 99287 594 0.882155 strain 99287:149 +1 NC_003197.2_198_0/1 99287 594 0.987374 strain 99287:175 +1 NC_003197.2_199_0/1 99287 594 0.972222 strain 99287:179 +1 NC_003197.2_200_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_201_0/1 99287 594 0.94697 strain 99287:175 +1 NC_003197.2_202_0/1 99287 594 0.876263 strain 99287:141 +1 NC_003197.2_203_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_204_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_205_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_206_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_207_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_208_0/1 99287 594 0.929293 strain 99287:163 +1 NC_003197.2_209_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_210_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_211_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_212_0/1 99287 594 0.954545 strain 99287:155 +1 NC_003197.2_213_0/1 99287 594 0.949495 strain 99287:167 +1 NC_003197.2_214_0/1 99287 594 0.95202 strain 99287:150 +1 NC_003197.2_215_0/1 99287 594 0.93771 strain 99287:158 +1 NC_003197.2_216_0/1 99287 594 0.976431 strain 99287:173 +1 NC_003197.2_217_0/1 99287 594 0.927609 strain 99287:152 +1 NC_003197.2_218_0/1 99287 594 0.99495 strain 99287:184 +1 NC_003197.2_219_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_220_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_221_0/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_222_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_223_0/1 99287 594 0.931818 strain 99287:129 +1 NC_003197.2_224_0/1 99287 594 0.990741 strain 99287:168 +1 NC_003197.2_225_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_226_0/1 99287 594 0.893939 strain 99287:143 +1 NC_003197.2_227_0/1 99287 594 0.915825 strain 99287:149 +1 NC_003197.2_228_0/1 99287 594 0.989899 strain 99287:176 +1 NC_003197.2_229_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_230_0/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_231_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_232_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_233_0/1 99287 594 0.919192 strain 99287:149 +1 NC_003197.2_234_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_235_0/1 99287 594 0.926768 strain 99287:156 +1 NC_003197.2_236_0/1 99287 594 0.977273 strain 99287:180 +1 NC_003197.2_237_0/1 99287 594 0.984848 strain 99287:175 +1 NC_003197.2_238_0/1 99287 594 0.979798 strain 99287:173 +1 NC_003197.2_239_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_240_0/1 99287 594 0.947811 strain 99287:168 +1 NC_003197.2_241_0/1 99287 594 0.929293 strain 99287:157 +1 NC_003197.2_242_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_243_0/1 99287 594 0.93771 strain 99287:158 +1 NC_003197.2_244_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_245_0/1 99287 594 0.969697 strain 99287:165 +1 NC_003197.2_246_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_247_0/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_248_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_249_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_0_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_1_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_2_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_3_1/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_4_1/1 99287 594 0.93771 strain 99287:173 +1 NC_003197.2_5_1/1 99287 594 0.858586 strain 99287:151 +1 NC_003197.2_6_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_7_1/1 99287 594 0.974747 strain 99287:168 +1 NC_003197.2_8_1/1 99287 594 0.928451 strain 99287:160 +1 NC_003197.2_9_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_10_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_11_1/1 99287 594 0.911616 strain 99287:140 +1 NC_003197.2_12_1/1 99287 594 0.967172 strain 99287:178 +1 NC_003197.2_13_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_14_1/1 99287 594 0.967172 strain 99287:179 +1 NC_003197.2_15_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_16_1/1 99287 594 0.944444 strain 99287:168 +1 NC_003197.2_17_1/1 99287 594 0.995791 strain 99287:184 +1 NC_003197.2_18_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_19_1/1 99287 594 0.939394 strain 99287:174 +1 NC_003197.2_20_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_21_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_22_1/1 99287 594 0.89899 strain 99287:127 +1 NC_003197.2_23_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_24_1/1 99287 594 0.979798 strain 99287:168 +1 NC_003197.2_25_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_26_1/1 99287 594 0.944444 strain 99287:168 +1 NC_003197.2_27_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_28_1/1 99287 594 0.753367 strain 99287:126 +1 NC_003197.2_29_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_30_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_31_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_32_1/1 99287 594 0.961279 strain 99287:176 +1 NC_003197.2_33_1/1 99287 594 0.974747 strain 99287:165 +1 NC_003197.2_34_1/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_35_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_36_1/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_37_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_38_1/1 99287 594 0.944444 strain 99287:166 +1 NC_003197.2_39_1/1 99287 594 0.95202 strain 99287:176 +1 NC_003197.2_40_1/1 99287 594 0.90404 strain 99287:160 +1 NC_003197.2_41_1/1 99287 594 0.999158 strain 99287:184 +1 NC_003197.2_42_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_43_1/1 99287 594 0.962121 strain 99287:156 +1 NC_003197.2_44_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_45_1/1 99287 594 0.989899 strain 99287:182 +1 NC_003197.2_46_1/1 99287 594 1 strain 99287:183 +1 NC_003197.2_47_1/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_48_1/1 99287 594 0.873737 strain 99287:145 +1 NC_003197.2_49_1/1 99287 594 0.974747 strain 99287:172 +1 NC_003197.2_50_1/1 99287 594 0.987374 strain 99287:176 +1 NC_003197.2_51_1/1 99287 594 0.979798 strain 99287:176 +1 NC_003197.2_52_1/1 99287 594 0.878788 strain 99287:163 +1 NC_003197.2_53_1/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_54_1/1 99287 594 0.939394 strain 99287:165 +1 NC_003197.2_55_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_56_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_57_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_58_1/1 99287 594 0.964646 strain 99287:157 +1 NC_003197.2_59_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_60_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_61_1/1 99287 594 0.954545 strain 99287:175 +1 NC_003197.2_62_1/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_63_1/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_64_1/1 99287 594 0.711279 strain 99287:116 +1 NC_003197.2_65_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_66_1/1 99287 594 0.987374 strain 99287:182 +1 NC_003197.2_67_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_68_1/1 99287 594 0.998317 strain 99287:176 +1 NC_003197.2_69_1/1 99287 594 0.956229 strain 99287:176 +1 NC_003197.2_70_1/1 99287 594 0.994108 strain 99287:176 +1 NC_003197.2_71_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_72_1/1 99287 594 0.949495 strain 99287:174 +1 NC_003197.2_73_1/1 99287 594 0.989899 strain 99287:176 +1 NC_003197.2_74_1/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_75_1/1 99287 594 0.722222 strain 99287:128 +1 NC_003197.2_76_1/1 99287 594 0.934343 strain 99287:150 +1 NC_003197.2_77_1/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_78_1/1 99287 594 0.90404 strain 99287:158 +1 NC_003197.2_79_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_80_1/1 99287 594 0.995791 strain 99287:184 +1 NC_003197.2_81_1/1 99287 594 0.961279 strain 99287:170 +1 NC_003197.2_82_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_83_1/1 99287 594 0.863636 strain 99287:152 +1 NC_003197.2_84_1/1 99287 594 0.934343 strain 99287:171 +1 NC_003197.2_85_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_86_1/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_87_1/1 99287 594 0.944444 strain 99287:176 +1 NC_003197.2_88_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_89_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_90_1/1 99287 594 0.990741 strain 99287:176 +1 NC_003197.2_91_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_92_1/1 99287 594 0.964646 strain 99287:177 +1 NC_003197.2_93_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_94_1/1 99287 594 0.969697 strain 99287:171 +1 NC_003197.2_95_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_96_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_97_1/1 99287 594 0.974747 strain 99287:168 +1 NC_003197.2_98_1/1 99287 594 0.981481 strain 99287:173 +1 NC_003197.2_99_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_100_1/1 99287 594 0.95202 strain 99287:168 +1 NC_003197.2_101_1/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_102_1/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_103_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_104_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_105_1/1 99287 594 0.912458 strain 99287:161 +1 NC_003197.2_106_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_107_1/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_108_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_109_1/1 99287 594 0.929293 strain 99287:170 +1 NC_003197.2_110_1/1 99287 594 0.810606 strain 99287:146 +1 NC_003197.2_111_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_112_1/1 99287 594 0.95202 strain 99287:168 +1 NC_003197.2_113_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_114_1/1 99287 594 0.964646 strain 99287:163 +1 NC_003197.2_115_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_116_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_117_1/1 99287 594 0.939394 strain 99287:165 +1 NC_003197.2_118_1/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_119_1/1 99287 594 0.882155 strain 99287:147 +1 NC_003197.2_120_1/1 99287 594 0.960438 strain 99287:176 +1 NC_003197.2_121_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_122_1/1 99287 594 0.969697 strain 99287:178 +1 NC_003197.2_123_1/1 99287 594 0.924242 strain 99287:135 +1 NC_003197.2_124_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_125_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_126_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_127_1/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_128_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_129_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_130_1/1 99287 594 0.967172 strain 99287:152 +1 NC_003197.2_131_1/1 99287 594 0.989899 strain 99287:169 +1 NC_003197.2_132_1/1 99287 594 0.972222 strain 99287:172 +1 NC_003197.2_133_1/1 99287 594 0.959596 strain 99287:163 +1 NC_003197.2_134_1/1 99287 594 0.992424 strain 99287:184 +1 NC_003197.2_135_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_136_1/1 99287 594 0.934343 strain 99287:157 +1 NC_003197.2_137_1/1 99287 594 0.84596 strain 99287:135 +1 NC_003197.2_138_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_139_1/1 99287 594 0.95202 strain 99287:161 +1 NC_003197.2_140_1/1 99287 594 0.991583 strain 99287:175 +1 NC_003197.2_141_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_142_1/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_143_1/1 99287 594 0.982323 strain 99287:168 +1 NC_003197.2_144_1/1 99287 594 0.977273 strain 99287:180 +1 NC_003197.2_145_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_146_1/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_147_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_148_1/1 99287 594 0.891414 strain 99287:152 +1 NC_003197.2_149_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_150_1/1 99287 594 0.941077 strain 99287:160 +1 NC_003197.2_151_1/1 99287 594 0.949495 strain 99287:160 +1 NC_003197.2_152_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_153_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_154_1/1 99287 594 0.933502 strain 99287:165 +1 NC_003197.2_155_1/1 99287 594 0.979798 strain 99287:159 +1 NC_003197.2_156_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_157_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_158_1/1 99287 594 0.934343 strain 99287:150 +1 NC_003197.2_159_1/1 99287 594 0.944444 strain 99287:174 +1 NC_003197.2_160_1/1 99287 594 0.994108 strain 99287:183 +1 NC_003197.2_161_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_162_1/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_163_1/1 99287 594 0.916667 strain 99287:156 +1 NC_003197.2_164_1/1 99287 594 0.99495 strain 99287:183 +1 NC_003197.2_165_1/1 99287 594 0.914141 strain 99287:147 +1 NC_003197.2_166_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_167_1/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_168_1/1 99287 594 0.998317 strain 99287:176 +1 NC_003197.2_169_1/1 99287 594 0.775253 strain 99287:132 +1 NC_003197.2_170_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_171_1/1 99287 594 0.772727 strain 99287:135 +1 NC_003197.2_172_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_173_1/1 99287 594 0.924242 strain 99287:171 +1 NC_003197.2_174_1/1 99287 594 0.939394 strain 99287:161 +1 NC_003197.2_175_1/1 99287 594 0.984848 strain 99287:167 +1 NC_003197.2_176_1/1 99287 594 0.895623 strain 99287:163 +1 NC_003197.2_177_1/1 99287 594 0.972222 strain 99287:172 +1 NC_003197.2_178_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_179_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_180_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_181_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_182_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_183_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_184_1/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_185_1/1 99287 594 0.974747 strain 99287:158 +1 NC_003197.2_186_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_187_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_188_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_189_1/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_190_1/1 99287 594 0.808081 strain 99287:134 +1 NC_003197.2_191_1/1 99287 594 0.958754 strain 99287:169 +1 NC_003197.2_192_1/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_193_1/1 99287 594 0.95202 strain 99287:175 +1 NC_003197.2_194_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_195_1/1 99287 594 0.991583 strain 99287:168 +1 NC_003197.2_196_1/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_197_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_198_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_199_1/1 99287 594 0.914141 strain 99287:169 +1 NC_003197.2_200_1/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_201_1/1 99287 594 0.939394 strain 99287:160 +1 NC_003197.2_202_1/1 99287 594 0.774411 strain 99287:127 +1 NC_003197.2_203_1/1 99287 594 0.964646 strain 99287:172 +1 NC_003197.2_204_1/1 99287 594 0.974747 strain 99287:179 +1 NC_003197.2_205_1/1 99287 594 0.979798 strain 99287:179 +1 NC_003197.2_206_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_207_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_208_1/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_209_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_210_1/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_211_1/1 99287 594 0.989899 strain 99287:182 +1 NC_003197.2_212_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_213_1/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_214_1/1 99287 594 0.853535 strain 99287:142 +1 NC_003197.2_215_1/1 99287 594 0.974747 strain 99287:172 +1 NC_003197.2_216_1/1 99287 594 0.992424 strain 99287:183 +1 NC_003197.2_217_1/1 99287 594 0.997475 strain 99287:180 +1 NC_003197.2_218_1/1 99287 594 0.944444 strain 99287:166 +1 NC_003197.2_219_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_220_1/1 99287 594 0.95202 strain 99287:161 +1 NC_003197.2_221_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_222_1/1 99287 594 0.967172 strain 99287:164 +1 NC_003197.2_223_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_224_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_225_1/1 99287 594 0.99495 strain 99287:183 +1 NC_003197.2_226_1/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_227_1/1 99287 594 0.944444 strain 99287:166 +1 NC_003197.2_228_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_229_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_230_1/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_231_1/1 99287 594 0.934343 strain 99287:171 +1 NC_003197.2_232_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_233_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_234_1/1 99287 594 0.90404 strain 99287:147 +1 NC_003197.2_235_1/1 99287 594 0.931818 strain 99287:176 +1 NC_003197.2_236_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_237_1/1 99287 594 0.914141 strain 99287:155 +1 NC_003197.2_238_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_239_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_240_1/1 99287 594 0.982323 strain 99287:160 +1 NC_003197.2_241_1/1 99287 594 0.992424 strain 99287:183 +1 NC_003197.2_242_1/1 99287 594 0.968855 strain 99287:171 +1 NC_003197.2_243_1/1 99287 594 0.95202 strain 99287:149 +1 NC_003197.2_244_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_245_1/1 99287 594 0.670034 strain 99287:116 +1 NC_003197.2_246_1/1 99287 594 0.972222 strain 99287:165 +1 NC_003197.2_247_1/1 99287 594 0.979798 strain 99287:173 +1 NC_003197.2_248_1/1 99287 594 0.951178 strain 99287:168 +1 NC_003197.2_249_1/1 99287 594 0.997475 strain 99287:184
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+ <script id="notfound">window.onload=function(){document.body.innerHTML=""}</script> + <script language="javascript" type="text/javascript"> +{//----------------------------------------------------------------------------- +// +// PURPOSE +// +// Krona is a flexible tool for exploring the relative proportions of +// hierarchical data, such as metagenomic classifications, using a +// radial, space-filling display. It is implemented using HTML5 and +// JavaScript, allowing charts to be explored locally or served over the +// Internet, requiring only a current version of any major web +// browser. Krona charts can be created using an Excel template or from +// common bioinformatic formats using the provided conversion scripts. +// +// +// COPYRIGHT LICENSE +// +// Copyright (c) 2011, Battelle National Biodefense Institute (BNBI); +// all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and +// Adam Phillippy +// +// This Software was prepared for the Department of Homeland Security +// (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as +// part of contract HSHQDC-07-C-00020 to manage and operate the National +// Biodefense Analysis and Countermeasures Center (NBACC), a Federally +// Funded Research and Development Center. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// * Neither the name of the Battelle National Biodefense Institute nor +// the names of its contributors may be used to endorse or promote +// products derived from this software without specific prior written +// permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +// HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// +// TRADEMARK LICENSE +// +// KRONA(TM) is a trademark of the Department of Homeland Security, and use +// of the trademark is subject to the following conditions: +// +// * Distribution of the unchanged, official code/software using the +// KRONA(TM) mark is hereby permitted by the Department of Homeland +// Security, provided that the software is distributed without charge +// and modification. +// +// * Distribution of altered source code/software using the KRONA(TM) mark +// is not permitted unless written permission has been granted by the +// Department of Homeland Security. +// +// +// FOR MORE INFORMATION VISIT +// +// https://github.com/marbl/Krona/wiki/ +// +//----------------------------------------------------------------------------- +} + + +var canvas; +var context; +var svg; // for snapshot mode +var collapse = true; +var collapseCheckBox; +var collapseLast; +var compress; +var compressCheckBox; +var maxAbsoluteDepthText; +var maxAbsoluteDepthButtonDecrease; +var maxAbsoluteDepthButtonIncrease; +var fontSize = 11; +var fontSizeText; +var fontSizeButtonDecrease; +var fontSizeButtonIncrease; +var fontSizeLast; +var radiusButtonDecrease; +var radiusButtonIncrease; +var shorten; +var shortenCheckBox; +var maxAbsoluteDepth; +var backButton; +var upButton; +var forwardButton; +var snapshotButton; +var snapshotMode = false; +var details; +var detailsName; +var search; +var searchResults; +var nSearchResults; +var useHueCheckBox; +var useHueDiv; +var datasetDropDown; +var datasetButtonLast; +var datasetButtonPrev; +var datasetButtonNext; +var keyControl; +var showKeys = true; +var linkButton; +var linkText; +var frame; + +// Node references. Note that the meanings of 'selected' and 'focused' are +// swapped in the docs. +// +var head; // the root of the entire tree +var selectedNode = 0; // the root of the current view +var focusNode = 0; // a node chosen for more info (single-click) +var highlightedNode = 0; // mouse hover node +var highlightingHidden = false; +var nodes = new Array(); +var currentNodeID = 0; // to iterate while loading + +var nodeHistory = new Array(); +var nodeHistoryPosition = 0; + +var dataEnabled = false; // true when supplemental files are present + +// store non-Krona GET variables so they can be passed on to links +// +var getVariables = new Array(); + +// selectedNodeLast is separate from the history, since we need to check +// properties of the last node viewed when browsing through the history +// +var selectedNodeLast = 0; +var zoomOut = false; + +// temporary zoom-in while holding the mouse button on a wedge +// +var quickLook = false; // true when in quick look state +var mouseDown = false; +var mouseDownTime; // to detect mouse button hold +var quickLookHoldLength = 200; + +var imageWidth; +var imageHeight; +var centerX; +var centerY; +var gRadius; +var updateViewNeeded = false; + +// Determines the angle that the pie chart starts at. 90 degrees makes the +// center label consistent with the children. +// +var rotationOffset = Math.PI / 2; + +var buffer; +var bufferFactor = .1; + +// The maps are the small pie charts showing the current slice being viewed. +// +var mapBuffer = 10; +var mapRadius = 0; +var maxMapRadius = 25; +var mapWidth = 150; +var maxLabelOverhang = Math.PI * 4.18; + +// Keys are the labeled boxes for slices in the highest level that are too thin +// to label. +// +var maxKeySizeFactor = 2; // will be multiplied by font size +var keySize; +var keys; +var keyBuffer = 10; +var currentKey; +var keyMinTextLeft; +var keyMinAngle; + +var minRingWidthFactor = 5; // will be multiplied by font size +var maxPossibleDepth; // the theoretical max that can be displayed +var maxDisplayDepth; // the actual depth that will be displayed +var headerHeight = 0;//document.getElementById('options').clientHeight; +var historySpacingFactor = 1.6; // will be multiplied by font size +var historyAlphaDelta = .25; + +// appearance +// +var lineOpacity = 0.3; +var saturation = 0.5; +var lightnessBase = 0.6; +var lightnessMax = .8; +var thinLineWidth = .3; +var highlightLineWidth = 1.5; +var labelBoxBuffer = 6; +var labelBoxRounding = 15; +var labelWidthFudge = 1.05; // The width of unshortened labels are set slightly + // longer than the name width so the animation + // finishes faster. +var fontNormal; +var fontBold; +var fontFamily = 'sans-serif'; +//var fontFaceBold = 'bold Arial'; +var nodeRadius; +var angleFactor; +var tickLength; +var compressedRadii; + +// colors +// +var highlightFill = 'rgba(255, 255, 255, .3)'; +var colorUnclassified = 'rgb(220,220,220)'; + +// label staggering +// +var labelOffsets; // will store the current offset at each depth +// +// This will store pointers to the last node that had a label in each offset (or "track") of a +// each depth. These will be used to shorten neighboring labels that would overlap. +// The [nLabelNodes] index will store the last node with a radial label. +// labelFirstNodes is the same, but to check for going all the way around and +// overlapping the first labels. +// +var labelLastNodes; +var labelFirstNodes; +// +var nLabelOffsets = 3; // the number of offsets to use + +var mouseX = -1; +var mouseY = -1; +var mouseXRel = -1; +var mouseYRel = -1; + +// tweening +// +var progress = 0; // for tweening; goes from 0 to 1. +var progressLast = 0; +var tweenFactor = 0; // progress converted by a curve for a smoother effect. +var tweenLength = 850; // in ms +var tweenCurvature = 13; +// +// tweenMax is used to scale the sigmoid function so its range is [0,1] for the +// domain [0,1] +// +var tweenMax = 1 / (1 + Math.exp(-tweenCurvature / 2)); +// +var tweenStartTime; + +// for framerate debug +// +var tweenFrames = 0; +var fpsDisplay = document.getElementById('frameRate'); + +// Arrays to translate xml attribute names into displayable attribute names +// +var attributes = new Array(); +// +var magnitudeIndex; // the index of attribute arrays used for magnitude +var membersAssignedIndex; +var membersSummaryIndex; + +// For defining gradients +// +var hueDisplayName; +var hueStopPositions; +var hueStopHues; +var hueStopText; + +// multiple datasets +// +var currentDataset = 0; +var lastDataset = 0; +var datasets = 1; +var datasetNames; +var datasetSelectSize = 30; +var datasetAlpha = new Tween(0, 0); +var datasetWidths = new Array(); +var datasetChanged; +var datasetSelectWidth = 50; + +window.onload = load; + +var image; +var hiddenPattern; +var loadingImage; +var logoImage; + +function backingScale() +{ + if ('devicePixelRatio' in window) + { + if (window.devicePixelRatio > 1) + { + return window.devicePixelRatio; + } + } + + return 1; +} + +function resize() +{ + imageWidth = window.innerWidth; + imageHeight = window.innerHeight; + + if ( ! snapshotMode ) + { + context.canvas.width = imageWidth * backingScale(); + context.canvas.height = imageHeight * backingScale(); + context.canvas.style.width = imageWidth + "px" + context.canvas.style.height = imageHeight + "px" + context.scale(backingScale(), backingScale()); + } + + if ( datasetDropDown ) + { + var ratio = + (datasetDropDown.offsetTop + datasetDropDown.clientHeight) * 2 / + imageHeight; + + if ( ratio > 1 ) + { + ratio = 1; + } + + ratio = Math.sqrt(ratio); + + datasetSelectWidth = + (datasetDropDown.offsetLeft + datasetDropDown.clientWidth) * ratio; + } + var leftMargin = datasets > 1 ? datasetSelectWidth + 30 : 0; + var minDimension = imageWidth - mapWidth - leftMargin > imageHeight ? + imageHeight : + imageWidth - mapWidth - leftMargin; + + maxMapRadius = minDimension * .03; + buffer = minDimension * bufferFactor; + margin = minDimension * .015; + centerX = (imageWidth - mapWidth - leftMargin) / 2 + leftMargin; + centerY = imageHeight / 2; + gRadius = minDimension / 2 - buffer; + //context.font = '11px sans-serif'; +} + +function handleResize() +{ + updateViewNeeded = true; +} + +function Attribute() +{ +} + +function Tween(start, end) +{ + this.start = start; + this.end = end; + this.current = this.start; + + this.current = function() + { + if ( progress == 1 || this.start == this.end ) + { + return this.end; + } + else + { + return this.start + tweenFactor * (this.end - this.start); + } + }; + + this.setTarget = function(target) + { + this.start = this.current(); + this.end = target; + } +} + +function Node() +{ + this.id = currentNodeID; + currentNodeID++; + nodes[this.id] = this; + + this.angleStart = new Tween(Math.PI, 0); + this.angleEnd = new Tween(Math.PI, 0); + this.radiusInner = new Tween(1, 1); + this.labelRadius = new Tween(1, 1); + this.labelWidth = new Tween(0, 0); + this.scale = new Tween(1, 1); // TEMP + this.radiusOuter = new Tween(1, 1); + + this.r = new Tween(255, 255); + this.g = new Tween(255, 255); + this.b = new Tween(255, 255); + + this.alphaLabel = new Tween(0, 1); + this.alphaLine = new Tween(0, 1); + this.alphaArc = new Tween(0, 0); + this.alphaWedge = new Tween(0, 1); + this.alphaOther = new Tween(0, 1); + this.alphaPattern = new Tween(0, 0); + this.children = Array(); + this.parent = 0; + + this.attributes = new Array(attributes.length); + + this.addChild = function(child) + { + this.children.push(child); + }; + + this.addLabelNode = function(depth, labelOffset) + { + if ( labelHeadNodes[depth][labelOffset] == 0 ) + { + // this will become the head node for this list + + labelHeadNodes[depth][labelOffset] = this; + this.labelPrev = this; + } + + var head = labelHeadNodes[depth][labelOffset]; + + this.labelNext = head; + this.labelPrev = head.labelPrev; + head.labelPrev.labelNext = this; + head.labelPrev = this; + } + + this.canDisplayDepth = function() + { + // whether this node is at a depth that can be displayed, according + // to the max absolute depth + + return this.depth <= maxAbsoluteDepth; + } + + this.canDisplayHistory = function() + { + var radiusInner; + + if ( compress ) + { + radiusInner = compressedRadii[0]; + } + else + { + radiusInner = nodeRadius; + } + + return ( + -this.labelRadius.end * gRadius + + historySpacingFactor * fontSize / 2 < + radiusInner * gRadius + ); + } + + this.canDisplayLabelCurrent = function() + { + return ( + (this.angleEnd.current() - this.angleStart.current()) * + (this.radiusInner.current() * gRadius + gRadius) >= + minWidth()); + } + + this.checkHighlight = function() + { + if ( this.children.length == 0 && this == focusNode ) + { + //return false; + } + + if ( this.hide ) + { + return false; + } + + if ( this.radiusInner.end == 1 ) + { + // compressed to the outside; don't check + + return false; + } + + var highlighted = false; + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + for ( var i = 0; i < this.children.length; i++ ) + { + highlighted = this.children[i].checkHighlight(); + + if ( highlighted ) + { + return true; + } + } + + if ( this.radial ) + { + var angleText = (angleStartCurrent + angleEndCurrent) / 2; + var radiusText = (gRadius + radiusInner) / 2; + + context.rotate(angleText); + context.beginPath(); + context.moveTo(radiusText, -fontSize); + context.lineTo(radiusText, fontSize); + context.lineTo(radiusText + centerX, fontSize); + context.lineTo(radiusText + centerX, -fontSize); + context.closePath(); + context.rotate(-angleText); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(this.getPercentage()) + '%' + ' ' + this.name; + + if ( this.searchResultChildren() ) + { + label += searchResultString(this.searchResultChildren()); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + radiusText + measureText(label) + ) + { + highlighted = true; + } + } + } + else + { + for ( var i = 0; i < this.hiddenLabels.length; i++ ) + { + var hiddenLabel = this.hiddenLabels[i]; + + context.rotate(hiddenLabel.angle); + context.beginPath(); + context.moveTo(gRadius, -fontSize); + context.lineTo(gRadius, fontSize); + context.lineTo(gRadius + centerX, fontSize); + context.lineTo(gRadius + centerX, -fontSize); + context.closePath(); + context.rotate(-hiddenLabel.angle); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + var label = String(hiddenLabel.value) + ' more'; + + if ( hiddenLabel.search ) + { + label += searchResultString(hiddenLabel.search); + } + + if + ( + Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < + gRadius + fontSize + measureText(label) + ) + { + highlighted = true; + break; + } + } + } + } + + if ( ! highlighted && this != selectedNode && ! this.getCollapse() ) + { + context.beginPath(); + context.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false); + context.arc(0, 0, gRadius, angleEndCurrent, angleStartCurrent, true); + context.closePath(); + + if ( context.isPointInPath(mouseXRel, mouseYRel) ) + { + highlighted = true; + } + + if + ( + ! highlighted && + (angleEndCurrent - angleStartCurrent) * + (radiusInner + gRadius) < + minWidth() && + this.getDepth() == selectedNode.getDepth() + 1 + ) + { + if ( showKeys && this.checkHighlightKey() ) + { + highlighted = true; + } + } + } + + if ( highlighted ) + { + if ( this != highlightedNode ) + { + // document.body.style.cursor='pointer'; + } + + highlightedNode = this; + } + + return highlighted; + } + + this.checkHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + var cx = centerX; + var cy = centerY - this.labelRadius.end * gRadius; + //var dim = context.measureText(this.name); + + var width = this.nameWidth; + + if ( this.searchResultChildren() ) + { + var results = searchResultString(this.searchResultChildren()); + var dim = context.measureText(results); + width += dim.width; + } + + if + ( + mouseX > cx - width / 2 && + mouseX < cx + width / 2 && + mouseY > cy - historySpacingFactor * fontSize / 2 && + mouseY < cy + historySpacingFactor * fontSize / 2 + ) + { + highlightedNode = this; + return; + } + + if ( this.getParent() ) + { + this.getParent().checkHighlightCenter(); + } + } + + this.checkHighlightKey = function() + { + var offset = keyOffset(); + + var xMin = imageWidth - keySize - margin - this.keyNameWidth - keyBuffer; + var xMax = imageWidth - margin; + var yMin = offset; + var yMax = offset + keySize; + + currentKey++; + + return ( + mouseX > xMin && + mouseX < xMax && + mouseY > yMin && + mouseY < yMax); + } + + this.checkHighlightMap = function() + { + if ( this.parent ) + { + this.parent.checkHighlightMap(); + } + + if ( this.getCollapse() || this == focusNode ) + { + return; + } + + var box = this.getMapPosition(); + + if + ( + mouseX > box.x - mapRadius && + mouseX < box.x + mapRadius && + mouseY > box.y - mapRadius && + mouseY < box.y + mapRadius + ) + { + highlightedNode = this; + } + } + +/* this.collapse = function() + { + for (var i = 0; i < this.children.length; i++ ) + { + this.children[i] = this.children[i].collapse(); + } + + if + ( + this.children.length == 1 && + this.children[0].magnitude == this.magnitude + ) + { + this.children[0].parent = this.parent; + this.children[0].getDepth() = this.parent.getDepth() + 1; + return this.children[0]; + } + else + { + return this; + } + } +*/ + this.draw = function(labelMode, selected, searchHighlighted) + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; +// var hidden = false; + + if ( selectedNode == this ) + { + selected = true; + } + + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + var canDisplayLabelCurrent = this.canDisplayLabelCurrent(); + var hiddenSearchResults = false; + +/* if ( ! this.hide ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.children[i].hide && this.children[i].searchResults ) + { + hiddenSearchResults = true; + } + } + } +*/ + var drawChildren = + ( ! this.hide || ! this.hidePrev && progress < 1 ) && + ( ! this.hideAlone || ! this.hideAlonePrev && progress < 1 ); + +// if ( this.alphaWedge.current() > 0 || this.alphaLabel.current() > 0 ) + { + var lastChildAngleEnd = angleStartCurrent; + + if ( this.hasChildren() )//canDisplayChildren ) + { + lastChildAngleEnd = + this.children[this.children.length - 1].angleEnd.current() + + rotationOffset; + } + + if ( labelMode ) + { + var drawRadial = + !( + this.parent && + this.parent != selectedNode && + angleEndCurrent == this.parent.angleEnd.current() + rotationOffset + ); + + //if ( angleStartCurrent != angleEndCurrent ) + { + this.drawLines(angleStartCurrent, angleEndCurrent, radiusInner, drawRadial, selected); + } + + var alphaOtherCurrent = this.alphaOther.current(); + var childRadiusInner; + + if ( this == selectedNode || alphaOtherCurrent ) + { + childRadiusInner = + this.children.length ? + this.children[this.children.length - 1].radiusInner.current() * gRadius + : radiusInner + } + + if ( this == selectedNode ) + { + this.drawReferenceRings(childRadiusInner); + } + + if + ( + selected && + ! searchHighlighted && + this != selectedNode && + ( + this.isSearchResult || + this.hideAlone && this.searchResultChildren() || + false +// this.hide && +// this.containsSearchResult + ) + ) + { + context.globalAlpha = this.alphaWedge.current(); + + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + + if + ( + this.keyed && + ! showKeys && + this.searchResults && + ! searchHighlighted && + this != highlightedNode && + this != focusNode + ) + { + var angle = (angleEndCurrent + angleStartCurrent) / 2; + this.drawLabel(angle, true, false, true, true); + } + + //this.drawHighlight(false); + searchHighlighted = true; + } + + if + ( + this == selectedNode || +// true + //(canDisplayLabelCurrent) && + this != highlightedNode && + this != focusNode + ) + { + if ( this.radial != this.radialPrev && this.alphaLabel.end == 1 ) + { + context.globalAlpha = tweenFactor; + } + else + { + context.globalAlpha = this.alphaLabel.current(); + } + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + this.hideAlone && this.searchResultChildren() || + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNode && ! this.radial, + selected, + this.radial + ); + + if ( this.radial != this.radialPrev && this.alphaLabel.start == 1 && progress < 1 ) + { + context.globalAlpha = 1 - tweenFactor; + + this.drawLabel + ( + (angleStartCurrent + angleEndCurrent) / 2, + (this.isSearchResult || hiddenSearchResults) && selected, + this == selectedNodeLast && ! this.radialPrev, + selected, + this.radialPrev + ); + } + } + + if + ( + alphaOtherCurrent && + lastChildAngleEnd != null + ) + { + if + ( + (angleEndCurrent - lastChildAngleEnd) * + (childRadiusInner + gRadius) >= + minWidth() + ) + { + //context.font = fontNormal; + context.globalAlpha = this.alphaOther.current(); + + drawTextPolar + ( + this.getUnclassifiedText(), + this.getUnclassifiedPercentage(), + (lastChildAngleEnd + angleEndCurrent) / 2, + (childRadiusInner + gRadius) / 2, + true, + false, + false, + 0, + 0 + ); + } + } + + if ( this == selectedNode && this.keyUnclassified && showKeys ) + { + this.drawKey + ( + (lastChildAngleEnd + angleEndCurrent) / 2, + false, + false + ); + } + } + else + { + var alphaWedgeCurrent = this.alphaWedge.current(); + + if ( alphaWedgeCurrent || this.alphaOther.current() ) + { + var currentR = this.r.current(); + var currentG = this.g.current(); + var currentB = this.b.current(); + + var fill = rgbText(currentR, currentG, currentB); + + var radiusOuter; + var lastChildAngle; + var truncateWedge = + ( + (this.hasChildren() || this == selectedNode ) && + ! this.keyed && + (compress || depth < maxDisplayDepth) && + drawChildren + ); + + if ( truncateWedge ) + { + radiusOuter = this.children.length ? this.children[0].radiusInner.current() * gRadius : radiusInner; + } + else + { + radiusOuter = gRadius; + } + /* + if ( this.hasChildren() ) + { + radiusOuter = this.children[0].getUncollapsed().radiusInner.current() * gRadius + 1; + } + else + { // TEMP + radiusOuter = radiusInner + nodeRadius * gRadius; + + if ( radiusOuter > gRadius ) + { + radiusOuter = gRadius; + } + } + */ + context.globalAlpha = alphaWedgeCurrent; + + if ( radiusInner != radiusOuter || truncateWedge ) + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + radiusOuter,//this.radiusOuter.current() * gRadius, + //'rgba(0, 200, 0, .1)', + fill, + this.alphaPattern.current() + ); + + if ( truncateWedge ) + { + // fill in the extra space if the sum of our childrens' + // magnitudes is less than ours + + if ( lastChildAngleEnd < angleEndCurrent )//&& false) // TEMP + { + if ( radiusOuter > 1 ) + { + // overlap slightly to hide the seam + + // radiusOuter -= 1; + } + + if ( alphaWedgeCurrent < 1 ) + { + context.globalAlpha = this.alphaOther.current(); + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius, + colorUnclassified, + 0 + ); + context.globalAlpha = alphaWedgeCurrent; + } + + drawWedge + ( + lastChildAngleEnd, + angleEndCurrent, + radiusOuter, + gRadius,//this.radiusOuter.current() * gRadius, + //'rgba(200, 0, 0, .1)', + fill, + this.alphaPattern.current() + ); + } + } + + if ( radiusOuter < gRadius ) + { + // patch up the seam + // + context.beginPath(); + context.arc(0, 0, radiusOuter, angleStartCurrent/*lastChildAngleEnd*/, angleEndCurrent, false); + context.strokeStyle = fill; + context.lineWidth = 1; + context.stroke(); + } + } + + if ( this.keyed && selected && showKeys )//&& progress == 1 ) + { + this.drawKey + ( + (angleStartCurrent + angleEndCurrent) / 2, + ( + this == highlightedNode || + this == focusNode || + this.searchResults + ), + this == highlightedNode || this == focusNode + ); + } + } + } + } + + this.hiddenLabels = Array(); + + if ( drawChildren ) + { + // draw children + // + for ( var i = 0; i < this.children.length; i++ ) + { + if ( this.drawHiddenChildren(i, selected, labelMode, searchHighlighted) ) + { + i = this.children[i].hiddenEnd; + } + else + { + this.children[i].draw(labelMode, selected, searchHighlighted); + } + } + } + }; + + this.drawHiddenChildren = function + ( + firstHiddenChild, + selected, + labelMode, + searchHighlighted + ) + { + var firstChild = this.children[firstHiddenChild]; + + if ( firstChild.hiddenEnd == null || firstChild.radiusInner.current() == 1 ) + { + return false; + } + + for ( var i = firstHiddenChild; i < firstChild.hiddenEnd; i++ ) + { + if ( ! this.children[i].hide || ! this.children[i].hidePrev && progress < 1 ) + { + return false; + } + } + + var angleStart = firstChild.angleStart.current() + rotationOffset; + var lastChild = this.children[firstChild.hiddenEnd]; + var angleEnd = lastChild.angleEnd.current() + rotationOffset; + var radiusInner = gRadius * firstChild.radiusInner.current(); + var hiddenChildren = firstChild.hiddenEnd - firstHiddenChild + 1; + + if ( labelMode ) + { + var hiddenSearchResults = 0; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + hiddenSearchResults += this.children[i].searchResults; + + if ( this.children[i].magnitude == 0 ) + { + hiddenChildren--; + } + } + + if + ( + selected && + (angleEnd - angleStart) * + (gRadius + gRadius) >= + minWidth() || + this == highlightedNode && + hiddenChildren || + hiddenSearchResults + ) + { + context.globalAlpha = this.alphaWedge.current(); + + this.drawHiddenLabel + ( + angleStart, + angleEnd, + hiddenChildren, + hiddenSearchResults + ); + } + } + + var drawWedges = true; + + for ( var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++ ) + { + // all hidden children must be completely hidden to draw together + + if ( this.children[i].alphaPattern.current() != this.children[i].alphaWedge.current() ) + { + drawWedges = false; + break; + } + } + + if ( labelMode ) + { + if ( drawWedges ) + { + var drawRadial = (angleEnd < this.angleEnd.current() + rotationOffset); + this.drawLines(angleStart, angleEnd, radiusInner, drawRadial); + } + + if ( hiddenSearchResults && ! searchHighlighted ) + { + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + highlightFill, + 0, + true + ); + } + } + else if ( drawWedges ) + { + context.globalAlpha = this.alphaWedge.current(); + + var fill = rgbText + ( + firstChild.r.current(), + firstChild.g.current(), + firstChild.b.current() + ); + + drawWedge + ( + angleStart, + angleEnd, + radiusInner, + gRadius,//this.radiusOuter.current() * gRadius, + fill, + context.globalAlpha, + false + ); + } + + return drawWedges; + } + + this.drawHiddenLabel = function(angleStart, angleEnd, value, hiddenSearchResults) + { + var textAngle = (angleStart + angleEnd) / 2; + var labelRadius = gRadius + fontSize;//(radiusInner + radius) / 2; + + var hiddenLabel = Array(); + + hiddenLabel.value = value; + hiddenLabel.angle = textAngle; + hiddenLabel.search = hiddenSearchResults; + + this.hiddenLabels.push(hiddenLabel); + + drawTick(gRadius - fontSize * .75, fontSize * 1.5, textAngle); + drawTextPolar + ( + value.toString() + ' more', + 0, // inner text + textAngle, + labelRadius, + true, // radial + hiddenSearchResults, // bubble + this == highlightedNode || this == focusNode, // bold + false, + hiddenSearchResults + ); + } + + this.drawHighlight = function(bold) + { + var angleStartCurrent = this.angleStart.current() + rotationOffset; + var angleEndCurrent = this.angleEnd.current() + rotationOffset; + var radiusInner = this.radiusInner.current() * gRadius; + + //this.setHighlightStyle(); + + if ( this == focusNode && this == highlightedNode && this.hasChildren() ) + { +// context.fillStyle = "rgba(255, 255, 255, .3)"; + arrow + ( + angleStartCurrent, + angleEndCurrent, + radiusInner + ); + } + else + { + drawWedge + ( + angleStartCurrent, + angleEndCurrent, + radiusInner, + gRadius, + highlightFill, + 0, + true + ); + } + + // check if hidden children should be highlighted + // + for ( var i = 0; i < this.children.length; i++ ) + { + if + ( + this.children[i].getDepth() - selectedNode.getDepth() + 1 <= + maxDisplayDepth && + this.children[i].hiddenEnd != null + ) + { + var firstChild = this.children[i]; + var lastChild = this.children[firstChild.hiddenEnd]; + var hiddenAngleStart = firstChild.angleStart.current() + rotationOffset; + var hiddenAngleEnd = lastChild.angleEnd.current() + rotationOffset; + var hiddenRadiusInner = gRadius * firstChild.radiusInner.current(); + + drawWedge + ( + hiddenAngleStart, + hiddenAngleEnd, + hiddenRadiusInner, + gRadius, + 'rgba(255, 255, 255, .3)', + 0, + true + ); + + if ( false && ! this.searchResults ) + { + this.drawHiddenLabel + ( + hiddenAngleStart, + hiddenAngleEnd, + firstChild.hiddenEnd - i + 1 + ); + } + + i = firstChild.hiddenEnd; + } + } + +// context.strokeStyle = 'black'; + context.fillStyle = 'black'; + + var highlight = ! ( progress < 1 && zoomOut && this == selectedNodeLast ); + + var angle = (angleEndCurrent + angleStartCurrent) / 2; + + if ( ! (this.keyed && showKeys) ) + { + this.drawLabel(angle, true, bold, true, this.radial); + } + } + + this.drawHighlightCenter = function() + { + if ( ! this.canDisplayHistory() ) + { + return; + } + + context.lineWidth = highlightLineWidth; + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .6)"; + + context.fillStyle = 'black'; + this.drawLabel(3 * Math.PI / 2, true, true, false); + context.font = fontNormal; + } + + this.drawKey = function(angle, highlight, bold) + { + var offset = keyOffset(); + var color; + var colorText = this.magnitude == 0 ? 'gray' : 'black'; + var patternAlpha = this.alphaPattern.end; + var boxLeft = imageWidth - keySize - margin; + var textY = offset + keySize / 2; + + var label; + var keyNameWidth; + + if ( this == selectedNode ) + { + color = colorUnclassified; + label = + this.getUnclassifiedText() + + ' ' + + this.getUnclassifiedPercentage(); + keyNameWidth = measureText(label, false); + } + else + { + label = this.keyLabel; + color = rgbText(this.r.end, this.g.end, this.b.end); + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + label = label + searchResultString(this.searchResultChildren()); + } + + keyNameWidth = measureText(label, bold); + } + else + { + keyNameWidth = this.keyNameWidth; + } + } + + var textLeft = boxLeft - keyBuffer - keyNameWidth - fontSize / 2; + var labelLeft = textLeft; + + if ( labelLeft > keyMinTextLeft - fontSize / 2 ) + { + keyMinTextLeft -= fontSize / 2; + + if ( keyMinTextLeft < centerX - gRadius + fontSize / 2 ) + { + keyMinTextLeft = centerX - gRadius + fontSize / 2; + } + + labelLeft = keyMinTextLeft; + } + + var lineX = new Array(); + var lineY = new Array(); + + var bendRadius; + var keyAngle = Math.atan((textY - centerY) / (labelLeft - centerX)); + var arcAngle; + + if ( keyAngle < 0 ) + { + keyAngle += Math.PI; + } + + if ( keyMinAngle == 0 || angle < keyMinAngle ) + { + keyMinAngle = angle; + } + + if ( angle > Math.PI && keyMinAngle > Math.PI ) + { + // allow lines to come underneath the chart + + angle -= Math.PI * 2; + } + + lineX.push(Math.cos(angle) * gRadius); + lineY.push(Math.sin(angle) * gRadius); + + if ( angle < keyAngle && textY > centerY + Math.sin(angle) * (gRadius + buffer * (currentKey - 1) / (keys + 1) / 2 + buffer / 2) ) + { + bendRadius = gRadius + buffer - buffer * currentKey / (keys + 1) / 2; + } + else + { + bendRadius = gRadius + buffer * currentKey / (keys + 1) / 2 + buffer / 2; + } + + var outside = + Math.sqrt + ( + Math.pow(labelLeft - centerX, 2) + + Math.pow(textY - centerY, 2) + ) > bendRadius; + + if ( ! outside ) + { + arcAngle = Math.asin((textY - centerY) / bendRadius); + + keyMinTextLeft = min(keyMinTextLeft, centerX + bendRadius * Math.cos(arcAngle) - fontSize / 2); + + if ( labelLeft < textLeft && textLeft > centerX + bendRadius * Math.cos(arcAngle) ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + else + { + keyMinTextLeft = min(keyMinTextLeft, labelLeft - fontSize / 2); + + if ( angle < keyAngle ) + { + // flip everything over y = x + // + arcAngle = Math.PI / 2 - keyLineAngle + ( + Math.PI / 2 - angle, + Math.PI / 2 - keyAngle, + bendRadius, + textY - centerY, + labelLeft - centerX, + lineY, + lineX + ); + + } + else + { + arcAngle = keyLineAngle + ( + angle, + keyAngle, + bendRadius, + labelLeft - centerX, + textY - centerY, + lineX, + lineY + ); + } + } + + if ( labelLeft > centerX + bendRadius * Math.cos(arcAngle) || + textY > centerY + bendRadius * Math.sin(arcAngle) + .01) +// if ( outside || ) + { + lineX.push(labelLeft - centerX); + lineY.push(textY - centerY); + + if ( textLeft != labelLeft ) + { + lineX.push(textLeft - centerX); + lineY.push(textY - centerY); + } + } + + context.globalAlpha = this.alphaWedge.current(); + + if ( snapshotMode ) + { + var labelSVG; + + if ( this == selectedNode ) + { + labelSVG = + this.getUnclassifiedText() + + spacer() + + this.getUnclassifiedPercentage(); + } + else + { + labelSVG = this.name + spacer() + this.getPercentage() + '%'; + } + + svg += + '<rect fill="' + color + '" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + + if ( patternAlpha ) + { + svg += + '<rect fill="url(#hiddenPattern)" style="stroke:none" ' + + 'x="' + boxLeft + '" y="' + offset + + '" width="' + keySize + '" height="' + keySize + '"/>'; + } + + svg += + '<path class="line' + + (highlight ? ' highlight' : '') + + '" d="M ' + (lineX[0] + centerX) + ',' + + (lineY[0] + centerY); + + if ( angle != arcAngle ) + { + svg += + ' L ' + (centerX + bendRadius * Math.cos(angle)) + ',' + + (centerY + bendRadius * Math.sin(angle)) + + ' A ' + bendRadius + ',' + bendRadius + ' 0 ' + + '0,' + (angle > arcAngle ? '0' : '1') + ' ' + + (centerX + bendRadius * Math.cos(arcAngle)) + ',' + + (centerY + bendRadius * Math.sin(arcAngle)); + } + + for ( var i = 1; i < lineX.length; i++ ) + { + svg += + ' L ' + (centerX + lineX[i]) + ',' + + (centerY + lineY[i]); + } + + svg += '"/>'; + + if ( highlight ) + { + if ( this.searchResultChildren() ) + { + labelSVG = labelSVG + searchResultString(this.searchResultChildren()); + } + + drawBubbleSVG + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + svg += svgText(labelSVG, boxLeft - keyBuffer, textY, 'end', bold, colorText); + } + else + { + context.fillStyle = color; + context.translate(-centerX, -centerY); + context.strokeStyle = 'black'; + context.globalAlpha = 1;//this.alphaWedge.current(); + + context.fillRect(boxLeft, offset, keySize, keySize); + + if ( patternAlpha ) + { + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + + // make clipping box for Firefox performance + context.beginPath(); + context.moveTo(boxLeft, offset); + context.lineTo(boxLeft + keySize, offset); + context.lineTo(boxLeft + keySize, offset + keySize); + context.lineTo(boxLeft, offset + keySize); + context.closePath(); + context.save(); + context.clip(); + + context.fillRect(boxLeft, offset, keySize, keySize); + context.fillRect(boxLeft, offset, keySize, keySize); + + context.restore(); // remove clipping region + } + + if ( highlight ) + { + this.setHighlightStyle(); + context.fillRect(boxLeft, offset, keySize, keySize); + } + else + { + context.lineWidth = thinLineWidth; + } + + context.strokeRect(boxLeft, offset, keySize, keySize); + + if ( lineX.length ) + { + context.beginPath(); + context.moveTo(lineX[0] + centerX, lineY[0] + centerY); + + context.arc(centerX, centerY, bendRadius, angle, arcAngle, angle > arcAngle); + + for ( var i = 1; i < lineX.length; i++ ) + { + context.lineTo(lineX[i] + centerX, lineY[i] + centerY); + } + + context.globalAlpha = this == selectedNode ? + this.children[0].alphaWedge.current() : + this.alphaWedge.current(); + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.stroke(); + context.globalAlpha = 1; + } + + if ( highlight ) + { + drawBubbleCanvas + ( + boxLeft - keyBuffer - keyNameWidth - fontSize / 2, + textY - fontSize, + keyNameWidth + fontSize, + fontSize * 2, + fontSize, + 0 + ); + + if ( this.isSearchResult ) + { + drawSearchHighlights + ( + label, + boxLeft - keyBuffer - keyNameWidth, + textY, + 0 + ) + } + } + + drawText(label, boxLeft - keyBuffer, offset + keySize / 2, 0, 'end', bold, colorText); + + context.translate(centerX, centerY); + } + + currentKey++; + } + + this.drawLabel = function(angle, bubble, bold, selected, radial) + { + if ( context.globalAlpha == 0 ) + { + return; + } + + var innerText; + var label; + var radius; + + if ( radial ) + { + radius = (this.radiusInner.current() + 1) * gRadius / 2; + } + else + { + radius = this.labelRadius.current() * gRadius; + } + + if ( radial && (selected || bubble ) ) + { + var percentage = this.getPercentage(); + innerText = percentage + '%'; + } + + if + ( + ! radial && + this != selectedNode && + ! bubble && + ( !zoomOut || this != selectedNodeLast) + ) + { + label = this.shortenLabel(); + } + else + { + label = this.name; + } + + var flipped = drawTextPolar + ( + label, + innerText, + angle, + radius, + radial, + bubble, + bold, +// this.isSearchResult && this.shouldAddSearchResultsString() && (!selected || this == selectedNode || highlight), + this.isSearchResult && (!selected || this == selectedNode || bubble), + (this.hideAlone || !selected || this == selectedNode ) ? this.searchResultChildren() : 0 + ); + + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + if + ( + ! radial && + ! bubble && + this != selectedNode && + this.angleEnd.end != this.angleStart.end && + nLabelOffsets[depth - 2] > 2 && + this.labelWidth.current() > (this.angleEnd.end - this.angleStart.end) * Math.abs(radius) && + ! ( zoomOut && this == selectedNodeLast ) && + this.labelRadius.end > 0 + ) + { + // name extends beyond wedge; draw tick mark towards the central + // radius for easier identification + + var radiusCenter = compress ? + (compressedRadii[depth - 1] + compressedRadii[depth - 2]) / 2 : + (depth - .5) * nodeRadius; + + if ( this.labelRadius.end > radiusCenter ) + { + if ( flipped ) + { + drawTick(radius - tickLength * 1.4 , tickLength, angle); + } + else + { + drawTick(radius - tickLength * 1.7, tickLength, angle); + } + } + else + { + if ( flipped ) + { + drawTick(radius + tickLength * .7, tickLength, angle); + } + else + { + drawTick(radius + tickLength * .4, tickLength, angle); + } + } + } + } + + this.drawLines = function(angleStart, angleEnd, radiusInner, drawRadial, selected) + { + if ( snapshotMode ) + { + if ( this != selectedNode) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + if ( this.alphaArc.end ) + { + var dArray = + [ + " M ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, + " 0 ", x1, ",", y1 + ]; + + svg += '<path class="line" d="' + dArray.join('') + '"/>'; + } + + if ( drawRadial && this.alphaLine.end ) + { + svg += '<line x1="' + x3 + '" y1="' + y3 + '" x2="' + x4 + '" y2="' + y4 + '"/>'; + } + } + } + else + { + context.lineWidth = thinLineWidth; + context.strokeStyle = 'black'; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.globalAlpha = this.alphaArc.current(); + context.stroke(); + + if ( drawRadial ) + { + var x1 = radiusInner * Math.cos(angleEnd); + var y1 = radiusInner * Math.sin(angleEnd); + var x2 = gRadius * Math.cos(angleEnd); + var y2 = gRadius * Math.sin(angleEnd); + + context.beginPath(); + context.moveTo(x1, y1); + context.lineTo(x2, y2); + +// if ( this.getCollapse() )//( selected && this != selectedNode ) + { + context.globalAlpha = this.alphaLine.current(); + } + + context.stroke(); + } + } + } + + this.drawMap = function(child) + { + if ( this.parent ) + { + this.parent.drawMap(child); + } + + if ( this.getCollapse() && this != child || this == focusNode ) + { + return; + } + + var angleStart = + (child.baseMagnitude - this.baseMagnitude) / this.magnitude * Math.PI * 2 + + rotationOffset; + var angleEnd = + (child.baseMagnitude - this.baseMagnitude + child.magnitude) / + this.magnitude * Math.PI * 2 + + rotationOffset; + + var box = this.getMapPosition(); + + context.save(); + context.fillStyle = 'black'; + context.textAlign = 'end'; + context.textBaseline = 'middle'; + + var textX = box.x - mapRadius - mapBuffer; + var percentage = getPercentage(child.magnitude / this.magnitude); + + var highlight = this == selectedNode || this == highlightedNode; + + if ( highlight ) + { + context.font = fontBold; + } + else + { + context.font = fontNormal; + } + + context.fillText(percentage + '% of', textX, box.y - mapRadius / 3); + context.fillText(this.name, textX, box.y + mapRadius / 3); + + if ( highlight ) + { + context.font = fontNormal; + } + + if ( this == highlightedNode && this != selectedNode ) + { + context.fillStyle = 'rgb(245, 245, 245)'; +// context.fillStyle = 'rgb(200, 200, 200)'; + } + else + { + context.fillStyle = 'rgb(255, 255, 255)'; + } + + context.beginPath(); + context.arc(box.x, box.y, mapRadius, 0, Math.PI * 2, true); + context.closePath(); + context.fill(); + + if ( this == selectedNode ) + { + context.lineWidth = 1; + context.fillStyle = 'rgb(100, 100, 100)'; + } + else + { + if ( this == highlightedNode ) + { + context.lineWidth = .2; + context.fillStyle = 'rgb(190, 190, 190)'; + } + else + { + context.lineWidth = .2; + context.fillStyle = 'rgb(200, 200, 200)'; + } + } + + var maxDepth = this.getMaxDepth(); + + if ( ! compress && maxDepth > maxPossibleDepth + this.getDepth() - 1 ) + { + maxDepth = maxPossibleDepth + this.getDepth() - 1; + } + + if ( this.getDepth() < selectedNode.getDepth() ) + { + if ( child.getDepth() - 1 >= maxDepth ) + { + maxDepth = child.getDepth(); + } + } + + var radiusInner; + + if ( compress ) + { + radiusInner = 0; +// Math.atan(child.getDepth() - this.getDepth()) / +// Math.PI * 2 * .9; + } + else + { + radiusInner = + (child.getDepth() - this.getDepth()) / + (maxDepth - this.getDepth() + 1); + } + + context.stroke(); + context.beginPath(); + + if ( radiusInner == 0 ) + { + context.moveTo(box.x, box.y); + } + else + { + context.arc(box.x, box.y, mapRadius * radiusInner, angleEnd, angleStart, true); + } + + context.arc(box.x, box.y, mapRadius, angleStart, angleEnd, false); + context.closePath(); + context.fill(); + + if ( this == highlightedNode && this != selectedNode ) + { + context.lineWidth = 1; + context.stroke(); + } + + context.restore(); + } + + this.drawReferenceRings = function(childRadiusInner) + { + if ( snapshotMode ) + { + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + childRadiusInner + '"/>'; + svg += + '<circle cx="' + centerX + '" cy="' + centerY + + '" r="' + gRadius + '"/>'; + } + else + { + context.globalAlpha = 1 - this.alphaLine.current();//this.getUncollapsed().alphaLine.current(); + context.beginPath(); + context.arc(0, 0, childRadiusInner, 0, Math.PI * 2, false); + context.stroke(); + context.beginPath(); + context.arc(0, 0, gRadius, 0, Math.PI * 2, false); + context.stroke(); + } + } + + this.getCollapse = function() + { + return ( + collapse && + this.collapse && + this.depth != maxAbsoluteDepth + ); + } + + this.getDepth = function() + { + if ( collapse ) + { + return this.depthCollapsed; + } + else + { + return this.depth; + } + } + + this.getMagnitude = function() + { + return this.attributes[magnitudeIndex][currentDataset]; + } + + this.getMapPosition = function() + { + return { + x : (details.offsetLeft + details.clientWidth - mapRadius), + y : ((focusNode.getDepth() - this.getDepth()) * + (mapBuffer + mapRadius * 2) - mapRadius) + + details.clientHeight + details.offsetTop + }; + } + + this.getMaxDepth = function(limit) + { + var max; + + if ( collapse ) + { + return this.maxDepthCollapsed; + } + else + { + if ( this.maxDepth > maxAbsoluteDepth ) + { + return maxAbsoluteDepth; + } + else + { + return this.maxDepth; + } + } + } + + this.getData = function(index, summary) + { + var files = new Array(); + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null && + this.attributes[index][currentDataset] != '' + ) + { + files.push + ( + document.location + + '.files/' + + this.attributes[index][currentDataset] + ); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + files = files.concat(this.children[i].getData(index, true)); + } + } + + return files; + } + + this.getList = function(index, summary) + { + var list; + + if + ( + this.attributes[index] != null && + this.attributes[index][currentDataset] != null + ) + { + list = this.attributes[index][currentDataset]; + } + else + { + list = new Array(); + } + + if ( summary ) + { + for ( var i = 0; i < this.children.length; i++ ) + { + list = list.concat(this.children[i].getList(index, true)); + } + } + + return list; + } + + this.getParent = function() + { + // returns parent, accounting for collapsing or 0 if doesn't exist + + var parent = this.parent; + + while ( parent != 0 && parent.getCollapse() ) + { + parent = parent.parent; + } + + return parent; + } + + this.getPercentage = function() + { + return getPercentage(this.magnitude / selectedNode.magnitude); + } + + this.getUnclassifiedPercentage = function() + { + if ( this.children.length ) + { + var lastChild = this.children[this.children.length - 1]; + + return getPercentage + ( + ( + this.baseMagnitude + + this.magnitude - + lastChild.magnitude - + lastChild.baseMagnitude + ) / this.magnitude + ) + '%'; + } + else + { + return '100%'; + } + } + + this.getUnclassifiedText = function() + { + return '[other '+ this.name + ']'; + } + + this.getUncollapsed = function() + { + // recurse through collapsed children until uncollapsed node is found + + if ( this.getCollapse() ) + { + return this.children[0].getUncollapsed(); + } + else + { + return this; + } + } + + this.hasChildren = function() + { + return this.children.length && this.depth < maxAbsoluteDepth && this.magnitude; + } + + this.hasParent = function(parent) + { + if ( this.parent ) + { + if ( this.parent == parent ) + { + return true; + } + else + { + return this.parent.hasParent(parent); + } + } + else + { + return false; + } + } + + this.maxVisibleDepth = function(maxDepth) + { + var childInnerRadius; + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var currentMaxDepth = depth; + + if ( this.hasChildren() && depth < maxDepth) + { + var lastChild = this.children[this.children.length - 1]; + + if ( this.name == 'Pseudomonadaceae' ) + { + var x = 3; + } + + if + ( + lastChild.baseMagnitude + lastChild.magnitude < + this.baseMagnitude + this.magnitude + ) + { + currentMaxDepth++; + } + + if ( compress ) + { + childInnerRadius = compressedRadii[depth - 1]; + } + else + { + childInnerRadius = (depth) / maxDepth; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + if + (//true || + this.children[i].magnitude * + angleFactor * + (childInnerRadius + 1) * + gRadius >= + minWidth() + ) + { + var childMaxDepth = this.children[i].maxVisibleDepth(maxDepth); + + if ( childMaxDepth > currentMaxDepth ) + { + currentMaxDepth = childMaxDepth; + } + } + } + } + + return currentMaxDepth; + } + + this.resetLabelWidth = function() + { + var nameWidthOld = this.nameWidth; + + if ( true || ! this.radial )//&& fontSize != fontSizeLast ) + { + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + } + + if ( fontSize != fontSizeLast && this.labelWidth.end == nameWidthOld * labelWidthFudge ) + { + // font size changed; adjust start of tween to match + + this.labelWidth.start = this.nameWidth * labelWidthFudge; + } + else + { + this.labelWidth.start = this.labelWidth.current(); + } + + this.labelWidth.end = this.nameWidth * labelWidthFudge; + } + + this.restrictLabelWidth = function(width) + { + if ( width < this.labelWidth.end ) + { + this.labelWidth.end = width; + } + } + + this.search = function() + { + this.isSearchResult = false; + this.searchResults = 0; + + if + ( + ! this.getCollapse() && + search.value != '' && + this.name.toLowerCase().indexOf(search.value.toLowerCase()) != -1 + ) + { + this.isSearchResult = true; + this.searchResults = 1; + nSearchResults++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.searchResults += this.children[i].search(); + } + + return this.searchResults; + } + + this.searchResultChildren = function() + { + if ( this.isSearchResult ) + { + return this.searchResults - 1; + } + else + { + return this.searchResults; + } + } + + this.setDepth = function(depth, depthCollapsed) + { + this.depth = depth; + this.depthCollapsed = depthCollapsed; + + if + ( + this.children.length == 1 && +// this.magnitude > 0 && + this.children[0].magnitude == this.magnitude && + ( head.children.length > 1 || this.children[0].children.length ) + ) + { + this.collapse = true; + } + else + { + this.collapse = false; + depthCollapsed++; + } + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setDepth(depth + 1, depthCollapsed); + } + } + + this.setHighlightStyle = function() + { + context.lineWidth = highlightLineWidth; + + if ( this.hasChildren() || this != focusNode || this != highlightedNode ) + { + context.strokeStyle = 'black'; + context.fillStyle = "rgba(255, 255, 255, .3)"; + } + else + { + context.strokeStyle = 'rgb(90,90,90)'; + context.fillStyle = "rgba(155, 155, 155, .3)"; + } + } + + this.setLabelWidth = function(node) + { + if ( ! shorten || this.radial ) + { + return; // don't need to set width + } + + if ( node.hide ) + { + alert('wtf'); + return; + } + + var angle = (this.angleStart.end + this.angleEnd.end) / 2; + var a; // angle difference + + if ( node == selectedNode ) + { + a = Math.abs(angle - node.angleOther); + } + else + { + a = Math.abs(angle - (node.angleStart.end + node.angleEnd.end) / 2); + } + + if ( a == 0 ) + { + return; + } + + if ( a > Math.PI ) + { + a = 2 * Math.PI - a; + } + + if ( node.radial || node == selectedNode ) + { + var nodeLabelRadius; + + if ( node == selectedNode ) + { + // radial 'other' label + + nodeLabelRadius = (node.children[0].radiusInner.end + 1) / 2; + } + else + { + nodeLabelRadius = (node.radiusInner.end + 1) / 2; + } + + if ( a < Math.PI / 2 ) + { + var r = this.labelRadius.end * gRadius + .5 * fontSize + var hypotenuse = r / Math.cos(a); + var opposite = r * Math.tan(a); + var fontRadius = .8 * fontSize; + + if + ( + nodeLabelRadius * gRadius < hypotenuse && + this.labelWidth.end / 2 + fontRadius > opposite + ) + { + this.labelWidth.end = 2 * (opposite - fontRadius); + } + } + } + else if + ( + this.labelRadius.end == node.labelRadius.end && + a < Math.PI / 4 + ) + { + // same radius with small angle; use circumferential approximation + + var dist = a * this.labelRadius.end * gRadius - fontSize * (1 - a * 4 / Math.PI) * 1.3; + + if ( this.labelWidth.end < dist ) + { + node.restrictLabelWidth((dist - this.labelWidth.end / 2) * 2); + } + else if ( node.labelWidth.end < dist ) + { + this.restrictLabelWidth((dist - node.labelWidth.end / 2) * 2); + } + else + { + // both labels reach halfway point; restrict both + + this.labelWidth.end = dist; + node.labelWidth.end = dist + } + } + else + { + var r1 = this.labelRadius.end * gRadius; + var r2 = node.labelRadius.end * gRadius; + + // first adjust the radii to account for the height of the font by shifting them + // toward each other + // + var fontFudge = .35 * fontSize; + // + if ( this.labelRadius.end < node.labelRadius.end ) + { + r1 += fontFudge; + r2 -= fontFudge; + } + else if ( this.labelRadius.end > node.labelRadius.end ) + { + r1 -= fontFudge; + r2 += fontFudge; + } + else + { + r1 -= fontFudge; + r2 -= fontFudge; + } + + var r1s = r1 * r1; + var r2s = r2 * r2; + + // distance between the centers of the two labels + // + var dist = Math.sqrt(r1s + r2s - 2 * r1 * r2 * Math.cos(a)); + + // angle at our label center between our radius and the line to the other label center + // + var b = Math.acos((r1s + dist * dist - r2s) / (2 * r1 * dist)); + + // distance from our label center to the intersection of the two tangents + // + var l1 = Math.sin(a + b - Math.PI / 2) * dist / Math.sin(Math.PI - a); + + // distance from other label center the the intersection of the two tangents + // + var l2 = Math.sin(Math.PI / 2 - b) * dist / Math.sin(Math.PI - a); + + l1 = Math.abs(l1) - .4 * fontSize; + l2 = Math.abs(l2) - .4 * fontSize; +/* + // amount to shorten the distances because of the height of the font + // + var l3 = 0; + var fontRadius = fontSize * .55; + // + if ( l1 < 0 || l2 < 0 ) + { + var l4 = fontRadius / Math.tan(a); + l1 = Math.abs(l1); + l2 = Math.abs(l2); + + l1 -= l4; + l2 -= l4; + } + else + { + var c = Math.PI - a; + + l3 = fontRadius * Math.tan(c / 2); + } +*/ + if ( this.labelWidth.end / 2 > l1 && node.labelWidth.end / 2 > l2 ) + { + // shorten the farthest one from the intersection + + if ( l1 > l2 ) + { + this.restrictLabelWidth(2 * (l1));// - l3 - fontRadius)); + } + else + { + node.restrictLabelWidth(2 * (l2));// - l3 - fontRadius)); + } + }/* + else if ( this.labelWidth.end / 2 > l1 + l3 && node.labelWidth.end / 2 > l2 - l3 ) + { + node.restrictLabelWidth(2 * (l2 - l3)); + } + else if ( this.labelWidth.end / 2 > l1 - l3 && node.labelWidth.end / 2 > l2 + l3 ) + { + this.restrictLabelWidth(2 * (l1 - l3)); + }*/ + } + } + + this.setMagnitudes = function(baseMagnitude) + { + this.magnitude = this.getMagnitude(); + this.baseMagnitude = baseMagnitude; + + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setMagnitudes(baseMagnitude); + baseMagnitude += this.children[i].magnitude; + } + + this.maxChildMagnitude = baseMagnitude; + } + + this.setMaxDepths = function() + { + this.maxDepth = this.depth; + this.maxDepthCollapsed = this.depthCollapsed; + + for ( i in this.children ) + { + var child = this.children[i]; + + child.setMaxDepths(); + + if ( child.maxDepth > this.maxDepth ) + { + this.maxDepth = child.maxDepth; + } + + if + ( + child.maxDepthCollapsed > this.maxDepthCollapsed && + (child.depth <= maxAbsoluteDepth || maxAbsoluteDepth == 0) + ) + { + this.maxDepthCollapsed = child.maxDepthCollapsed; + } + } + } + + this.setTargetLabelRadius = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var index = depth - 2; + var labelOffset = labelOffsets[index]; + + if ( this.radial ) + { + //this.labelRadius.setTarget((this.radiusInner.end + 1) / 2); + var max = + depth == maxDisplayDepth ? + 1 : + compressedRadii[index + 1]; + + this.labelRadius.setTarget((compressedRadii[index] + max) / 2); + } + else + { + var radiusCenter; + var width; + + if ( compress ) + { + if ( nLabelOffsets[index] > 1 ) + { + this.labelRadius.setTarget + ( + lerp + ( + labelOffset + .75, + 0, + nLabelOffsets[index] + .5, + compressedRadii[index], + compressedRadii[index + 1] + ) + ); + } + else + { + this.labelRadius.setTarget((compressedRadii[index] + compressedRadii[index + 1]) / 2); + } + } + else + { + radiusCenter = + nodeRadius * (depth - 1) + + nodeRadius / 2; + width = nodeRadius; + + this.labelRadius.setTarget + ( + radiusCenter + width * ((labelOffset + 1) / (nLabelOffsets[index] + 1) - .5) + ); + } + } + + if ( ! this.hide && ! this.keyed && nLabelOffsets[index] ) + { + // check last and first labels in each track for overlap + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + var last = labelLastNodes[i][j]; + var first = labelFirstNodes[i][j]; + + if ( last ) + { + if ( j == nLabelOffsets[i] ) + { + // last is radial + this.setLabelWidth(last); + } + else + { + last.setLabelWidth(this); + } + } + + if ( first ) + { + if ( j == nLabelOffsets[i] ) + { + this.setLabelWidth(first); + } + else + { + first.setLabelWidth(this); + } + } + } + } + + if ( selectedNode.canDisplayLabelOther ) + { + this.setLabelWidth(selectedNode); // in case there is an 'other' label + } + + if ( this.radial ) + { + // use the last 'track' of this depth for radial + + labelLastNodes[index][nLabelOffsets[index]] = this; + + if ( labelFirstNodes[index][nLabelOffsets[index]] == 0 ) + { + labelFirstNodes[index][nLabelOffsets[index]] = this; + } + } + else + { + labelLastNodes[index][labelOffset] = this; + + // update offset + + labelOffsets[index] += 1; + + if ( labelOffsets[index] > nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]--; + } + } + else if ( labelOffsets[index] == nLabelOffsets[index] ) + { + labelOffsets[index] -= nLabelOffsets[index]; + + if ( false && !(nLabelOffsets[index] & 1) ) + { + labelOffsets[index]++; + } + } + + if ( labelFirstNodes[index][labelOffset] == 0 ) + { + labelFirstNodes[index][labelOffset] = this; + } + } + } + else if ( this.hide ) + { + this.labelWidth.end = 0; + } + } + + this.setTargets = function() + { + if ( this == selectedNode ) + { + this.setTargetsSelected + ( + 0, + 1, + lightnessBase, + false, + false + ); + return; + } + + var depthRelative = this.getDepth() - selectedNode.getDepth(); + + var parentOfSelected = selectedNode.hasParent(this); +/* ( +// ! this.getCollapse() && + this.baseMagnitude <= selectedNode.baseMagnitude && + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ); +*/ + if ( parentOfSelected ) + { + this.resetLabelWidth(); + } + else + { + //context.font = fontNormal; + var dim = context.measureText(this.name); + this.nameWidth = dim.width; + //this.labelWidth.setTarget(this.labelWidth.end); + this.labelWidth.setTarget(0); + } + + // set angles + // + if ( this.baseMagnitude <= selectedNode.baseMagnitude ) + { + this.angleStart.setTarget(0); + } + else + { + this.angleStart.setTarget(Math.PI * 2); + } + // + if + ( + parentOfSelected || + this.baseMagnitude + this.magnitude >= + selectedNode.baseMagnitude + selectedNode.magnitude + ) + { + this.angleEnd.setTarget(Math.PI * 2); + } + else + { + this.angleEnd.setTarget(0); + } + + // children + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargets(); + } + + if ( this.getDepth() <= selectedNode.getDepth() ) + { + // collapse in + + this.radiusInner.setTarget(0); + + if ( parentOfSelected ) + { + this.labelRadius.setTarget + ( + (depthRelative) * + historySpacingFactor * fontSize / gRadius + ); + //this.scale.setTarget(1 - (selectedNode.getDepth() - this.getDepth()) / 18); // TEMP + } + else + { + this.labelRadius.setTarget(0); + //this.scale.setTarget(1); // TEMP + } + } + else if ( depthRelative + 1 > maxDisplayDepth ) + { + // collapse out + + this.radiusInner.setTarget(1); + this.labelRadius.setTarget(1); + //this.scale.setTarget(1); // TEMP + } + else + { + // don't collapse + + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depthRelative - 1]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depthRelative)); + } + + //this.scale.setTarget(1); // TEMP + + if ( this == selectedNode ) + { + this.labelRadius.setTarget(0); + } + else + { + if ( compress ) + { + this.labelRadius.setTarget + ( + (compressedRadii[depthRelative - 1] + compressedRadii[depthRelative]) / 2 + ); + } + else + { + this.labelRadius.setTarget(nodeRadius * (depthRelative) + nodeRadius / 2); + } + } + } + +// this.r.start = this.r.end; +// this.g.start = this.g.end; +// this.b.start = this.b.end; + + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + + this.alphaLine.setTarget(0); + this.alphaArc.setTarget(0); + this.alphaWedge.setTarget(0); + this.alphaPattern.setTarget(0); + this.alphaOther.setTarget(0); + + if ( parentOfSelected && ! this.getCollapse() ) + { + var alpha = + ( + 1 - + (selectedNode.getDepth() - this.getDepth()) / + (Math.floor((compress ? compressedRadii[0] : nodeRadius) * gRadius / (historySpacingFactor * fontSize) - .5) + 1) + ); + + if ( alpha < 0 ) + { + alpha = 0; + } + + this.alphaLabel.setTarget(alpha); + this.radial = false; + } + else + { + this.alphaLabel.setTarget(0); + } + + this.hideAlonePrev = this.hideAlone; + this.hidePrev = this.hide; + + if ( parentOfSelected ) + { + this.hideAlone = false; + this.hide = false; + } + + if ( this.getParent() == selectedNode.getParent() ) + { + this.hiddenEnd = null; + } + + this.radialPrev = this.radial; + } + + this.setTargetsSelected = function(hueMin, hueMax, lightness, hide, nextSiblingHidden) + { + var collapse = this.getCollapse(); + var depth = this.getDepth() - selectedNode.getDepth() + 1; + var canDisplayChildLabels = false; + var lastChild; + + if ( this.hasChildren() )//&& ! hide ) + { + lastChild = this.children[this.children.length - 1]; + this.hideAlone = true; + } + else + { + this.hideAlone = false; + } + + // set child wedges + // + for ( var i = 0; i < this.children.length; i++ ) + { + this.children[i].setTargetWedge(); + + if + ( + ! this.children[i].hide && + ( collapse || depth < maxDisplayDepth ) && + this.depth < maxAbsoluteDepth + ) + { + canDisplayChildLabels = true; + this.hideAlone = false; + } + } + + if ( this == selectedNode || lastChild && lastChild.angleEnd.end < this.angleEnd.end - .01) + { + this.hideAlone = false; + } + + if ( this.hideAlonePrev == undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + if ( this == selectedNode ) + { + var otherArc = + this.children.length ? + angleFactor * + ( + this.baseMagnitude + this.magnitude - + lastChild.baseMagnitude - lastChild.magnitude + ) + : this.baseMagnitude + this.magnitude; + this.canDisplayLabelOther = + this.children.length ? + otherArc * + (this.children[0].radiusInner.end + 1) * gRadius >= + minWidth() + : true; + + this.keyUnclassified = false; + + if ( this.canDisplayLabelOther ) + { + this.angleOther = Math.PI * 2 - otherArc / 2; + } + else if ( otherArc > 0.0000000001 ) + { + this.keyUnclassified = true; + keys++; + } + + this.angleStart.setTarget(0); + this.angleEnd.setTarget(Math.PI * 2); + + if ( this.children.length ) + { + this.radiusInner.setTarget(0); + } + else + { + this.radiusInner.setTarget(compressedRadii[0]); + } + + this.hidePrev = this.hide; + this.hide = false; + this.hideAlonePrev = this.hideAlone; + this.hideAlone = false; + this.keyed = false; + } + + if ( hueMax - hueMin > 1 / 12 ) + { + hueMax = hueMin + 1 / 12; + } + + // set lightness + // + if ( ! ( hide || this.hideAlone ) ) + { + if ( useHue() ) + { + lightness = (lightnessBase + lightnessMax) / 2; + } + else + { + lightness = lightnessBase + (depth - 1) * lightnessFactor; + + if ( lightness > lightnessMax ) + { + lightness = lightnessMax; + } + } + } + + if ( hide ) + { + this.hide = true; + } + + if ( this.hidePrev == undefined ) + { + this.hidePrev = this.hide; + } + + var hiddenStart = -1; + var hiddenHueNumer = 0; + var hiddenHueDenom = 0; + var i = 0; + + if ( ! this.hide ) + { + this.hiddenEnd = null; + } + + while ( true ) + { + if ( ! this.hideAlone && ! hide && ( i == this.children.length || ! this.children[i].hide ) ) + { + // reached a non-hidden child or the end; set targets for + // previous group of hidden children (if any) using their + // average hue + + if ( hiddenStart != -1 ) + { + var hiddenHue = hiddenHueDenom ? hiddenHueNumer / hiddenHueDenom : hueMin; + + for ( var j = hiddenStart; j < i; j++ ) + { + this.children[j].setTargetsSelected + ( + hiddenHue, + null, + lightness, + false, + j < i - 1 + ); + + this.children[j].hiddenEnd = null; + } + + this.children[hiddenStart].hiddenEnd = i - 1; + } + } + + if ( i == this.children.length ) + { + break; + } + + var child = this.children[i]; + var childHueMin; + var childHueMax; + + if ( this.magnitude > 0 && ! this.hide && ! this.hideAlone ) + { + if ( useHue() ) + { + childHueMin = child.hues[currentDataset]; + } + else if ( this == selectedNode ) + { + var min = 0.0; + var max = 1.0; + + if ( this.children.length > 6 ) + { + childHueMin = lerp((1 - Math.pow(1 - i / this.children.length, 1.4)) * .95, 0, 1, min, max); + childHueMax = lerp((1 - Math.pow(1 - (i + .55) / this.children.length, 1.4)) * .95, 0, 1, min, max); + } + else + { + childHueMin = lerp(i / this.children.length, 0, 1, min, max); + childHueMax = lerp((i + .55) / this.children.length, 0, 1, min, max); + } + } + else + { + childHueMin = lerp + ( + child.baseMagnitude, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + childHueMax = lerp + ( + child.baseMagnitude + child.magnitude * .99, + this.baseMagnitude, + this.baseMagnitude + this.magnitude, + hueMin, + hueMax + ); + } + } + else + { + childHueMin = hueMin; + childHueMax = hueMax; + } + + if ( ! this.hideAlone && ! hide && ! this.hide && child.hide ) + { + if ( hiddenStart == -1 ) + { + hiddenStart = i; + } + + if ( useHue() ) + { + hiddenHueNumer += childHueMin * child.magnitude; + hiddenHueDenom += child.magnitude; + } + else + { + hiddenHueNumer += childHueMin; + hiddenHueDenom++; + } + } + else + { + hiddenStart = -1; + + this.children[i].setTargetsSelected + ( + childHueMin, + childHueMax, + lightness, + hide || this.keyed || this.hideAlone || this.hide && ! collapse, + false + ); + } + + i++; + } + + if ( this.hue && this.magnitude ) + { + this.hue.setTarget(this.hues[currentDataset]); + + if ( this.attributes[magnitudeIndex][lastDataset] == 0 ) + { + this.hue.start = this.hue.end; + } + } + + this.radialPrev = this.radial; + + if ( this == selectedNode ) + { + this.resetLabelWidth(); + this.labelWidth.setTarget(this.nameWidth * labelWidthFudge); + this.alphaWedge.setTarget(0); + this.alphaLabel.setTarget(1); + this.alphaOther.setTarget(1); + this.alphaArc.setTarget(0); + this.alphaLine.setTarget(0); + this.alphaPattern.setTarget(0); + this.r.setTarget(255); + this.g.setTarget(255); + this.b.setTarget(255); + this.radial = false; + this.labelRadius.setTarget(0); + } + else + { + var rgb = hslToRgb + ( + hueMin, + saturation, + lightness + ); + + this.r.setTarget(rgb.r); + this.g.setTarget(rgb.g); + this.b.setTarget(rgb.b); + this.alphaOther.setTarget(0); + + this.alphaWedge.setTarget(1); + + if ( this.hide || this.hideAlone ) + { + this.alphaPattern.setTarget(1); + } + else + { + this.alphaPattern.setTarget(0); + } + + // set radial + // + if ( ! ( hide || this.hide ) )//&& ! this.keyed ) + { + if ( this.hideAlone ) + { + this.radial = true; + } + else if ( false && canDisplayChildLabels ) + { + this.radial = false; + } + else + { + this.radial = true; + + if ( this.hasChildren() && depth < maxDisplayDepth ) + { + var lastChild = this.children[this.children.length - 1]; + + if + ( + lastChild.angleEnd.end == this.angleEnd.end || + ( + (this.angleStart.end + this.angleEnd.end) / 2 - + lastChild.angleEnd.end + ) * (this.radiusInner.end + 1) * gRadius * 2 < + minWidth() + ) + { + this.radial = false; + } + } + } + } + + // set alphaLabel + // + if + ( + collapse || + hide || + this.hide || + this.keyed || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLabel.setTarget(0); + } + else + { + if + ( + (this.radial || nLabelOffsets[depth - 2]) + ) + { + this.alphaLabel.setTarget(1); + } + else + { + this.alphaLabel.setTarget(0); + + if ( this.radialPrev ) + { + this.alphaLabel.start = 0; + } + } + } + + // set alphaArc + // + if + ( + collapse || + hide || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaArc.setTarget(0); + } + else + { + this.alphaArc.setTarget(1); + } + + // set alphaLine + // + if + ( + hide || + this.hide && nextSiblingHidden || + depth > maxDisplayDepth || + ! this.canDisplayDepth() + ) + { + this.alphaLine.setTarget(0); + } + else + { + this.alphaLine.setTarget(1); + } + + //if ( ! this.radial ) + { + this.resetLabelWidth(); + } + + // set labelRadius target + // + if ( collapse ) + { + this.labelRadius.setTarget(this.radiusInner.end); + } + else + { + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.labelRadius.setTarget(1); + } + else + { + this.setTargetLabelRadius(); + } + } + } + } + + this.setTargetWedge = function() + { + var depth = this.getDepth() - selectedNode.getDepth() + 1; + + // set angles + // + var baseMagnitudeRelative = this.baseMagnitude - selectedNode.baseMagnitude; + // + this.angleStart.setTarget(baseMagnitudeRelative * angleFactor); + this.angleEnd.setTarget((baseMagnitudeRelative + this.magnitude) * angleFactor); + + // set radiusInner + // + if ( depth > maxDisplayDepth || ! this.canDisplayDepth() ) + { + this.radiusInner.setTarget(1); + } + else + { + if ( compress ) + { + this.radiusInner.setTarget(compressedRadii[depth - 2]); + } + else + { + this.radiusInner.setTarget(nodeRadius * (depth - 1)); + } + } + + if ( this.hide != undefined ) + { + this.hidePrev = this.hide; + } + + if ( this.hideAlone != undefined ) + { + this.hideAlonePrev = this.hideAlone; + } + + // set hide + // + if + ( + (this.angleEnd.end - this.angleStart.end) * + (this.radiusInner.end * gRadius + gRadius) < + minWidth() + ) + { + if ( depth == 2 && ! this.getCollapse() && this.depth <= maxAbsoluteDepth ) + { + this.keyed = true; + keys++; + this.hide = false; + + var percentage = this.getPercentage(); + this.keyLabel = this.name + ' ' + percentage + '%'; + var dim = context.measureText(this.keyLabel); + this.keyNameWidth = dim.width; + } + else + { + this.keyed = false; + this.hide = depth > 2; + } + } + else + { + this.keyed = false; + this.hide = false; + } + } + + this.shortenLabel = function() + { + var label = this.name; + + var labelWidth = this.nameWidth; + var maxWidth = this.labelWidth.current(); + var minEndLength = 0; + + if ( labelWidth > maxWidth && label.length > minEndLength * 2 ) + { + var endLength = + Math.floor((label.length - 1) * maxWidth / labelWidth / 2); + + if ( endLength < minEndLength ) + { + endLength = minEndLength; + } + + return ( + label.substring(0, endLength) + + '...' + + label.substring(label.length - endLength)); + } + else + { + return label; + } + } + +/* this.shouldAddSearchResultsString = function() + { + if ( this.isSearchResult ) + { + return this.searchResults > 1; + } + else + { + return this.searchResults > 0; + } + } +*/ + this.sort = function() + { + this.children.sort(function(a, b){return b.getMagnitude() - a.getMagnitude()}); + + for (var i = 0; i < this.children.length; i++) + { + this.children[i].sort(); + } + } +} + +var options; + +function addOptionElement(position, innerHTML, title) +{ + var div = document.createElement("div"); +// div.style.position = 'absolute'; +// div.style.top = position + 'px'; + div.innerHTML = innerHTML; +// div.style.display = 'block'; + div.style.padding = '2px'; + + if ( title ) + { + div.title = title; + } + + options.appendChild(div); + var height = 0;//div.clientHeight; + return position + height; +} + +function addOptionElements(hueName, hueDefault) +{ + options = document.createElement('div'); + options.style.position = 'absolute'; + options.style.top = '0px'; + options.addEventListener('mousedown', function(e) {mouseClick(e)}, false); +// options.onmouseup = function(e) {mouseUp(e)} + document.body.appendChild(options); + + document.body.style.font = '11px sans-serif'; + var position = 5; + + details = document.createElement('div'); + details.style.position = 'absolute'; + details.style.top = '1%'; + details.style.right = '2%'; + details.style.textAlign = 'right'; + document.body.insertBefore(details, canvas); +// <div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"> + + details.innerHTML = '\ +<span id="detailsName" style="font-weight:bold"></span> \ +<input type="button" id="detailsExpand" onclick="expand(focusNode);"\ +value="↔" title="Expand this wedge to become the new focus of the chart"/><br/>\ +<div id="detailsInfo" style="float:right"></div>'; + + keyControl = document.createElement('input'); + keyControl.type = 'button'; + keyControl.value = showKeys ? 'x' : '…'; + keyControl.style.position = ''; + keyControl.style.position = 'fixed'; + keyControl.style.visibility = 'hidden'; + + document.body.insertBefore(keyControl, canvas); + + var logoElement = document.getElementById('logo'); + + if ( logoElement ) + { + logoImage = logoElement.src; + } + else + { + logoImage = 'http://marbl.github.io/Krona/img/logo-med.png'; + } + +// document.getElementById('options').style.fontSize = '9pt'; + position = addOptionElement + ( + position, +'<a style="margin:2px" target="_blank" href="https://github.com/marbl/Krona/wiki"><img style="vertical-align:middle;width:108px;height:30px;" src="' + logoImage + '" alt="Logo of Krona"/></a><input type="button" id="back" value="←" title="Go back (Shortcut: ←)"/>\ +<input type="button" id="forward" value="→" title="Go forward (Shortcut: →)"/> \ + Search: <input type="text" id="search"/>\ +<input id="searchClear" type="button" value="x" onclick="clearSearch()"/> \ +<span id="searchResults"></span>' + ); + + if ( datasets > 1 ) + { + var size = datasets < datasetSelectSize ? datasets : datasetSelectSize; + + var select = + '<table style="border-collapse:collapse;padding:0px"><tr><td style="padding:0px">' + + '<select id="datasets" style="min-width:100px" size="' + size + '" onchange="onDatasetChange()">'; + + for ( var i = 0; i < datasetNames.length; i++ ) + { + select += '<option>' + datasetNames[i] + '</option>'; + } + + select += + '</select></td><td style="vertical-align:top;padding:1px;">' + + '<input style="display:block" title="Previous dataset (Shortcut: ↑)" id="prevDataset" type="button" value="↑" onclick="prevDataset()" disabled="true"/>' + + '<input title="Next dataset (Shortcut: ↓)" id="nextDataset" type="button" value="↓" onclick="nextDataset()"/><br/></td>' + + '<td style="padding-top:1px;vertical-align:top"><input title="Switch to the last dataset that was viewed (Shortcut: TAB)" id="lastDataset" type="button" style="font:11px Times new roman" value="last" onclick="selectLastDataset()"/></td></tr></table>'; + + position = addOptionElement(position + 5, select); + + datasetDropDown = document.getElementById('datasets'); + datasetButtonLast = document.getElementById('lastDataset'); + datasetButtonPrev = document.getElementById('prevDataset'); + datasetButtonNext = document.getElementById('nextDataset'); + + position += datasetDropDown.clientHeight; + } + + position = addOptionElement + ( + position + 5, +'<input type="button" id="maxAbsoluteDepthDecrease" value="-"/>\ +<span id="maxAbsoluteDepth"></span>\ + <input type="button" id="maxAbsoluteDepthIncrease" value="+"/> Max depth', +'Maximum depth to display, counted from the top level \ +and including collapsed wedges.' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="fontSizeDecrease" value="-"/>\ +<span id="fontSize"></span>\ + <input type="button" id="fontSizeIncrease" value="+"/> Font size' + ); + + position = addOptionElement + ( + position, +'<input type="button" id="radiusDecrease" value="-"/>\ +<input type="button" id="radiusIncrease" value="+"/> Chart size' + ); + + if ( hueName ) + { + hueDisplayName = attributes[attributeIndex(hueName)].displayName; + + position = addOptionElement + ( + position + 5, + '<input type="checkbox" id="useHue" style="float:left" ' + + '/><div>Color by<br/>' + hueDisplayName + + '</div>' + ); + + useHueCheckBox = document.getElementById('useHue'); + useHueCheckBox.checked = hueDefault; + useHueCheckBox.onclick = handleResize; + useHueCheckBox.onmousedown = suppressEvent; + } + /* + position = addOptionElement + ( + position + 5, + ' <input type="checkbox" id="shorten" checked="checked" />Shorten labels</div>', + 'Prevent labels from overlapping by shortening them' + ); + + position = addOptionElement + ( + position, + ' <input type="checkbox" id="compress" checked="checked" />Compress', + 'Compress wedges if needed to show the entire depth' + ); + */ + position = addOptionElement + ( + position, + '<input type="checkbox" id="collapse" checked="checked" />Collapse', + 'Collapse wedges that are redundant (entirely composed of another wedge)' + ); + + position = addOptionElement + ( + position + 5, + '<input type="button" id="snapshot" value="Snapshot"/>', +'Render the current view as SVG (Scalable Vector Graphics), a publication-\ +quality format that can be printed and saved (see Help for browser compatibility)' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="linkButton" value="Link"/>\ +<input type="text" size="30" id="linkText"/>', +'Show a link to this view that can be copied for bookmarking or sharing' + ); + + position = addOptionElement + ( + position + 5, +'<input type="button" id="help" value="?"\ +onclick="window.open(\'https://github.com/marbl/Krona/wiki/Browsing%20Krona%20charts\', \'help\')"/>', +'Help' + ); +} + +function arrow(angleStart, angleEnd, radiusInner) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + var angleCenter = (angleStart + angleEnd) / 2; + var radiusArrowInner = radiusInner - gRadius / 10;//nodeRadius * gRadius; + var radiusArrowOuter = gRadius * 1.1;//(1 + nodeRadius); + var radiusArrowCenter = (radiusArrowInner + radiusArrowOuter) / 2; + var pointLength = (radiusArrowOuter - radiusArrowInner) / 5; + + context.fillStyle = highlightFill; + context.lineWidth = highlightLineWidth; + + // First, mask out the first half of the arrow. This will prevent the tips + // from superimposing if the arrow goes most of the way around the circle. + // Masking is done by setting the clipping region to the inverse of the + // half-arrow, which is defined by cutting the half-arrow out of a large + // rectangle + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter, true); + context.closePath(); + context.moveTo(-imageWidth, -imageHeight); + context.lineTo(imageWidth, -imageHeight); + context.lineTo(imageWidth, imageHeight); + context.lineTo(-imageWidth, imageHeight); + context.closePath(); + context.save(); + context.clip(); + + // Next, draw the other half-arrow with the first half masked out + // + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter, angleStart, true); + context.lineTo + ( + radiusArrowInner * Math.cos(angleStart), + radiusArrowInner * Math.sin(angleStart) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleStart) + pointLength * Math.sin(angleStart), + radiusArrowCenter * Math.sin(angleStart) - pointLength * Math.cos(angleStart) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleStart), + radiusArrowOuter * Math.sin(angleStart) + ); + context.arc(0, 0, gRadius, angleStart, angleCenter, false); + context.fill(); + context.stroke(); + + // Finally, remove the clipping region and draw the first half-arrow. This + // half is extended slightly to fill the seam. + // + context.restore(); + context.beginPath(); + context.arc(0, 0, radiusInner, angleCenter - 2 / (2 * Math.PI * radiusInner), angleEnd, false); + context.lineTo + ( + radiusArrowInner * Math.cos(angleEnd), + radiusArrowInner * Math.sin(angleEnd) + ); + context.lineTo + ( + radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), + radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) + ); + context.lineTo + ( + radiusArrowOuter * Math.cos(angleEnd), + radiusArrowOuter * Math.sin(angleEnd) + ); + context.arc(0, 0, gRadius, angleEnd, angleCenter - 2 / (2 * Math.PI * gRadius), true); + context.fill(); + context.stroke(); +} + +function attributeIndex(aname) +{ + for ( var i = 0 ; i < attributes.length; i++ ) + { + if ( aname == attributes[i].name ) + { + return i; + } + } + + return null; +} + +function checkHighlight() +{ + var lastHighlightedNode = highlightedNode; + var lastHighlightingHidden = highlightingHidden; + + highlightedNode = selectedNode; + resetKeyOffset(); + + if ( progress == 1 ) + { + selectedNode.checkHighlight(); + if ( selectedNode.getParent() ) + { + selectedNode.getParent().checkHighlightCenter(); + } + + focusNode.checkHighlightMap(); + } + + if ( highlightedNode != selectedNode ) + { + if ( highlightedNode == focusNode ) + { +// canvas.style.display='none'; +// window.resizeBy(1,0); +// canvas.style.cursor='ew-resize'; +// window.resizeBy(-1,0); +// canvas.style.display='inline'; + } + else + { +// canvas.style.cursor='pointer'; + } + } + else + { +// canvas.style.cursor='auto'; + } + + if + ( + ( + true || + highlightedNode != lastHighlightedNode || + highlightingHidden != highlightingHiddenLast + ) && + progress == 1 + ) + { + draw(); // TODO: handle in update() + } +} + +function checkSelectedCollapse() +{ + var newNode = selectedNode; + + while ( newNode.getCollapse() ) + { + newNode = newNode.children[0]; + } + + if ( newNode.children.length == 0 && newNode.getParent() ) + { + newNode = newNode.getParent(); + } + + if ( newNode != selectedNode ) + { + selectNode(newNode); + } +} + +function clearSearch() +{ + if ( search.value != '' ) + { + search.value = ''; + onSearchChange(); + } +} + +function createSVG() +{ + svgNS = "http://www.w3.org/2000/svg"; + var SVG = {}; + SVG.xlinkns = "http://www.w3.org/1999/xlink"; + + var newSVG = document.createElementNS(svgNS, "svg:svg"); + + newSVG.setAttribute("id", "canvas"); + // How big is the canvas in pixels + newSVG.setAttribute("width", '100%'); + newSVG.setAttribute("height", '100%'); + // Set the coordinates used by drawings in the canvas +// newSVG.setAttribute("viewBox", "0 0 " + imageWidth + " " + imageHeight); + // Define the XLink namespace that SVG uses + newSVG.setAttributeNS + ( + "http://www.w3.org/2000/xmlns/", + "xmlns:xlink", + SVG.xlinkns + ); + + return newSVG; +} + +function degrees(radians) +{ + return radians * 180 / Math.PI; +} + +function draw() +{ + tweenFrames++; + //resize(); +// context.fillRect(0, 0, imageWidth, imageHeight); + context.clearRect(0, 0, imageWidth, imageHeight); + + context.font = fontNormal; + context.textBaseline = 'middle'; + + //context.strokeStyle = 'rgba(0, 0, 0, 0.3)'; + context.translate(centerX, centerY); + + resetKeyOffset(); + + head.draw(false, false); // draw pie slices + head.draw(true, false); // draw labels + + var pathRoot = selectedNode; + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + pathRoot = focusNode; + } + + if + ( + highlightedNode && + highlightedNode.getDepth() >= selectedNode.getDepth() && + highlightedNode != focusNode + ) + { + if + ( + progress == 1 && + highlightedNode != selectedNode && + ( + highlightedNode != focusNode || + focusNode.children.length > 0 + ) + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlight(true); + } + + //pathRoot = highlightedNode; + } + else if + ( + progress == 1 && + highlightedNode.getDepth() < selectedNode.getDepth() + ) + { + context.globalAlpha = 1; + highlightedNode.drawHighlightCenter(); + } + + if ( quickLook && false) // TEMP + { + context.globalAlpha = 1 - progress / 2; + selectedNode.drawHighlight(true); + } + else if ( progress < 1 )//&& zoomOut() ) + { + if ( !zoomOut)//() ) + { + context.globalAlpha = selectedNode.alphaLine.current(); + selectedNode.drawHighlight(true); + } + else if ( selectedNodeLast ) + { + context.globalAlpha = 1 - 4 * Math.pow(progress - .5, 2); + selectedNodeLast.drawHighlight(false); + } + } + + drawDatasetName(); + + //drawHistory(); + + context.translate(-centerX, -centerY); + context.globalAlpha = 1; + + mapRadius = + (imageHeight / 2 - details.clientHeight - details.offsetTop) / + (pathRoot.getDepth() - 1) * 3 / 4 / 2; + + if ( mapRadius > maxMapRadius ) + { + mapRadius = maxMapRadius; + } + + mapBuffer = mapRadius / 2; + + //context.font = fontNormal; + pathRoot.drawMap(pathRoot); + + if ( hueDisplayName && useHue() ) + { + drawLegend(); + } +} + +function drawBubble(angle, radius, width, radial, flip) +{ + var height = fontSize * 2; + var x; + var y; + + width = width + fontSize; + + if ( radial ) + { + y = -fontSize; + + if ( flip ) + { + x = radius - width + fontSize / 2; + } + else + { + x = radius - fontSize / 2; + } + } + else + { + x = -width / 2; + y = -radius - fontSize; + } + + if ( snapshotMode ) + { + drawBubbleSVG(x + centerX, y + centerY, width, height, fontSize, angle); + } + else + { + drawBubbleCanvas(x, y, width, height, fontSize, angle); + } +} + +function drawBubbleCanvas(x, y, width, height, radius, rotation) +{ + context.strokeStyle = 'black'; + context.lineWidth = highlightLineWidth; + context.fillStyle = 'rgba(255, 255, 255, .75)'; + context.rotate(rotation); + roundedRectangle(x, y, width, fontSize * 2, fontSize); + context.fill(); + context.stroke(); + context.rotate(-rotation); +} + +function drawBubbleSVG(x, y, width, height, radius, rotation) +{ + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" fill="rgba(255, 255, 255, .75)' + + '" class="highlight" ' + + 'transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; +} + +function drawDatasetName() +{ + var alpha = datasetAlpha.current(); + + if ( alpha > 0 ) + { + var radius = gRadius * compressedRadii[0] / -2; + + if ( alpha > 1 ) + { + alpha = 1; + } + + context.globalAlpha = alpha; + + drawBubble(0, -radius, datasetWidths[currentDataset], false, false); + drawText(datasetNames[currentDataset], 0, radius, 0, 'center', true); + } +} + +function drawHistory() +{ + var alpha = 1; + context.textAlign = 'center'; + + for ( var i = 0; i < nodeHistoryPosition && alpha > 0; i++ ) + { + + context.globalAlpha = alpha - historyAlphaDelta * tweenFactor; + context.fillText + ( + nodeHistory[nodeHistoryPosition - i - 1].name, + 0, + (i + tweenFactor) * historySpacingFactor * fontSize - 1 + ); + + if ( alpha > 0 ) + { + alpha -= historyAlphaDelta; + } + } + + context.globalAlpha = 1; +} + +function drawLegend() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + context.fillStyle = 'black'; + context.textAlign = 'start'; + context.font = fontNormal; +// context.fillText(valueStartText, textLeft, top + height); +// context.fillText(valueEndText, textLeft, top); + context.fillText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var gradient = context.createLinearGradient(0, top + height, 0, top); + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + gradient.addColorStop(hueStopPositions[i], hueStopHsl[i]); + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + context.fillText(hueStopText[i], textLeft, textY); + } + } + + context.fillStyle = gradient; + context.fillRect(left, top, width, height); + context.lineWidth = thinLineWidth; + context.strokeRect(left, top, width, height); +} + +function drawLegendSVG() +{ + var left = imageWidth * .01; + var width = imageHeight * .0265; + var height = imageHeight * .15; + var top = imageHeight - fontSize * 3.5 - height; + var textLeft = left + width + fontSize / 2; + + var text = ''; + + text += svgText(hueDisplayName, left, imageHeight - fontSize * 1.5); + + var svgtest = '<linearGradient id="gradient" x1="0%" y1="100%" x2="0%" y2="0%">'; + + for ( var i = 0; i < hueStopPositions.length; i++ ) + { + svgtest += + '<stop offset="' + round(hueStopPositions[i] * 100) + + '%" style="stop-color:' + hueStopHsl[i] + '"/>'; + + var textY = top + (1 - hueStopPositions[i]) * height; + + if + ( + i == 0 || + i == hueStopPositions.length - 1 || + textY > top + fontSize && textY < top + height - fontSize + ) + { + text += svgText(hueStopText[i], textLeft, textY); + } + } + + svgtest += '</linearGradient>'; + //alert(svgtest); + svg += svgtest; + svg += + '<rect style="fill:url(#gradient)" x="' + left + '" y="' + top + + '" width="' + width + '" height="' + height + '"/>'; + + svg += text; +} + +function drawSearchHighlights(label, bubbleX, bubbleY, rotation, center) +{ + var index = -1; + var labelLength = label.length; + + bubbleX -= fontSize / 4; + + do + { + index = label.toLowerCase().indexOf(search.value.toLowerCase(), index + 1); + + if ( index != -1 && index < labelLength ) + { + var dim = context.measureText(label.substr(0, index)); + var x = bubbleX + dim.width; + + dim = context.measureText(label.substr(index, search.value.length)); + + var y = bubbleY - fontSize * 3 / 4; + var width = dim.width + fontSize / 2; + var height = fontSize * 3 / 2; + var radius = fontSize / 2; + + if ( snapshotMode ) + { + if ( center ) + { + x += centerX; + y += centerY; + } + + svg += + '<rect x="' + x + '" y="' + y + + '" width="' + width + + '" height="' + height + + '" rx="' + radius + + '" ry="' + radius + + '" class="searchHighlight' + + '" transform="rotate(' + + degrees(rotation) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.fillStyle = 'rgb(255, 255, 100)'; + context.rotate(rotation); + roundedRectangle(x, y, width, height, radius); + context.fill(); + context.rotate(-rotation); + } + } + } + while ( index != -1 && index < labelLength ); +} + +function drawText(text, x, y, angle, anchor, bold, color) +{ + if ( color == undefined ) + { + color = 'black'; + } + + if ( snapshotMode ) + { + svg += + '<text x="' + (centerX + x) + '" y="' + (centerY + y) + + '" text-anchor="' + anchor + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" transform="rotate(' + degrees(angle) + ',' + centerX + ',' + centerY + ')">' + + text + '</text>'; + } + else + { + context.fillStyle = color; + context.textAlign = anchor; + context.font = bold ? fontBold : fontNormal; + context.rotate(angle); + context.fillText(text, x, y); + context.rotate(-angle); + } +} + +function drawTextPolar +( + text, + innerText, + angle, + radius, + radial, + bubble, + bold, + searchResult, + searchResults +) +{ + var anchor; + var textX; + var textY; + var spacer; + var totalText = text; + var flip; + + if ( snapshotMode ) + { + spacer = '   '; + } + else + { + spacer = ' '; + } + + if ( radial ) + { + flip = angle < 3 * Math.PI / 2; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + anchor = 'end'; + + if ( innerText ) + { + totalText = text + spacer + innerText; + } + } + else + { + anchor = 'start'; + + if ( innerText ) + { + totalText = innerText + spacer + text; + } + } + + textX = radius; + textY = 0; + } + else + { + flip = angle < Math.PI || angle > 2 * Math.PI; + var label; + + anchor = snapshotMode ? 'middle' : 'center'; + + if ( flip ) + { + angle -= Math.PI; + radius = -radius; + } + + angle += Math.PI / 2; + textX = 0; + textY = -radius; + } + + if ( bubble ) + { + var textActual = totalText; + + if ( innerText && snapshotMode ) + { + if ( flip ) + { + textActual = text + ' ' + innerText; + } + else + { + textActual = innerText + ' ' + text; + } + } + + if ( searchResults ) + { + textActual = textActual + searchResultString(searchResults); + } + + var textWidth = measureText(textActual, bold); + + var x = textX; + + if ( anchor == 'end' ) + { + x -= textWidth; + } + else if ( anchor != 'start' ) + { + // centered + x -= textWidth / 2; + } + + drawBubble(angle, radius, textWidth, radial, flip); + + if ( searchResult ) + { + drawSearchHighlights + ( + textActual, + x, + textY, + angle, + true + ) + } + } + + if ( searchResults ) + { + totalText = totalText + searchResultString(searchResults); + } + + drawText(totalText, textX, textY, angle, anchor, bold); + + return flip; +} + +function drawTick(start, length, angle) +{ + if ( snapshotMode ) + { + svg += + '<line x1="' + (centerX + start) + + '" y1="' + centerY + + '" x2="' + (centerX + start + length) + + '" y2="' + centerY + + '" class="tick" transform="rotate(' + + degrees(angle) + ',' + centerX + ',' + centerY + + ')"/>'; + } + else + { + context.rotate(angle); + context.beginPath(); + context.moveTo(start, 0); + context.lineTo(start + length, 0); + context.lineWidth = thinLineWidth * 2; + context.stroke(); + context.rotate(-angle); + } +} + +function drawWedge +( + angleStart, + angleEnd, + radiusInner, + radiusOuter, + color, + patternAlpha, + highlight +) +{ + if ( context.globalAlpha == 0 ) + { + return; + } + + if ( snapshotMode ) + { + if ( angleEnd == angleStart + Math.PI * 2 ) + { + // fudge to prevent overlap, which causes arc ambiguity + // + angleEnd -= .1 / gRadius; + } + + var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; + + var x1 = centerX + radiusInner * Math.cos(angleStart); + var y1 = centerY + radiusInner * Math.sin(angleStart); + + var x2 = centerX + gRadius * Math.cos(angleStart); + var y2 = centerY + gRadius * Math.sin(angleStart); + + var x3 = centerX + gRadius * Math.cos(angleEnd); + var y3 = centerY + gRadius * Math.sin(angleEnd); + + var x4 = centerX + radiusInner * Math.cos(angleEnd); + var y4 = centerY + radiusInner * Math.sin(angleEnd); + + var dArray = + [ + " M ", x1, ",", y1, + " L ", x2, ",", y2, + " A ", gRadius, ",", gRadius, " 0 ", longArc, ",1 ", x3, ",", y3, + " L ", x4, ",", y4, + " A ", radiusInner, ",", radiusInner, " 0 ", longArc, " 0 ", x1, ",", y1, + " Z " + ]; + + svg += + '<path class="'+ (highlight ? 'highlight' : 'wedge') + '" fill="' + color + + '" d="' + dArray.join('') + '"/>'; + + if ( patternAlpha > 0 ) + { + svg += + '<path class="wedge" fill="url(#hiddenPattern)" d="' + + dArray.join('') + '"/>'; + } + } + else + { + // fudge to prevent seams during animation + // + angleEnd += 1 / gRadius; + + context.fillStyle = color; + context.beginPath(); + context.arc(0, 0, radiusInner, angleStart, angleEnd, false); + context.arc(0, 0, radiusOuter, angleEnd, angleStart, true); + context.closePath(); + context.fill(); + + if ( patternAlpha > 0 ) + { + context.save(); + context.clip(); + context.globalAlpha = patternAlpha; + context.fillStyle = hiddenPattern; + context.fill(); + context.restore(); + } + + if ( highlight ) + { + context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; + context.strokeStyle = 'black'; + context.stroke(); + } + } +} + +function expand(node) +{ + selectNode(node); + updateView(); +} + +function focusLost() +{ + mouseX = -1; + mouseY = -1; + checkHighlight(); + document.body.style.cursor = 'auto'; +} + +function fontSizeDecrease() +{ + if ( fontSize > 1 ) + { + fontSize--; + updateViewNeeded = true; + } +} + +function fontSizeIncrease() +{ + fontSize++; + updateViewNeeded = true; +} + +function getGetString(name, value, bool) +{ + return name + '=' + (bool ? value ? 'true' : 'false' : value); +} + +function hideLink() +{ + hide(linkText); + show(linkButton); +} + +function show(object) +{ + object.style.display = 'inline'; +} + +function hide(object) +{ + object.style.display = 'none'; +} + +function showLink() +{ + var urlHalves = String(document.location).split('?'); + var newGetVariables = new Array(); + + newGetVariables.push + ( + getGetString('dataset', currentDataset, false), + getGetString('node', selectedNode.id, false), + getGetString('collapse', collapse, true), + getGetString('color', useHue(), true), + getGetString('depth', maxAbsoluteDepth - 1, false), + getGetString('font', fontSize, false), + getGetString('key', showKeys, true) + ); + + hide(linkButton); + show(linkText); + linkText.value = urlHalves[0] + '?' + getVariables.concat(newGetVariables).join('&'); + //linkText.disabled = false; + linkText.focus(); + linkText.select(); + //linkText.disabled = true; +// document.location = urlHalves[0] + '?' + getVariables.join('&'); +} + +function getFirstChild(element) +{ + element = element.firstChild; + + if ( element && element.nodeType != 1 ) + { + element = getNextSibling(element); + } + + return element; +} + +function getNextSibling(element) +{ + do + { + element = element.nextSibling; + } + while ( element && element.nodeType != 1 ); + + return element; +} + +function getPercentage(fraction) +{ + return round(fraction * 100); +} + +function hslText(hue) +{ + if ( 1 || snapshotMode ) + { + // Safari doesn't seem to allow hsl() in SVG + + var rgb = hslToRgb(hue, saturation, (lightnessBase + lightnessMax) / 2); + + return rgbText(rgb.r, rgb.g, rgb.b); + } + else + { + var hslArray = + [ + 'hsl(', + Math.floor(hue * 360), + ',', + Math.floor(saturation * 100), + '%,', + Math.floor((lightnessBase + lightnessMax) * 50), + '%)' + ]; + + return hslArray.join(''); + } +} + +function hslToRgb(h, s, l) +{ + var m1, m2; + var r, g, b; + + if (s == 0) + { + r = g = b = Math.floor((l * 255)); + } + else + { + if (l <= 0.5) + { + m2 = l * (s + 1); + } + else + { + m2 = l + s - l * s; + } + + m1 = l * 2 - m2; + + r = Math.floor(hueToRgb(m1, m2, h + 1 / 3)); + g = Math.floor(hueToRgb(m1, m2, h)); + b = Math.floor(hueToRgb(m1, m2, h - 1/3)); + } + + return {r: r, g: g, b: b}; +} + +function hueToRgb(m1, m2, hue) +{ + var v; + + while (hue < 0) + { + hue += 1; + } + + while (hue > 1) + { + hue -= 1; + } + + if (6 * hue < 1) + v = m1 + (m2 - m1) * hue * 6; + else if (2 * hue < 1) + v = m2; + else if (3 * hue < 2) + v = m1 + (m2 - m1) * (2/3 - hue) * 6; + else + v = m1; + + return 255 * v; +} + +function interpolateHue(hueStart, hueEnd, valueStart, valueEnd) +{ + // since the gradient will be RGB based, we need to add stops to hit all the + // colors in the hue spectrum + + hueStopPositions = new Array(); + hueStopHsl = new Array(); + hueStopText = new Array(); + + hueStopPositions.push(0); + hueStopHsl.push(hslText(hueStart)); + hueStopText.push(round(valueStart)); + + for + ( + var i = (hueStart > hueEnd ? 5 / 6 : 1 / 6); + (hueStart > hueEnd ? i > 0 : i < 1); + i += (hueStart > hueEnd ? -1 : 1) / 6 + ) + { + if + ( + hueStart > hueEnd ? + i > hueEnd && i < hueStart : + i > hueStart && i < hueEnd + ) + { + hueStopPositions.push(lerp(i, hueStart, hueEnd, 0, 1)); + hueStopHsl.push(hslText(i)); + hueStopText.push(round(lerp + ( + i, + hueStart, + hueEnd, + valueStart, + valueEnd + ))); + } + } + + hueStopPositions.push(1); + hueStopHsl.push(hslText(hueEnd)); + hueStopText.push(round(valueEnd)); +} + +function keyLineAngle(angle, keyAngle, bendRadius, keyX, keyY, pointsX, pointsY) +{ + if ( angle < Math.PI / 2 && keyY < bendRadius * Math.sin(angle) + || angle > Math.PI / 2 && keyY < bendRadius) + { + return Math.asin(keyY / bendRadius); + } + else + { + // find the angle of the normal to a tangent line that goes to + // the label + + var textDist = Math.sqrt + ( + Math.pow(keyX, 2) + + Math.pow(keyY, 2) + ); + + var tanAngle = Math.acos(bendRadius / textDist) + keyAngle; + + if ( angle < tanAngle || angle < Math.PI / 2 )//|| labelLeft < centerX ) + { + // angle doesn't reach far enough for tangent; collapse and + // connect directly to label + + if ( keyY / Math.tan(angle) > 0 ) + { + pointsX.push(keyY / Math.tan(angle)); + pointsY.push(keyY); + } + else + { + pointsX.push(bendRadius * Math.cos(angle)); + pointsY.push(bendRadius * Math.sin(angle)); + } + + return angle; + } + else + { + return tanAngle; + } + } +} + +function keyOffset() +{ + return imageHeight - (keys - currentKey + 1) * (keySize + keyBuffer) + keyBuffer - margin; +} + +function lerp(value, fromStart, fromEnd, toStart, toEnd) +{ + return (value - fromStart) * + (toEnd - toStart) / + (fromEnd - fromStart) + + toStart; +} + +function createCanvas() +{ + canvas = document.createElement('canvas'); + document.body.appendChild(canvas); + context = canvas.getContext('2d'); +} + +function load() +{ + document.body.style.overflow = "hidden"; + document.body.style.margin = 0; + + createCanvas(); + + if ( context == undefined ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + if ( typeof context.fillText != 'function' ) + { + document.body.innerHTML = '\ +<br/>This browser does not support HTML5 canvas text (see \ +<a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).\ + '; + return; + } + + resize(); + + var kronaElement = document.getElementsByTagName('krona')[0]; + + var magnitudeName; + var hueName; + var hueDefault; + var hueStart; + var hueEnd; + var valueStart; + var valueEnd; + + if ( kronaElement.getAttribute('collapse') != undefined ) + { + collapse = kronaElement.getAttribute('collapse') == 'true'; + } + + if ( kronaElement.getAttribute('key') != undefined ) + { + showKeys = kronaElement.getAttribute('key') == 'true'; + } + + for + ( + var element = getFirstChild(kronaElement); + element; + element = getNextSibling(element) + ) + { + switch ( element.tagName.toLowerCase() ) + { + case 'attributes': + magnitudeName = element.getAttribute('magnitude'); + // + for + ( + var attributeElement = getFirstChild(element); + attributeElement; + attributeElement = getNextSibling(attributeElement) + ) + { + var tag = attributeElement.tagName.toLowerCase(); + + if ( tag == 'attribute' ) + { + var attribute = new Attribute(); + attribute.name = attributeElement.firstChild.nodeValue.toLowerCase(); + attribute.displayName = attributeElement.getAttribute('display'); + + if ( attributeElement.getAttribute('hrefBase') ) + { + attribute.hrefBase = attributeElement.getAttribute('hrefBase'); + } + + if ( attributeElement.getAttribute('target') ) + { + attribute.target = attributeElement.getAttribute('target'); + } + + if ( attribute.name == magnitudeName ) + { + magnitudeIndex = attributes.length; + } + + if ( attributeElement.getAttribute('listAll') ) + { + attribute.listAll = attributeElement.getAttribute('listAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('listNode') ) + { + attribute.listNode = attributeElement.getAttribute('listNode').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataAll') ) + { + attribute.dataAll = attributeElement.getAttribute('dataAll').toLowerCase(); + } + else if ( attributeElement.getAttribute('dataNode') ) + { + attribute.dataNode = attributeElement.getAttribute('dataNode').toLowerCase(); + } + + if ( attributeElement.getAttribute('postUrl') ) + { + attribute.postUrl = attributeElement.getAttribute('postUrl'); + } + + if ( attributeElement.getAttribute('postVar') ) + { + attribute.postVar = attributeElement.getAttribute('postVar'); + } + + if ( attributeElement.getAttribute('mono') ) + { + attribute.mono = true; + } + + attributes.push(attribute); + } + else if ( tag == 'list' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.list = true; + attributes.push(attribute); + } + else if ( tag == 'data' ) + { + var attribute = new Attribute(); + + attribute.name = attributeElement.firstChild.nodeValue; + attribute.data = true; + attributes.push(attribute); + + var enableScript = document.createElement('script'); + var date = new Date(); + enableScript.src = + attributeElement.getAttribute('enable') + '?' + + date.getTime(); + document.body.appendChild(enableScript); + } + } + break; + + case 'color': + hueName = element.getAttribute('attribute'); + hueStart = Number(element.getAttribute('hueStart')) / 360; + hueEnd = Number(element.getAttribute('hueEnd')) / 360; + valueStart = Number(element.getAttribute('valueStart')); + valueEnd = Number(element.getAttribute('valueEnd')); + // + interpolateHue(hueStart, hueEnd, valueStart, valueEnd); + // + if ( element.getAttribute('default') == 'true' ) + { + hueDefault = true; + } + break; + + case 'datasets': + datasetNames = new Array(); + // + for ( j = getFirstChild(element); j; j = getNextSibling(j) ) + { + datasetNames.push(j.firstChild.nodeValue); + } + datasets = datasetNames.length; + break; + + case 'node': + head = loadTreeDOM + ( + element, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + break; + } + } + + // get GET options + // + var urlHalves = String(document.location).split('?'); + var datasetDefault = 0; + var maxDepthDefault; + var nodeDefault = 0; + // + if ( urlHalves[1] ) + { + var vars = urlHalves[1].split('&'); + + for ( i = 0; i < vars.length; i++ ) + { + var pair = vars[i].split('='); + + switch ( pair[0] ) + { + case 'collapse': + collapse = pair[1] == 'true'; + break; + + case 'color': + hueDefault = pair[1] == 'true'; + break; + + case 'dataset': + datasetDefault = Number(pair[1]); + break; + + case 'depth': + maxDepthDefault = Number(pair[1]) + 1; + break; + + case 'key': + showKeys = pair[1] == 'true'; + break; + + case 'font': + fontSize = Number(pair[1]); + break; + + case 'node': + nodeDefault = Number(pair[1]); + break; + + default: + getVariables.push(pair[0] + '=' + pair[1]); + break; + } + } + } + + addOptionElements(hueName, hueDefault); + setCallBacks(); + + head.sort(); + maxAbsoluteDepth = 0; + selectDataset(datasetDefault); + + if ( maxDepthDefault && maxDepthDefault < head.maxDepth ) + { + maxAbsoluteDepth = maxDepthDefault; + } + else + { + maxAbsoluteDepth = head.maxDepth; + } + + selectNode(nodes[nodeDefault]); + + setInterval(update, 20); + + window.onresize = handleResize; + updateMaxAbsoluteDepth(); + updateViewNeeded = true; +} + +function loadTreeDOM +( + domNode, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd +) +{ + var newNode = new Node(); + + newNode.name = domNode.getAttribute('name'); + + if ( domNode.getAttribute('href') ) + { + newNode.href = domNode.getAttribute('href'); + } + + if ( hueName ) + { + newNode.hues = new Array(); + } + + for ( var i = getFirstChild(domNode); i; i = getNextSibling(i) ) + { + switch ( i.tagName.toLowerCase() ) + { + case 'node': + var newChild = loadTreeDOM + ( + i, + magnitudeName, + hueName, + hueStart, + hueEnd, + valueStart, + valueEnd + ); + newChild.parent = newNode; + newNode.children.push(newChild); + break; + + default: + var attributeName = i.tagName.toLowerCase(); + var index = attributeIndex(attributeName); + // + newNode.attributes[index] = new Array(); + // + for ( var j = getFirstChild(i); j; j = getNextSibling(j) ) + { + if ( attributes[index] == undefined ) + { + var x = 5; + } + if ( attributes[index].list ) + { + newNode.attributes[index].push(new Array()); + + for ( var k = getFirstChild(j); k; k = getNextSibling(k) ) + { + newNode.attributes[index][newNode.attributes[index].length - 1].push(k.firstChild.nodeValue); + } + } + else + { + var value = j.firstChild ? j.firstChild.nodeValue : ''; + + if ( j.getAttribute('href') ) + { + var target; + + if ( attributes[index].target ) + { + target = ' target="' + attributes[index].target + '"'; + } + + value = '<a href="' + attributes[index].hrefBase + j.getAttribute('href') + '"' + target + '>' + value + '</a>'; + } + + newNode.attributes[index].push(value); + } + } + // + if ( attributeName == magnitudeName || attributeName == hueName ) + { + for ( j = 0; j < datasets; j++ ) + { + var value = newNode.attributes[index][j] == undefined ? 0 : Number(newNode.attributes[index][j]); + + newNode.attributes[index][j] = value; + + if ( attributeName == hueName ) + { + var hue = lerp + ( + value, + valueStart, + valueEnd, + hueStart, + hueEnd + ); + + if ( hue < hueStart == hueStart < hueEnd ) + { + hue = hueStart; + } + else if ( hue > hueEnd == hueStart < hueEnd ) + { + hue = hueEnd; + } + + newNode.hues[j] = hue; + } + } + + if ( attributeName == hueName ) + { + newNode.hue = new Tween(newNode.hues[0], newNode.hues[0]); + } + } + break; + } + } + + return newNode; +} + +function maxAbsoluteDepthDecrease() +{ + if ( maxAbsoluteDepth > 2 ) + { + maxAbsoluteDepth--; + head.setMaxDepths(); + handleResize(); + } +} + +function maxAbsoluteDepthIncrease() +{ + if ( maxAbsoluteDepth < head.maxDepth ) + { + maxAbsoluteDepth++; + head.setMaxDepths(); + handleResize(); + } +} + +function measureText(text, bold) +{ + context.font = bold ? fontBold : fontNormal; + var dim = context.measureText(text); + return dim.width; +} + +function min(a, b) +{ + return a < b ? a : b; +} + +function minWidth() +{ + // Min wedge width (at center) for displaying a node (or for displaying a + // label if it's at the highest level being viewed, multiplied by 2 to make + // further calculations simpler + + return (fontSize * 2.3); +} + +function mouseMove(e) +{ + mouseX = e.pageX; + mouseY = e.pageY - headerHeight; + mouseXRel = (mouseX - centerX) * backingScale() + mouseYRel = (mouseY - centerY) * backingScale() + + if ( head && ! quickLook ) + { + checkHighlight(); + } +} + +function mouseClick(e) +{ + if ( highlightedNode == focusNode && focusNode != selectedNode || selectedNode.hasParent(highlightedNode) ) + { + if ( highlightedNode.hasChildren() ) + { + expand(highlightedNode); + } + } + else if ( progress == 1 )//( highlightedNode != selectedNode ) + { + setFocus(highlightedNode); +// document.body.style.cursor='ew-resize'; + draw(); + checkHighlight(); + var date = new Date(); + mouseDownTime = date.getTime(); + mouseDown = true; + } +} + +function mouseUp(e) +{ + if ( quickLook ) + { + navigateBack(); + quickLook = false; + } + + mouseDown = false; +} + +function navigateBack() +{ + if ( nodeHistoryPosition > 0 ) + { + nodeHistory[nodeHistoryPosition] = selectedNode; + nodeHistoryPosition--; + + if ( nodeHistory[nodeHistoryPosition].collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + setSelectedNode(nodeHistory[nodeHistoryPosition]); + updateDatasetButtons(); + updateView(); + } +} + +function navigateUp() +{ + if ( selectedNode.getParent() ) + { + selectNode(selectedNode.getParent()); + updateView(); + } +} + +function navigateForward() +{ + if ( nodeHistoryPosition < nodeHistory.length - 1 ) + { + nodeHistoryPosition++; + var newNode = nodeHistory[nodeHistoryPosition]; + + if ( newNode.collapse ) + { + collapseCheckBox.checked = collapse = false; + } + + if ( nodeHistoryPosition == nodeHistory.length - 1 ) + { + // this will ensure the forward button is disabled + + nodeHistory.length = nodeHistoryPosition; + } + + setSelectedNode(newNode); + updateDatasetButtons(); + updateView(); + } +} + +function nextDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == datasets - 1 ) + { + newDataset = 0; + } + else + { + newDataset++; + } + } + while ( datasetDropDown.options[newDataset].disabled ) + + selectDataset(newDataset); +} + +function onDatasetChange() +{ + selectDataset(datasetDropDown.selectedIndex); +} + +function onKeyDown(event) +{ + if + ( + event.keyCode == 37 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateBack(); + event.preventDefault(); + } + else if + ( + event.keyCode == 39 && + document.activeElement.id != 'search' && + document.activeElement.id != 'linkText' + ) + { + navigateForward(); + event.preventDefault(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { + prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { + nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 9 && datasets > 1 ) + { + selectLastDataset(); + event.preventDefault(); + } + else if ( event.keyCode == 83 ) + { + progress += .2; + } + else if ( event.keyCode == 66 ) + { + progress -= .2; + } + else if ( event.keyCode == 70 ) + { + progress = 1; + } +} + +function onKeyPress(event) +{ + if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onKeyUp(event) +{ + if ( event.keyCode == 27 && document.activeElement.id == 'search' ) + { + search.value = ''; + onSearchChange(); + } + else if ( event.keyCode == 38 && datasets > 1 ) + { +// prevDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } + else if ( event.keyCode == 40 && datasets > 1 ) + { +// nextDataset(); + + //if ( document.activeElement.id == 'datasets' ) + { + event.preventDefault(); + } + } +} + +function onSearchChange() +{ + nSearchResults = 0; + head.search(); + + if ( search.value == '' ) + { + searchResults.innerHTML = ''; + } + else + { + searchResults.innerHTML = nSearchResults + ' results'; + } + + setFocus(selectedNode); + draw(); +} + +function post(url, variable, value, postWindow) +{ + var form = document.createElement('form'); + var input = document.createElement('input'); + var inputDataset = document.createElement('input'); + + form.appendChild(input); + form.appendChild(inputDataset); + + form.method = "POST"; + form.action = url; + + if ( postWindow == undefined ) + { + form.target = '_blank'; + postWindow = window; + } + + input.type = 'hidden'; + input.name = variable; + input.value = value; + + inputDataset.type = 'hidden'; + inputDataset.name = 'dataset'; + inputDataset.value = currentDataset; + + postWindow.document.body.appendChild(form); + form.submit(); +} + +function prevDataset() +{ + var newDataset = currentDataset; + + do + { + if ( newDataset == 0 ) + { + newDataset = datasets - 1; + } + else + { + newDataset--; + } + } + while ( datasetDropDown.options[newDataset].disabled ); + + selectDataset(newDataset); +} + +function radiusDecrease() +{ + if ( bufferFactor < .309 ) + { + bufferFactor += .03; + updateViewNeeded = true; + } +} + +function radiusIncrease() +{ + if ( bufferFactor > .041 ) + { + bufferFactor -= .03; + updateViewNeeded = true; + } +} + +function resetKeyOffset() +{ + currentKey = 1; + keyMinTextLeft = centerX + gRadius + buffer - buffer / (keys + 1) / 2 + fontSize / 2; + keyMinAngle = 0; +} + +function rgbText(r, g, b) +{ + var rgbArray = + [ + "rgb(", + Math.floor(r), + ",", + Math.floor(g), + ",", + Math.floor(b), + ")" + ]; + + return rgbArray.join(''); +} + +function round(number) +{ + if ( number >= 1 || number <= -1 ) + { + return number.toFixed(0); + } + else + { + return number.toPrecision(1); + } +} + +function roundedRectangle(x, y, width, height, radius) +{ + if ( radius * 2 > width ) + { + radius = width / 2; + } + + if ( radius * 2 > height ) + { + radius = height / 2; + } + + context.beginPath(); + context.arc(x + radius, y + radius, radius, Math.PI, Math.PI * 3 / 2, false); + context.lineTo(x + width - radius, y); + context.arc(x + width - radius, y + radius, radius, Math.PI * 3 / 2, Math.PI * 2, false); + context.lineTo(x + width, y + height - radius); + context.arc(x + width - radius, y + height - radius, radius, 0, Math.PI / 2, false); + context.lineTo(x + radius, y + height); + context.arc(x + radius, y + height - radius, radius, Math.PI / 2, Math.PI, false); + context.lineTo(x, y + radius); +} + +function passClick(e) +{ + mouseClick(e); +} + +function searchResultString(results) +{ + var searchResults = this.searchResults; + + if ( this.isSearchResult ) + { + // don't count ourselves + searchResults--; + } + + return ' - ' + results + (results > 1 ? ' results' : ' result'); +} + +function setCallBacks() +{ + canvas.onselectstart = function(){return false;} // prevent unwanted highlighting + options.onselectstart = function(){return false;} // prevent unwanted highlighting + document.onmousemove = mouseMove; + window.onblur = focusLost; + window.onmouseout = focusLost; + document.onkeyup = onKeyUp; + document.onkeydown = onKeyDown; + canvas.onmousedown = mouseClick; + document.onmouseup = mouseUp; + keyControl.onclick = toggleKeys; + collapseCheckBox = document.getElementById('collapse'); + collapseCheckBox.checked = collapse; + collapseCheckBox.onclick = handleResize; + collapseCheckBox.onmousedown = suppressEvent; + maxAbsoluteDepthText = document.getElementById('maxAbsoluteDepth'); + maxAbsoluteDepthButtonDecrease = document.getElementById('maxAbsoluteDepthDecrease'); + maxAbsoluteDepthButtonIncrease = document.getElementById('maxAbsoluteDepthIncrease'); + maxAbsoluteDepthButtonDecrease.onclick = maxAbsoluteDepthDecrease; + maxAbsoluteDepthButtonIncrease.onclick = maxAbsoluteDepthIncrease; + maxAbsoluteDepthButtonDecrease.onmousedown = suppressEvent; + maxAbsoluteDepthButtonIncrease.onmousedown = suppressEvent; + fontSizeText = document.getElementById('fontSize'); + fontSizeButtonDecrease = document.getElementById('fontSizeDecrease'); + fontSizeButtonIncrease = document.getElementById('fontSizeIncrease'); + fontSizeButtonDecrease.onclick = fontSizeDecrease; + fontSizeButtonIncrease.onclick = fontSizeIncrease; + fontSizeButtonDecrease.onmousedown = suppressEvent; + fontSizeButtonIncrease.onmousedown = suppressEvent; + radiusButtonDecrease = document.getElementById('radiusDecrease'); + radiusButtonIncrease = document.getElementById('radiusIncrease'); + radiusButtonDecrease.onclick = radiusDecrease; + radiusButtonIncrease.onclick = radiusIncrease; + radiusButtonDecrease.onmousedown = suppressEvent; + radiusButtonIncrease.onmousedown = suppressEvent; + maxAbsoluteDepth = 0; + backButton = document.getElementById('back'); + backButton.onclick = navigateBack; + backButton.onmousedown = suppressEvent; + forwardButton = document.getElementById('forward'); + forwardButton.onclick = navigateForward; + forwardButton.onmousedown = suppressEvent; + snapshotButton = document.getElementById('snapshot'); + snapshotButton.onclick = snapshot; + snapshotButton.onmousedown = suppressEvent; + detailsName = document.getElementById('detailsName'); + detailsExpand = document.getElementById('detailsExpand'); + detailsInfo = document.getElementById('detailsInfo'); + search = document.getElementById('search'); + search.onkeyup = onSearchChange; + search.onmousedown = suppressEvent; + searchResults = document.getElementById('searchResults'); + useHueDiv = document.getElementById('useHueDiv'); + linkButton = document.getElementById('linkButton'); + linkButton.onclick = showLink; + linkButton.onmousedown = suppressEvent; + linkText = document.getElementById('linkText'); + linkText.onblur = hideLink; + linkText.onmousedown = suppressEvent; + hide(linkText); + var helpButton = document.getElementById('help'); + helpButton.onmousedown = suppressEvent; + var searchClear = document.getElementById('searchClear'); + searchClear.onmousedown = suppressEvent; + if ( datasets > 1 ) + { + datasetDropDown.onmousedown = suppressEvent; + var prevDatasetButton = document.getElementById('prevDataset'); + prevDatasetButton.onmousedown = suppressEvent; + var nextDatasetButton = document.getElementById('nextDataset'); + nextDatasetButton.onmousedown = suppressEvent; + var lastDatasetButton = document.getElementById('lastDataset'); + lastDatasetButton.onmousedown = suppressEvent; + } + + image = document.getElementById('hiddenImage'); + image.onload = function() + { + hiddenPattern = context.createPattern(image, 'repeat'); + } + + var loadingImageElement = document.getElementById('loadingImage'); + + if ( loadingImageElement ) + { + loadingImage = loadingImageElement.src; + } +} + +function selectDataset(newDataset) +{ + lastDataset = currentDataset; + currentDataset = newDataset + if ( datasets > 1 ) + { + datasetDropDown.selectedIndex = currentDataset; + updateDatasetButtons(); + datasetAlpha.start = 1.5; + datasetChanged = true; + } + head.setMagnitudes(0); + head.setDepth(1, 1); + head.setMaxDepths(); + handleResize(); +} + +function selectLastDataset() +{ + selectDataset(lastDataset); + handleResize(); +} + +function selectNode(newNode) +{ + if ( selectedNode != newNode ) + { + // truncate history at current location to create a new branch + // + nodeHistory.length = nodeHistoryPosition; + + if ( selectedNode != 0 ) + { + nodeHistory.push(selectedNode); + nodeHistoryPosition++; + } + + setSelectedNode(newNode); + //updateView(); + } + + updateDatasetButtons(); +} + +function setFocus(node) +{ + if ( node == focusNode ) + { +// return; + } + + focusNode = node; + + if ( node.href ) + { + detailsName.innerHTML = + '<a target="_blank" href="' + node.href + '">' + node.name + '</a>'; + } + else + { + detailsName.innerHTML = node.name; + } + + var table = '<table>'; + //TODO: use CSS margins instead of an additional column + table += '<tr><td></td><td></td></tr>'; + + for ( var i = 0; i < node.attributes.length; i++ ) + { + if ( attributes[i].displayName && node.attributes[i] != undefined ) + { + var index = node.attributes[i].length == 1 && attributes[i].mono ? 0 : currentDataset; + + if ( typeof node.attributes[i][currentDataset] == 'number' || node.attributes[i][index] != undefined && node.attributes[i][currentDataset] != '' ) + { + var value = node.attributes[i][index]; + + if ( attributes[i].listNode != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listNode) + ',' + i + + ',false);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].listAll != undefined ) + { + value = + '<a href="" onclick="showList(' + + attributeIndex(attributes[i].listAll) + ',' + i + + ',true);return false;" title="Show list">' + + value + '</a>'; + } + else if ( attributes[i].dataNode != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataNode) + ',' + i + + ',false);return false;" title="Show data">' + + value + '</a>'; + } + else if ( attributes[i].dataAll != undefined && dataEnabled ) + { + value = + '<a href="" onclick="showData(' + + attributeIndex(attributes[i].dataAll) + ',' + i + + ',true);return false;" title="Show data">' + + value + '</a>'; + } + + table += + '<tr><td><strong>' + attributes[i].displayName + ':</strong></td><td>' + + value + '</td></tr>'; + } + } + } + + table += '</table>'; + detailsInfo.innerHTML = table; + + detailsExpand.disabled = !focusNode.hasChildren() || focusNode == selectedNode; +} + +function setSelectedNode(newNode) +{ + if ( selectedNode && selectedNode.hasParent(newNode) ) + { + zoomOut = true; + } + else + { + zoomOut = false; + } + + selectedNodeLast = selectedNode; + selectedNode = newNode; + + //if ( focusNode != selectedNode ) + { + setFocus(selectedNode); + } +} + +function waitForData(dataWindow, target, title, time, postUrl, postVar) +{ + if ( nodeData.length == target ) + { + if ( postUrl != undefined ) + { + for ( var i = 0; i < nodeData.length; i++ ) + { + nodeData[i] = nodeData[i].replace(/\n/g, ','); + } + + var postString = nodeData.join(''); + postString = postString.slice(0, -1); + + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + + post(postUrl, postVar, postString, dataWindow); + } + else + { + //dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + //document.body.removeChild(document.getElementById('data')); + + dataWindow.document.open(); + dataWindow.document.write('<pre>' + nodeData.join('') + '</pre>'); + dataWindow.document.close(); + } + + dataWindow.document.title = title; // replace after document.write() + } + else + { + var date = new Date(); + + if ( date.getTime() - time > 10000 ) + { + dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); + document.body.removeChild(document.getElementById('data')); + dataWindow.document.body.innerHTML = + 'Timed out loading supplemental files for:<br/>' + document.location; + } + else + { + setTimeout(function() {waitForData(dataWindow, target, title, time, postUrl, postVar);}, 100); + } + } +} + +function data(newData) +{ + nodeData.push(newData); +} + +function enableData() +{ + dataEnabled = true; +} + +function showData(indexData, indexAttribute, summary) +{ + var dataWindow = window.open('', '_blank'); + var title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + dataWindow.document.title = title; + + nodeData = new Array(); + + if ( dataWindow && dataWindow.document && dataWindow.document.body != null ) + { + //var loadImage = document.createElement('img'); + //loadImage.src = "file://localhost/Users/ondovb/Krona/KronaTools/img/loading.gif"; + //loadImage.id = "loading"; + //loadImage.alt = "Loading..."; + //dataWindow.document.body.appendChild(loadImage); + dataWindow.document.body.innerHTML = + '<img id="loading" src="' + loadingImage + '" alt="Loading..."></img>'; + } + + var scripts = document.createElement('div'); + scripts.id = 'data'; + document.body.appendChild(scripts); + + var files = focusNode.getData(indexData, summary); + + var date = new Date(); + var time = date.getTime(); + + for ( var i = 0; i < files.length; i++ ) + { + var script = document.createElement('script'); + script.src = files[i] + '?' + time; + scripts.appendChild(script); + } + + waitForData(dataWindow, files.length, title, time, attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar); + + return false; +} + +function showList(indexList, indexAttribute, summary) +{ + var list = focusNode.getList(indexList, summary); + + if ( attributes[indexAttribute].postUrl != undefined ) + { + post(attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar, list.join(',')); + } + else + { + var dataWindow = window.open('', '_blank'); + + if ( true || navigator.appName == 'Microsoft Internet Explorer' ) // :( + { + dataWindow.document.open(); + dataWindow.document.write('<pre>' + list.join('\n') + '</pre>'); + dataWindow.document.close(); + } + else + { + var pre = document.createElement('pre'); + dataWindow.document.body.appendChild(pre); + pre.innerHTML = list; + } + + dataWindow.document.title = 'Krona - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; + } +} + +function snapshot() +{ + svg = svgHeader(); + + resetKeyOffset(); + + snapshotMode = true; + + selectedNode.draw(false, true); + selectedNode.draw(true, true); + + if ( focusNode != 0 && focusNode != selectedNode ) + { + context.globalAlpha = 1; + focusNode.drawHighlight(true); + } + + if ( hueDisplayName && useHue() ) + { + drawLegendSVG(); + } + + snapshotMode = false; + + svg += svgFooter(); + + var snapshotWindow = window.open('', '_blank', '', 'replace=false'); + snapshotWindow.document.write('<html><body><a href="data:image/svg+xml,' + encodeURIComponent(svg) + '" download="snapshot.svg">Download Snapshot</a></html></body>'); + snapshotWindow.document.write(svg); +} + +function save() +{ + alert(document.body.innerHTML); +} + +function spacer() +{ + if ( snapshotMode ) + { + return '   '; + } + else + { + return ' '; + } +} + +function suppressEvent(e) +{ + e.cancelBubble = true; + if (e.stopPropagation) e.stopPropagation(); +} + +function svgFooter() +{ + return '</svg>'; +} + +function svgHeader() +{ + var patternWidth = fontSize * .6;//radius / 50; + + return '\ +<?xml version="1.0" standalone="no"?>\ +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" \ + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\ +<svg width="' + imageWidth + '" height="' + imageHeight + '" version="1.1"\ + xmlns="http://www.w3.org/2000/svg">\ +<title>Krona (snapshot) - ' + +(datasets > 1 ? datasetNames[currentDataset] + ' - ' : '') + selectedNode.name + +'</title>\ +<defs>\ + <style type="text/css">\ + text {font-size: ' + fontSize + 'px; font-family: ' + fontFamily + '; dominant-baseline:central}\ + path {stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + path.wedge {stroke:none}\ + path.line {fill:none;stroke:black;}\ + line {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + line.tick {stroke-width:' + thinLineWidth * fontSize / 6 + ';}\ + line.pattern {stroke-width:' + thinLineWidth * fontSize / 18 + ';}\ + circle {fill:none;stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + rect {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ + .highlight {stroke:black;stroke-width:'+ highlightLineWidth * fontSize / 12 + ';}\ + .searchHighlight {fill:rgb(255, 255, 100);stroke:none;}\ + </style>\ +<pattern id="hiddenPattern" patternUnits="userSpaceOnUse" \ +x="0" y="0" width="' + patternWidth + '" height="' + patternWidth + '">\ +<line class="pattern" x1="0" y1="0" x2="' + patternWidth / 2 + '" y2="' + patternWidth / 2 + '"/>\ +<line class="pattern" x1="' + patternWidth / 2 + '" y1="' + patternWidth + +'" x2="' + patternWidth + '" y2="' + patternWidth / 2 + '"/>\ +</pattern>\ +</defs>\ +'; +} + +function svgText(text, x, y, anchor, bold, color) +{ + if ( typeof(anchor) == 'undefined' ) + { + anchor = 'start'; + } + + if ( color == undefined ) + { + color = 'black'; + } + + return '<text x="' + x + '" y="' + y + + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + + '" text-anchor="' + anchor + '">' + text + '</text>'; +} + +function toggleKeys() +{ + if ( showKeys ) + { + keyControl.value = '…'; + showKeys = false; + } + else + { + keyControl.value = 'x'; + showKeys = true; + } + + updateKeyControl(); + + if ( progress == 1 ) + { + draw(); + } +} + +function update() +{ + if ( ! head ) + { + return; + } + + if ( mouseDown && focusNode != selectedNode ) + { + var date = new Date(); + + if ( date.getTime() - mouseDownTime > quickLookHoldLength ) + { + if ( focusNode.hasChildren() ) + { + expand(focusNode); + quickLook = true; + } + } + } + + if ( updateViewNeeded ) + { + resize(); + mouseX = -1; + mouseY = -1; + + collapse = collapseCheckBox.checked; + compress = true;//compressCheckBox.checked; + shorten = true;//shortenCheckBox.checked; + + checkSelectedCollapse(); + updateMaxAbsoluteDepth(); + + if ( focusNode.getCollapse() || focusNode.depth > maxAbsoluteDepth ) + { + setFocus(selectedNode); + } + else + { + setFocus(focusNode); + } + + updateView(); + + updateViewNeeded = false; + } + + var date = new Date(); + progress = (date.getTime() - tweenStartTime) / tweenLength; +// progress += .01; + + if ( progress >= 1 ) + { + progress = 1; + } + + if ( progress != progressLast ) + { + tweenFactor =// progress; + (1 / (1 + Math.exp(-tweenCurvature * (progress - .5))) - .5) / + (tweenMax - .5) / 2 + .5; + + if ( progress == 1 ) + { + snapshotButton.disabled = false; + zoomOut = false; + + //updateKeyControl(); + + if ( ! quickLook ) + { + //checkHighlight(); + } + + + if ( fpsDisplay ) + { + fpsDisplay.innerHTML = 'fps: ' + Math.round(tweenFrames * 1000 / tweenLength); + } + } + + draw(); + } + + progressLast = progress; +} + +function updateDatasetButtons() +{ + if ( datasets == 1 ) + { + return; + } + + var node = selectedNode ? selectedNode : head; + + datasetButtonLast.disabled = + node.attributes[magnitudeIndex][lastDataset] == 0; + + datasetButtonPrev.disabled = true; + datasetButtonNext.disabled = true; + + for ( var i = 0; i < datasets; i++ ) + { + var disable = node.attributes[magnitudeIndex][i] == 0; + + datasetDropDown.options[i].disabled = disable; + + if ( ! disable ) + { + if ( i != currentDataset ) + { + datasetButtonPrev.disabled = false; + datasetButtonNext.disabled = false; + } + } + } +} + +function updateDatasetWidths() +{ + if ( datasets > 1 ) + { + for ( var i = 0; i < datasets; i++ ) + { + context.font = fontBold; + var dim = context.measureText(datasetNames[i]); + datasetWidths[i] = dim.width; + } + } +} + +function updateKeyControl() +{ + if ( keys == 0 )//|| progress != 1 ) + { + keyControl.style.visibility = 'hidden'; + } + else + { + keyControl.style.visibility = 'visible'; + keyControl.style.right = margin + 'px'; + + if ( showKeys ) + { + keyControl.style.top = + imageHeight - + ( + keys * (keySize + keyBuffer) - + keyBuffer + + margin + + keyControl.clientHeight * 1.5 + ) + 'px'; + } + else + { + keyControl.style.top = + (imageHeight - margin - keyControl.clientHeight) + 'px'; + } + } +} + +function updateView() +{ + if ( selectedNode.depth > maxAbsoluteDepth - 1 ) + { + maxAbsoluteDepth = selectedNode.depth + 1; + } + + highlightedNode = selectedNode; + + angleFactor = 2 * Math.PI / (selectedNode.magnitude); + + maxPossibleDepth = Math.floor(gRadius / (fontSize * minRingWidthFactor)); + + if ( maxPossibleDepth < 4 ) + { + maxPossibleDepth = 4; + } + + var minRadiusInner = fontSize * 8 / gRadius; + var minRadiusFirst = fontSize * 6 / gRadius; + var minRadiusOuter = fontSize * 5 / gRadius; + + if ( .25 < minRadiusInner ) + { + minRadiusInner = .25; + } + + if ( .15 < minRadiusFirst ) + { + minRadiusFirst = .15; + } + + if ( .15 < minRadiusOuter ) + { + minRadiusOuter = .15; + } + + // visibility of nodes depends on the depth they are displayed at, + // so we need to set the max depth assuming they can all be displayed + // and iterate it down based on the deepest child node we can display + // + var maxDepth; + var newMaxDepth = selectedNode.getMaxDepth() - selectedNode.getDepth() + 1; + // + do + { + maxDepth = newMaxDepth; + + if ( ! compress && maxDepth > maxPossibleDepth ) + { + maxDepth = maxPossibleDepth; + } + + if ( compress ) + { + compressedRadii = new Array(maxDepth); + + compressedRadii[0] = minRadiusInner; + + var offset = 0; + + while + ( + lerp + ( + Math.atan(offset + 2), + Math.atan(offset + 1), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) - minRadiusInner > minRadiusFirst && + offset < 10 + ) + { + offset++; + } + + offset--; + + for ( var i = 1; i < maxDepth; i++ ) + { + compressedRadii[i] = lerp + ( + Math.atan(i + offset), + Math.atan(offset), + Math.atan(maxDepth + offset - 1), + minRadiusInner, + 1 - minRadiusOuter + ) + } + } + else + { + nodeRadius = 1 / maxDepth; + } + + newMaxDepth = selectedNode.maxVisibleDepth(maxDepth); + + if ( compress ) + { + if ( newMaxDepth <= maxPossibleDepth ) + { +// compress + } + } + else + { + if ( newMaxDepth > maxPossibleDepth ) + { + newMaxDepth = maxPossibleDepth; + } + } + } + while ( newMaxDepth < maxDepth ); + + maxDisplayDepth = maxDepth; + + lightnessFactor = (lightnessMax - lightnessBase) / (maxDepth > 8 ? 8 : maxDepth); + keys = 0; + + nLabelOffsets = new Array(maxDisplayDepth - 1); + labelOffsets = new Array(maxDisplayDepth - 1); + labelLastNodes = new Array(maxDisplayDepth - 1); + labelFirstNodes = new Array(maxDisplayDepth - 1); + + for ( var i = 0; i < maxDisplayDepth - 1; i++ ) + { + if ( compress ) + { + if ( i == maxDisplayDepth - 1 ) + { + nLabelOffsets[i] = 0; + } + else + { + var width = + (compressedRadii[i + 1] - compressedRadii[i]) * + gRadius; + + nLabelOffsets[i] = Math.floor(width / fontSize / 1.2); + + if ( nLabelOffsets[i] > 2 ) + { + nLabelOffsets[i] = min + ( + Math.floor(width / fontSize / 1.75), + 5 + ); + } + } + } + else + { + nLabelOffsets[i] = Math.max + ( + Math.floor(Math.sqrt((nodeRadius * gRadius / fontSize)) * 1.5), + 3 + ); + } + + labelOffsets[i] = Math.floor((nLabelOffsets[i] - 1) / 2); + labelLastNodes[i] = new Array(nLabelOffsets[i] + 1); + labelFirstNodes[i] = new Array(nLabelOffsets[i] + 1); + + for ( var j = 0; j <= nLabelOffsets[i]; j++ ) + { + // these arrays will allow nodes with neighboring labels to link to + // each other to determine max label length + + labelLastNodes[i][j] = 0; + labelFirstNodes[i][j] = 0; + } + } + + fontSizeText.innerHTML = fontSize; + fontNormal = fontSize + 'px ' + fontFamily; + context.font = fontNormal; + fontBold = 'bold ' + fontSize + 'px ' + fontFamily; + tickLength = fontSize * .7; + + head.setTargets(0); + + keySize = ((imageHeight - margin * 3) * 1 / 2) / keys * 3 / 4; + + if ( keySize > fontSize * maxKeySizeFactor ) + { + keySize = fontSize * maxKeySizeFactor; + } + + keyBuffer = keySize / 3; + + fontSizeLast = fontSize; + + if ( datasetChanged ) + { + datasetChanged = false; + } + else + { + datasetAlpha.start = 0; + } + + var date = new Date(); + tweenStartTime = date.getTime(); + progress = 0; + tweenFrames = 0; + + updateKeyControl(); + updateDatasetWidths(); + + document.title = 'Krona - ' + selectedNode.name; + updateNavigationButtons(); + snapshotButton.disabled = true; + + maxAbsoluteDepthText.innerHTML = maxAbsoluteDepth - 1; + + maxAbsoluteDepthButtonDecrease.disabled = (maxAbsoluteDepth == 2); + maxAbsoluteDepthButtonIncrease.disabled = (maxAbsoluteDepth == head.maxDepth); + + if ( collapse != collapseLast && search.value != '' ) + { + onSearchChange(); + collapseLast = collapse; + } +} + +function updateMaxAbsoluteDepth() +{ + while ( maxAbsoluteDepth > 1 && selectedNode.depth > maxAbsoluteDepth - 1 ) + { + selectedNode = selectedNode.getParent(); + } +} + +function updateNavigationButtons() +{ + backButton.disabled = (nodeHistoryPosition == 0); +// upButton.disabled = (selectedNode.getParent() == 0); + forwardButton.disabled = (nodeHistoryPosition == nodeHistory.length); +} + +function useHue() +{ + return useHueCheckBox && useHueCheckBox.checked; +} +/* +function zoomOut() +{ + return ( + selectedNodeLast != 0 && + selectedNodeLast.getDepth() < selectedNode.getDepth()); +} +*/ + </script> +</head> +<body> +<img id="hiddenImage" src="data:image/png;base64,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" style="display:none"/> +<img id="loadingImage" 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style="display:none"/> +<noscript>Javascript must be enabled to view this page.</noscript> +<div style="display:none"> + <krona collapse="true" key="true"> + <attributes magnitude="magnitude"> + <attribute display="Total">magnitude</attribute> + </attributes> + <datasets> + <dataset>kt</dataset> + </datasets> + +<node name="all"><magnitude><val>1500</val></magnitude><node name="root"><magnitude><val>1500</val></magnitude><node name="cellular organisms"><magnitude><val>1500</val></magnitude><node name="Bacteria"><magnitude><val>1500</val></magnitude><node name="Pseudomonadota"><magnitude><val>1500</val></magnitude><node name="Gammaproteobacteria"><magnitude><val>1500</val></magnitude><node name="Enterobacterales"><magnitude><val>1000</val></magnitude><node name="Enterobacteriaceae"><magnitude><val>1000</val></magnitude><node name="Escherichia"><magnitude><val>500</val></magnitude><node name="Escherichia coli"><magnitude><val>500</val></magnitude><node name="Escherichia coli K-12"><magnitude><val>500</val></magnitude><node name="Escherichia coli str. K-12 substr. MG1655"><magnitude><val>500</val></magnitude></node></node></node></node><node name="Salmonella"><magnitude><val>500</val></magnitude><node name="Salmonella enterica"><magnitude><val>500</val></magnitude><node name="Salmonella enterica subsp. enterica"><magnitude><val>500</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium"><magnitude><val>500</val></magnitude><node name="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"><magnitude><val>500</val></magnitude></node></node></node></node></node></node></node><node name="Pseudomonadales"><magnitude><val>500</val></magnitude><node name="Pseudomonadaceae"><magnitude><val>500</val></magnitude><node name="Pseudomonas"><magnitude><val>500</val></magnitude><node name="Pseudomonas aeruginosa group"><magnitude><val>500</val></magnitude><node name="Pseudomonas aeruginosa"><magnitude><val>500</val></magnitude><node name="Pseudomonas aeruginosa PAO1"><magnitude><val>500</val></magnitude></node></node></node></node></node></node></node></node></node></node></node></node></krona></div></body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sr_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,22 @@ +100.0000 1500 0 no rank 1 root +100.0000 1500 0 no rank 131567 cellular organisms +100.0000 1500 0 superkingdom 2 Bacteria +100.0000 1500 0 phylum 1224 Pseudomonadota +100.0000 1500 0 class 1236 Gammaproteobacteria +66.6667 1000 0 order 91347 Enterobacterales +66.6667 1000 0 family 543 Enterobacteriaceae +33.3333 500 0 genus 561 Escherichia +33.3333 500 0 species 562 Escherichia coli +33.3333 500 0 strain 83333 Escherichia coli K-12 +33.3333 500 500 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +33.3333 500 0 genus 590 Salmonella +33.3333 500 0 species 28901 Salmonella enterica +33.3333 500 0 subspecies 59201 Salmonella enterica subsp. enterica +33.3333 500 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +33.3333 500 500 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +33.3333 500 0 order 72274 Pseudomonadales +33.3333 500 0 family 135621 Pseudomonadaceae +33.3333 500 0 genus 286 Pseudomonas +33.3333 500 0 species group 136841 Pseudomonas aeruginosa group +33.3333 500 0 species 287 Pseudomonas aeruginosa +33.3333 500 500 strain 208964 Pseudomonas aeruginosa PAO1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy.loc Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,4 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}/path/to/GTDB +taxonomy taxonomy ${__HERE__}/taxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy/names.dmp Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,397 @@ +1 | all | | synonym | +1 | root | | scientific name | +2 | Bacteria | Bacteria <bacteria> | scientific name | +2 | bacteria | | blast name | +2 |" ""Bacteria"" Cavalier-Smith 1987 "| | authority | +2 | Bacteria (ex Cavalier-Smith 1987) | | synonym | +2 | Bacteria Woese et al. 2024 | | synonym | +2 |" ""Bacteriobiota"" Luketa 2012 "| | authority | +2 | Bacteriobiota | | synonym | +2 | eubacteria | | genbank common name | +2 | Monera | Monera <bacteria> | in-part | +2 | Procaryotae | Procaryotae <bacteria> | in-part | +2 | Prokaryotae | Prokaryotae <bacteria> | in-part | +2 | Prokaryota | Prokaryota <bacteria> | in-part | +2 | prokaryote | prokaryote <bacteria> | in-part | +2 | prokaryotes | prokaryotes <bacteria> | in-part | +286 |" ""Chlorobacterium"" Guillebeau 1890, nom. rejic. Opin. 6 (not ""Chlorobacterium"" Lauterborn 1916) "| | synonym | +286 | Chryseomonas Holmes et al. 1986 | | authority | +286 | Chryseomonas | | synonym | +286 | Flavimonas Holmes et al. 1987 | | authority | +286 | Flavimonas | | synonym | +286 |" ""Liquidomonas"" Orla-Jensen 1909 "| | authority | +286 | Liquidomonas | | synonym | +286 |" ""Loefflerella"" Holden 1935 "| | authority | +286 | Loefflerella | | synonym | +286 | Pseudomonas Migula 1894 (Approved Lists 1980) | | authority | +286 | Pseudomonas Migula 1894 emend. Yang et al. 2013 | | authority | +286 | Pseudomonas | | scientific name | +286 | RNA similarity group I | | common name | +286 | Serpens Hespell 1977 (Approved Lists 1980) | | authority | +286 | Serpens | | synonym | +287 |" ""Bacillus aeruginosus"" (Schroeter 1872) Trevisan 1885 "| | authority | +287 | Bacillus aeruginosus | | synonym | +287 | Bacillus pyocyaneus | | synonym | +287 |" ""Bacillus pyocyaneus"" (Zopf 1884) Flugge 1886 "| | authority | +287 |" ""Bacterium aeruginosum"" Cohn 1872 "| | authority | +287 |" ""Bacterium aeruginosum"" Schroeter 1872 "| | authority | +287 | Bacterium aeruginosum | | synonym | +287 | bacterium ASFP-37 | | includes | +287 | bacterium ASFP-38 | | includes | +287 | bacterium ASFP-45 | | includes | +287 | bacterium ASFP-46 | | includes | +287 | bacterium ASFP-48 | | includes | +287 | bacterium CRM125 | | includes | +287 | Bacterium pyocyaneum | | synonym | +287 |" ""Bacterium pyocyaneum"" (Zopf 1884) Lehmann and Neumann 1896 "| | authority | +287 | Micrococcus pyocyaneus | | synonym | +287 |" ""Micrococcus pyocyaneus"" Zopf 1884 "| | authority | +287 |" probable synonym or variety: ""Pseudomonas polycolor"" Clara 1930 "| | synonym | +287 | Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (Approved Lists 1980) | | authority | +287 | Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (Approved Lists 1980) emend. Rudra et al. 2022 | | authority | +287 | Pseudomonas aeruginosa | | scientific name | +287 | Pseudomonas polycolor | | synonym | +287 | Pseudomonas pyocyanea | | synonym | +287 |" ""Pseudomonas pyocyanea"" (Zopf 1884) Migula 1895 "| | authority | +287 | Pseudomonas sp. 2_1_26 | | includes | +287 | Pseudomonas sp. ACP_02 | | includes | +287 | Pseudomonas sp. CRRI 93 | | includes | +287 | Pseudomonas sp. HSA1/2016 | | includes | +287 | Pseudomonas sp. NCIM 2036 | | includes | +287 | Pseudomonas sp. NCIM 2862 | | includes | +287 | Pseudomonas sp. PR_01 | | includes | +287 | Pseudomonas sp. PSE5 | | includes | +287 | Pseudomonas sp. RV3 | | includes | +287 | Pseudomonas sp. UFT2/2016 | | includes | +543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982 | | authority | +543 | Enterobacteraceae | | synonym | +543 | enterobacteria | | blast name | +543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980 | | authority | +543 | Enterobacteriaceae Rahn 1937 (Approved Lists 1980) emend. Adeolu et al. 2016 | | authority | +543 | Enterobacteriaceae | | scientific name | +543 | gamma-3 proteobacteria | gamma-3 proteobacteria <enterobacteria,Enterobacteriaceae> | in-part | +561 | Escherichia Castellani and Chalmers 1919 | | authority | +561 | Escherichia | | scientific name | +562 | Achromobacter sp. ATCC 35328 | | includes | +562 |" ""Bacillus coli"" Migula 1895 "| | authority | +562 | Bacillus coli | | synonym | +562 | bacterium 10a | | includes | +562 |" ""Bacterium coli commune"" Escherich 1885 "| | authority | +562 | Bacterium coli commune | | synonym | +562 |" ""Bacterium coli"" (Migula 1895) Lehmann and Neumann 1896 "| | authority | +562 | Bacterium coli | | synonym | +562 | bacterium E3 | | includes | +562 | E. coli | | common name | +562 | Enterococcus coli | | synonym | +562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (Approved Lists 1980) | | authority | +562 | Escherichia coli | | scientific name | +562 | Escherichia/Shigella coli | | equivalent name | +562 | Escherichia sp. 3_2_53FAA | | includes | +562 | Escherichia sp. MAR | | includes | +590 | Salmonella Lignieres 1900 | | authority | +590 | Salmonella | | scientific name | +1224 | Alphaproteobacteriota | | synonym | +1224 |" ""Alphaproteobacteriota"" Whitman et al. 2018 "| | synonym | +1224 | proteobacteria | | blast name | +1224 |" ""Proteobacteria"" Garrity et al. 2005 "| | authority | +1224 | Proteobacteria Stackebrandt et al. 1988 | | authority | +1224 | Proteobacteria | | synonym | +1224 |" ""Proteobacteriota"" Panda et al. 2022 "| | authority | +1224 | Proteobacteriota | | synonym | +1224 | Pseudomonadota corrig. Garrity et al. 2021 | | authority | +1224 | Pseudomonadota | | scientific name | +1224 | purple photosynthetic bacteria and relatives | | common name | +1236 | Gammaproteobacteria Garrity et al. 2005 emend. Williams and Kelly 2013 | | authority | +1236 | Gammaproteobacteria | | scientific name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1236 | g-proteobacteria | | blast name | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 |" ""Pseudomonadia"" Oren et al. 2016 "| | authority | +1236 | Pseudomonadia | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +28901 |" ""Bacillus cholerae-suis"" Smith 1894 "| | authority | +28901 | Bacillus cholerae-suis | | synonym | +28901 | Salmonella choleraesuis corrig. (Smith 1894) Weldin 1927 (Approved Lists 1980) | | authority | +28901 | Salmonella cholerae-suis | | synonym | +28901 | Salmonella choleraesuis | | synonym | +28901 | Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 | | authority | +28901 |" ""Salmonella enterica"" Kauffmann and Edwards 1952 "| | authority | +28901 | Salmonella enterica | | scientific name | +28901 | Salmonella enterica ser. choleraesuis | | synonym | +28901 | Salmonella sp. 22OH10_CL01-S1 | | includes | +28901 | Salmonella sp. 22OH12_PC07-S1 | | includes | +28901 | Salmonella sp. 23OH01_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH01_GT01-S1 | | includes | +28901 | Salmonella sp. 23OH01_GT02-S1 | | includes | +28901 | Salmonella sp. 23OH02_GT02-S1 | | includes | +28901 | Salmonella sp. 23OH04_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH05_CB01-S1 | | includes | +28901 | Salmonella sp. 23OH06_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH06_CH01-S1 | | includes | +28901 | Salmonella sp. 23OH06_GT01-S1 | | includes | +28901 | Salmonella sp. 23OH07_CB02-S1 | | includes | +28901 | Salmonella sp. 23OH07_GT04-S1 | | includes | +28901 | Salmonella sp. 23OH08_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH10_CB03-S1 | | includes | +28901 | Salmonella sp. 23OH10_CG01-S1 | | includes | +28901 | Salmonella sp. AMC 200 | | includes | +28901 | Salmonella sp. AMC 238 | | includes | +28901 | Salmonella sp. AMC 239 | | includes | +28901 | Salmonella sp. AMC 240 | | includes | +28901 | Salmonella sp. AMC 253 | | includes | +28901 | Salmonella sp. AMC 257 | | includes | +28901 | Salmonella sp. AMC 265 | | includes | +28901 | Salmonella sp. AMC 266 | | includes | +28901 | Salmonella sp. AMC 267 | | includes | +28901 | Salmonella sp. AMC 268 | | includes | +28901 | Salmonella sp. AMC 270 | | includes | +28901 | Salmonella sp. AMC 289 | | includes | +28901 | Salmonella sp. AMC 28 | | includes | +28901 | Salmonella sp. AMC 291 | | includes | +28901 | Salmonella sp. AMC 294 | | includes | +28901 | Salmonella sp. AMC 299 | | includes | +28901 | Salmonella sp. AMC 301 | | includes | +28901 | Salmonella sp. AMC 327 | | includes | +28901 | Salmonella sp. AMC 90 | | includes | +28901 | Salmonella sp. FDA00013420 | | includes | +28901 | Salmonella sp. FDA00013433 | | includes | +28901 | Salmonella sp. FDA00013434 | | includes | +28901 | Salmonella sp. FDA00013435 | | includes | +28901 | Salmonella sp. FDA00013436 | | includes | +28901 | Salmonella sp. FDA00013437 | | includes | +28901 | Salmonella sp. FDA00013438 | | includes | +28901 | Salmonella sp. FDA00013439 | | includes | +28901 | Salmonella sp. FDA00013440 | | includes | +28901 | Salmonella sp. FDA00013468 | | includes | +28901 | Salmonella sp. FDA00013469 | | includes | +28901 | Salmonella sp. FDA00013470 | | includes | +28901 | Salmonella sp. FDA00013495 | | includes | +28901 | Salmonella sp. FDA00013496 | | includes | +28901 | Salmonella sp. FDA00013499 | | includes | +28901 | Salmonella sp. FDA00013500 | | includes | +28901 | Salmonella sp. FDA00013513 | | includes | +28901 | Salmonella sp. FDA00013514 | | includes | +28901 | Salmonella sp. FDA00013515 | | includes | +28901 | Salmonella sp. FDA00013516 | | includes | +28901 | Salmonella sp. FDA00013517 | | includes | +28901 | Salmonella sp. FDA00013518 | | includes | +28901 | Salmonella sp. FDA00013519 | | includes | +28901 | Salmonella sp. FDA00013520 | | includes | +28901 | Salmonella sp. FDA00013521 | | includes | +28901 | Salmonella sp. FDA00013522 | | includes | +28901 | Salmonella sp. FDA00013523 | | includes | +28901 | Salmonella sp. FDA00013524 | | includes | +28901 | Salmonella sp. FDA00013525 | | includes | +28901 | Salmonella sp. FDA00013526 | | includes | +28901 | Salmonella sp. FDA00013597 | | includes | +28901 | Salmonella sp. HC-257 | | includes | +28901 | Salmonella sp. IA1-174 | | includes | +28901 | Salmonella sp. MH3-A1 | | includes | +28901 | Salmonella sp. MH3-A2 | | includes | +28901 | Salmonella sp. MH3-A3 | | includes | +28901 | Salmonella sp. MH3-C | | includes | +28901 | Salmonella sp. MH3-D1 | | includes | +28901 | Salmonella sp. MH3-D2 | | includes | +28901 | Salmonella sp. MH3-D3 | | includes | +28901 | Salmonella sp. MH3-D4 | | includes | +28901 | Salmonella sp. MH3-Z1 | | includes | +28901 | Salmonella sp. MH3-Z2 | | includes | +28901 | Salmonella sp. MH4-A2 | | includes | +28901 | Salmonella sp. MH4-A3 | | includes | +28901 | Salmonella sp. MH4-A4 | | includes | +28901 | Salmonella sp. MH4-Z2 | | includes | +28901 | Salmonella sp. NYVetLIRN-85 | | includes | +28901 | Salmonella sp. NYVetLIRN-86 | | includes | +28901 | Salmonella sp. NYVetLIRN-87 | | includes | +28901 | Salmonella sp. NYVetLIRN-88 | | includes | +28901 | Salmonella sp. OH-18-15149 | | includes | +28901 | Salmonella sp. OH-18-15334 | | includes | +28901 | Salmonella sp. OH-18-15363 | | includes | +28901 | Salmonella sp. OH-18-16886 | | includes | +28901 | Salmonella sp. OH-18-16934 | | includes | +28901 | Salmonella sp. OH-18-18132-10 | | includes | +28901 | Salmonella sp. OH-18-18132-11 | | includes | +28901 | Salmonella sp. OH-18-18132-12 | | includes | +28901 | Salmonella sp. OH-18-18132-13 | | includes | +28901 | Salmonella sp. OH-18-18132-14 | | includes | +28901 | Salmonella sp. OH-18-18132-15 | | includes | +28901 | Salmonella sp. OH-18-18132-1 | | includes | +28901 | Salmonella sp. OH-18-18132-2 | | includes | +28901 | Salmonella sp. OH-18-18132-3 | | includes | +28901 | Salmonella sp. OH-18-18132-4 | | includes | +28901 | Salmonella sp. OH-18-18132-5 | | includes | +28901 | Salmonella sp. OH-18-18132-6 | | includes | +28901 | Salmonella sp. OH-18-18132-7 | | includes | +28901 | Salmonella sp. OH-18-18132-8 | | includes | +28901 | Salmonella sp. OH-18-18132-9 | | includes | +28901 | Salmonella sp. OH-18-18281-1 | | includes | +28901 | Salmonella sp. OH-18-18281-2 | | includes | +28901 | Salmonella sp. OH-18-18411 | | includes | +28901 | Salmonella sp. OH-18-18446 | | includes | +28901 | Salmonella sp. OH-18-18447 | | includes | +28901 | Salmonella sp. OH-18-18941 | | includes | +28901 | Salmonella sp. OH-18-19201 | | includes | +28901 | Salmonella sp. OH-18-19951-1 | | includes | +28901 | Salmonella sp. OH-18-20073-2T | | includes | +28901 | Salmonella sp. OH-18-20117-1 | | includes | +28901 | Salmonella sp. OH-18-20132-7 | | includes | +28901 | Salmonella sp. OH-18-20225-1-S | | includes | +28901 | Salmonella sp. OH-18-20225-2-S | | includes | +28901 | Salmonella sp. OH-18-20299-1 | | includes | +28901 | Salmonella sp. OH-18-20299-2 | | includes | +28901 | Salmonella sp. OH-18-20299-3 | | includes | +28901 | Salmonella sp. OH-18-20299-4 | | includes | +28901 | Salmonella sp. OH-18-20299-5 | | includes | +28901 | Salmonella sp. OH-18-20299-6 | | includes | +28901 | Salmonella sp. OH-18-20299-7 | | includes | +28901 | Salmonella sp. OH-18-20299-8 | | includes | +28901 | Salmonella sp. OH-18-20386 | | includes | +28901 | Salmonella sp. OH-18-20895 | | includes | +28901 | Salmonella sp. OH-18-20897 | | includes | +28901 | Salmonella sp. OH-18-21102 | | includes | +28901 | Salmonella sp. OH-18-21112 | | includes | +28901 | Salmonella sp. OH-18-21175 | | includes | +28901 | Salmonella sp. OH-18-21493-S | | includes | +28901 | Salmonella sp. OH-18-21628 | | includes | +28901 | Salmonella sp. OH-18-21629 | | includes | +28901 | Salmonella sp. OH-18-21765 | | includes | +28901 | Salmonella sp. OH-18-21865-2 | | includes | +28901 | Salmonella sp. OH-18-22026 | | includes | +28901 | Salmonella sp. OH-18-22045 | | includes | +28901 | Salmonella sp. OH-18-22168 | | includes | +28901 | Salmonella sp. OH-18-22269-1 | | includes | +28901 | Salmonella sp. OH-18-22479 | | includes | +28901 | Salmonella sp. SAL-18-VL-LA-TX-0007 | | includes | +28901 | Salmonella sp. SAL-18-VL-LA-TX-0008 | | includes | +28901 | Salmonella sp. SAL-18-VL-LA-TX-0009 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-MS-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-MS-0002 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-MS-0003 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-NJ-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0004 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0005 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0006 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0007 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0002 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0003 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0005 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0007 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0012 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0013 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0014 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0017 | | includes | +28901 | Salmonella sp. TTU_251 | | includes | +28901 | Salmonella sp. TTU_258 | | includes | +28901 | Salmonella sp. TTU_262 | | includes | +28901 | Salmonella sp. TTU_264 | | includes | +28901 | Salmonella sp. TTU_265 | | includes | +28901 | Salmonella sp. TTU_266 | | includes | +28901 | Salmonella sp. TTU_267 | | includes | +28901 | Salmonella sp. TTU_269 | | includes | +28901 | Salmonella sp. TTU_274 | | includes | +28901 | Salmonella sp. TTU_279 | | includes | +28901 | Salmonella sp. TTU_282 | | includes | +28901 | Salmonella sp. TTU_284 | | includes | +28901 | Salmonella sp. TTU_287 | | includes | +28901 | Salmonella sp. TTU_289 | | includes | +28901 | Salmonella sp. TTU_297 | | includes | +28901 | Salmonella sp. TTU_298 | | includes | +28901 | Salmonella sp. TTU_299 | | includes | +28901 | Salmonella sp. TTU_303 | | includes | +28901 | Salmonella sp. TTU_304 | | includes | +28901 | Salmonella sp. TTU_305 | | includes | +28901 | Salmonella sp. TTU_306 | | includes | +28901 | Salmonella sp. TTU_307 | | includes | +28901 | Salmonella sp. TTU_308 | | includes | +28901 | Salmonella sp. TTU_309 | | includes | +28901 | Salmonella sp. TTU_310 | | includes | +28901 | Salmonella sp. TTU_311 | | includes | +28901 | Salmonella sp. TTU_312 | | includes | +28901 | Salmonella sp. TTU_313 | | includes | +28901 | Salmonella sp. TTU_314 | | includes | +28901 | Salmonella sp. TTU_315 | | includes | +28901 | Salmonella sp. TTU_316 | | includes | +28901 | Salmonella sp. TTU_317 | | includes | +28901 | Salmonella sp. TTU_318 | | includes | +28901 | Salmonella sp. TTU_319 | | includes | +28901 | Salmonella sp. TTU_320 | | includes | +28901 | Salmonella sp. TTU_321 | | includes | +28901 | Salmonella sp. TTU_322 | | includes | +28901 | Salmonella sp. TTU_323 | | includes | +28901 | Salmonella sp. TTU_324 | | includes | +28901 | Salmonella sp. TTU_325 | | includes | +28901 | Salmonella sp. TTU_326 | | includes | +28901 | Salmonella sp. TTU_327 | | includes | +28901 | Salmonella sp. TTU_328 | | includes | +28901 | Salmonella sp. TTU_329 | | includes | +28901 | Salmonella sp. TTU_330 | | includes | +28901 | Salmonella sp. TTU_331 | | includes | +28901 | Salmonella sp. TTU_332 | | includes | +28901 | Salmonella sp. TTU_333 | | includes | +28901 | Salmonella sp. TTU_334 | | includes | +28901 | Salmonella sp. TTU_335 | | includes | +28901 | Salmonella sp. TTU_338 | | includes | +28901 | Salmonella sp. TTU_345 | | includes | +28901 | Salmonella sp. TTU_352 | | includes | +28901 | Salmonella sp. TTU_353 | | includes | +28901 | Salmonella sp. TTU_357 | | includes | +28901 | Salmonella sp. TTU_358 | | includes | +28901 | Salmonella sp. TTU_359 | | includes | +28901 | Salmonella sp. TXACF1801691 | | includes | +28901 | Salmonella sp. Z-172 | | includes | +28901 | Salmonella sp. ZH-248 | | includes | +59201 | Salmonella choleraesuis subsp. choleraesuis corrig. (Smith 1894) Weldin 1927 | | authority | +59201 | Salmonella cholerae-suis subsp. cholerae-suis | | synonym | +59201 | Salmonella choleraesuis subsp. choleraesuis | | synonym | +59201 | Salmonella enterica I | | synonym | +59201 | Salmonella enterica subsp. enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 | | authority | +59201 | Salmonella enterica subsp. enterica | | scientific name | +59201 | Salmonella enterica subsp. I | | synonym | +59201 | Salmonella enterica subsp. Subsp. I | | synonym | +59201 | Salmonella enterica subsp. Subsp. Ixxx | | synonym | +72274 | gamma-3 proteobacteria | gamma-3 proteobacteria <g-proteobacteria,Pseudomonadales> | in-part | +72274 | Pseudomonaceae/Moraxellaceae group | | synonym | +72274 | Pseudomonadales Orla-Jensen 1921 emend. Liao et al. 2020 | | authority | +72274 | Pseudomonadales | | scientific name | +83333 | Escherichia coli K12 | | equivalent name | +83333 | Escherichia coli K-12 | | scientific name | +90371 |" ""Bacillus typhimurium"" Loeffler 1892 "| | authority | +90371 | Bacillus typhimurium | | synonym | +90371 | Salmonella choleraesuis serotype typhimurium | | synonym | +90371 | Salmonella enterica 1,4,[5],12,:i:1,2 | | synonym | +90371 | Salmonella enterica serotype Typhimurium | | synonym | +90371 | Salmonella enterica serovar Typhimurium | | synonym | +90371 | Salmonella enterica ser. typhimurium | | synonym | +90371 | Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:1,2 | | synonym | +90371 | Salmonella enterica subsp. enterica serovar Typhimurium | | scientific name | +90371 | Salmonella typhimurium (Loeffler 1892) Castellani and Chalmers 1919 | | authority | +90371 |" ""Salmonella typhi-murium"" (sic) (Loeffler 1892) Castellani and Chalmers 1919 "| | authority | +90371 | Salmonella typhi-murium | | synonym | +90371 | Salmonella typhimurium | | synonym | +91347 | Enterobacterales Adeolu et al. 2016 | | authority | +91347 | Enterobacterales | | scientific name | +91347 | Enterobacteriaceae and related endosymbionts | | synonym | +91347 | Enterobacteriaceae group | | synonym | +91347 | Enterobacteriales | | synonym | +91347 | gamma-3 proteobacteria | gamma-3 proteobacteria <enterobacteria,Enterobacterales> | in-part | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium LT2 | | equivalent name | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 | | equivalent name | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium strain LT2-LTL2 | | equivalent name | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | | scientific name | +99287 | Salmonella typhimurium LT2 | | synonym | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | +135621 | Pseudomonadaceae | | scientific name | +135621 | Pseudomonadaceae Winslow et al. 1917 | | authority | +136841 | Pseudomonas aeruginosa group | | scientific name | +208964 | Pseudomonas aeruginosa PAO1 | | scientific name | +208964 | Pseudomonas sp. PAO1 | | equivalent name | +511145 | Escherichia coli MG1655 | | synonym | +511145 | Escherichia coli strain MG1655 | | equivalent name | +511145 | Escherichia coli str. K12 substr. MG1655 | | equivalent name | +511145 | Escherichia coli str. K-12 substr. MG1655 | | scientific name | +511145 | Escherichia coli str. MG1655 | | equivalent name |
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy/nodes.dmp Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,22 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | | | 0 | 0 | 0 | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | | | 0 | 0 | 1 | +286 | 135621 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +287 | 136841 | species | PA | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +590 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | | | 0 | 0 | 1 | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +28901 | 590 | species | SE | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +59201 | 28901 | subspecies | SE | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +72274 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +83333 | 562 | strain | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +90371 | 59201 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +99287 | 90371 | strain | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +135621 | 72274 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +136841 | 286 | species group | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +208964 | 287 | strain | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +511145 | 83333 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 |
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metabuli_databases.loc.sample Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}/path/to/GTDB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/taxonomy.loc.sample Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}/path/to/GTDB \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="metabuli_databases" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="tool-data/metabuli_databases.loc" /> + </table> + <table name="taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/taxonomy.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of model folders --> + <table name="metabuli_databases" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="${__HERE__}/test-data/metabuli_databases.loc" /> + </table> + <!-- Locations of reference genome files in fasta format --> + <table name="taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/taxonomy.loc" /> + </table> +</tables>