Mercurial > repos > iuc > quast
changeset 5:81df4950d65b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
| author | iuc |
|---|---|
| date | Tue, 04 Dec 2018 06:49:05 -0500 |
| parents | 0834c823d4b9 |
| children | f30d03867854 |
| files | README.txt quast.xml test-data/test1_output.tsv test-data/test2_report.html test-data/test2_report.pdf |
| diffstat | 5 files changed, 4878 insertions(+), 85 deletions(-) [+] |
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--- a/README.txt Mon Feb 12 09:05:20 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -**Tool Information** - -- QUAST Tool v4.1: - + Release Date: May 2016 - + URL: http://bioinf.spbau.ru/quast - + Source URL: https://downloads.sourceforge.net/project/quast/quast-4.1.tar.gz - ------ - -**QUAST Galaxy Wrapper Author and Contact Information** - -+ Delphine Lariviere -+ Galaxy Team -+ Email: delphine.lariviere@galaxyproject.org -+ Nekrutenko's Lab, Pennsylvania State University, State College, PA, USA - - -- From the wrapper of : - + Jacob Jablonski - + AAFC-MBB Team - + Email: mbb@agr.gc.ca - + Agriculture and Agri-foods Canada, Ottawa, ON, Canada
--- a/quast.xml Mon Feb 12 09:05:20 2018 -0500 +++ b/quast.xml Tue Dec 04 06:49:05 2018 -0500 @@ -1,60 +1,46 @@ -<tool id="quast" name="Quast" version="4.6.3" > +<tool id="quast" name="Quast" version="5.0.2" > <description>Genome assembly Quality</description> <requirements> - <requirement type="package" version="4.6.3">quast</requirement> + <requirement type="package" version="5.0.2">quast</requirement> </requirements> - <stdio> - <regex match="ERROR! exception caught!" - source="both" - level="fatal" - description="Something went wrong. Check the following errors : No labels..." /> - </stdio> - <command> + <command detect_errors="exit_code"> <![CDATA[ - #import re - quast - --threads \${GALAXY_SLOTS:-4} - -o outputdir - #if $gene_selection == "eukaryote": - --eukaryote - #else if $gene_selection == "metagenes": - --meta - #end if - #if $input_ref: - -R '$input_ref' - #if $input_operon: - -O '$input_operon' - #end if - #if $annot: - -G '$annot' - #end if - #end if - #if $input_size: - --est-ref-size $input_size - #end if - --min-contig $min_contig - -l - #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.element_identifier))+'"' for $x in $input ]) +#import re +quast +--threads \${GALAXY_SLOTS:-4} +-o outputdir +#if $gene_selection == "eukaryote": + --eukaryote +#else if $gene_selection == "metagenes": + --meta +#end if +$large +#if $input_ref: + -R '$input_ref' + #if $input_operon: + -O '$input_operon' + #end if + #if $annot: + -g '$annot' + #end if +#end if +#if $input_size: + --est-ref-size $input_size +#end if +--min-contig $min_contig +-l +#set names = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $input ]) - $names - --contig-thresholds $threshold_contig - #for $k in $input: - $k - #end for - && - mv outputdir/report.tsv '$quast_tsv' && - ## The sed string below removes non-functional "Main menu" button from the viewer - sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/contig_size_viewer.html > '$contig_size_viewer' && - #if $input_ref: - ## The sed string below removes non-functional "Main menu" button from the viewer - sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/alignment_viewer.html > '$alignment_viewer' && - #end if - ## The sed string below removes non-functional link from the report page - sed "\:<div id='icarus-json'>:,\:</div>:d" outputdir/report.html > '$report_html' && - mv outputdir/report.pdf '$report_pdf' && - mv outputdir/contigs_reports/misassemblies_report.tsv '$mis_ass_tsv' && - mv outputdir/contigs_reports/unaligned_report.tsv '$unalign_tsv' && - mv outputdir/quast.log '$log_txt' +'$names' +--contig-thresholds $threshold_contig +#for $k in $input: + $k +#end for +&& mkdir '$report_html.files_path' +&& cp outputdir/*.html '$report_html.files_path' +#if str($input_ref): + && cp -R outputdir/icarus_viewers '$report_html.files_path' +#end if ]]> </command> <inputs> @@ -65,6 +51,7 @@ </param> <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size" help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/> + <param argument="--large" type="boolean" truevalue="--large" falsevalue="" label="Run quast in --large mode for large genomes" help="Uses minimap2 aligner, improves transposable element handling and alignment thresholds"/> <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True" argument="-R" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/> <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G" @@ -80,20 +67,16 @@ help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/> </inputs> <outputs> - <data format="txt" name="log_txt" label="Quast: Log" /> - <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies"> - <filter>input_ref is not None</filter> - </data> - <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs"> + <data format="txt" name="log_txt" label="Quast: Log" from_work_dir="outputdir/quast.log"/> + <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt"> <filter>input_ref is not None</filter> </data> - <data format="html" name="contig_size_viewer" label="Quast: Contig view"/> - <data format="html" name="alignment_viewer" label="Quast: Alignment view"> + <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv"> <filter>input_ref is not None</filter> </data> - <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)"/> - <data format="html" name="report_html" label="Quast: Report (HTML)"/> - <data format="pdf" name="report_pdf" label="Quast: Report (PDF)"/> + <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)" from_work_dir="outputdir/report.tsv"/> + <data format="html" name="report_html" label="Quast: Report (HTML)" from_work_dir="outputdir/report.html"/> + <data format="pdf" name="report_pdf" label="Quast: Report (PDF)" from_work_dir="outputdir/report.pdf"/> </outputs> <tests> <test> @@ -103,6 +86,7 @@ <param name="type_file" value="contig"/> <param name="annot" value="genes.gff"/> <param name="gene_selection" value="prokaryotes"/> + <param name="large" value="true"/> <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/> </test> <test> @@ -110,6 +94,8 @@ <param name="input" value="contigs2.fna,contigs1.fna"/> <param name="type_file" value="contig"/> <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/> + <output name="report_html" file="test2_report.html" lines_diff="50"/> + <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/> </test> </tests> <help>
--- a/test-data/test1_output.tsv Mon Feb 12 09:05:20 2018 -0500 +++ b/test-data/test1_output.tsv Tue Dec 04 06:49:05 2018 -0500 @@ -21,6 +21,9 @@ # misassembled contigs 0 0 Misassembled contigs length 0 0 # local misassemblies 0 0 +# scaffold gap ext. mis. 0 0 +# scaffold gap loc. mis. 0 0 +# possible TEs 0 0 # unaligned mis. contigs 0 0 # unaligned contigs 0 + 0 part 0 + 1 part Unaligned length 0 1950 @@ -29,7 +32,7 @@ # N's per 100 kbp 0.00 0.00 # mismatches per 100 kbp 0.00 0.00 # indels per 100 kbp 0.00 0.00 -# genes 6 + 0 part 3 + 3 part +# genomic features 13 + 1 part 7 + 7 part Largest alignment 6650 2030 Total aligned length 6650 4760 NA50 6650 1610
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font-size: 26px; + padding: 0 -3px 0 5px; + -webkit-margin-before: 5px; + -webkit-margin-after: 0px; + -webkit-margin-start: 0px; + -webkit-margin-end: 0px; + font-weight: bold; +} + +#header { + display: block; + width: 100%; + margin-bottom: 10px; +} + +.logo_img { + height: 40px; + margin-bottom: -10px; + margin-left: -6px; + margin-right: -7px; +} +</style> + + <style rel="stylesheet"> +.report-and-plots { + margin-top: 15px; +} + +/****************/ +/* REPORT TABLE */ +.report { + margin: 0 100px 50px 0; + float: left; + font-size: 1em; +} + +#main_report { + /*min-width: 600px;*/ +} + +/*#extended_link {*/ + /*margin-top: 5px;*/ +/*}*/ + +#ref_report { + /*min-width: 300px;*/ + margin-right: 0; + margin-bottom: 20px; + /*margin-right: 200px;*/ +} + +.report td { + margin: 0; + padding: 2px 0.6em 0 14px; + /*min-width: 100px;*/ + max-width: 400px; + white-space: nowrap; +} +.report td.number { + text-align: right; +} + +.report tr.top_row_tr td, +.report tr.group_header td { + font-weight: bold; + border-bottom: 1px solid #ddd; +} +.report tr.group_header td { + height: 20px; + vertical-align: bottom; +} + +#ref_report tr.top_row_tr td, +#ref_report tr.group_header td { + font-weight: normal; +} + +.report tr td:first-child { + padding-left: 0; +} +.report tr td:last-child { + padding-right: 0; +} + +.report tr.row_hidden, tr.group_empty { + display: none; +} + +.report tr.secondary_hidden { + display: none; +} + +/*.report td.secondary_td {*/ + /*padding-left: 10px !important;*/ +/*}*/ + +span.heatmap_legend { + font-size: 11px; + display: inline-block; +} + +#heatmap_header { + margin-right: 30px; +} + +#combined_reference_length { + padding-top: 1px; + padding-bottom: 15px; +} + +span.metric-name.expandable { + margin-left: -13px; +} + +span.metric-name.secondary { + margin-left: 13px; +} + +span.metric-name.expandable.collapsed::before { + content: '+ '; + color: #CCC; + cursor: pointer; +} + +span.metric-name.expandable.expanded::before { + content: '\2212\a0'; /* &minus  */ + color: #CCC; + cursor: pointer; +} + +.report_legend { + padding-left: 15px; /* compensate drag handles */ +} + +#contigs_are_ordered { + z-index: 0; + position: relative; +} + + +/*.report .report-table-header { + font-weight: bold; +}*/ + +/*.report thead td { + border-bottom: 1px solid #bbb; +}*/ + + +/*************/ +/* Draggable */ +table.moving_table { + box-shadow: -0px 0px 5px 1px #888888; + -moz-box-shadow: -0px 0px 5px 1px #888888; + -webkit-box-shadow: -0px 0px 5px 1px #888888; + /*outline: 1px solid #888888;*/ + background-color: white; + z-index: 3 !important; +} + +table.draggable .drag_handle { + padding: 2px 1px 0 1px; + margin: 0 2px 0 1px; + + cursor: grab; + cursor: -moz-grab; + cursor: -webkit-grab; +} + +table.draggable .drag_handle .drag_image { + height: 9px; + width: 9px; + display: inline-block; + background: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAkAAAAJCAIAAABv85FHAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAiElEQVQImV2OsQ3FIAxEz2AhCAukyATZf5ZMQI8okZUjhfWj6F/pd09n6b1f1wUgxkgSAACS53lqSmnfdxHBLyJCMucsc877vv201nobKSUl2VoLIeATksdxKEmf+UqOxczGGDHGP7Ztm5qZmfmkYx8upehaq/fu4P2WZK1VAdRaAbjqXghBVR9BvlQcgtQsKgAAAABJRU5ErkJggg==") no-repeat; +} + +table.draggable .drag_handle:active, +table.draggable td.cell_of_moving_table .drag_handle { + cursor: grabbing !important; + cursor: -moz-grabbing !important; + cursor: -webkit-grabbing !important; +} + +/* Override the styles for the first and the last columns of the table.report. + The cloned table contains a single column which is both first and last, + and we don't need it to inherit those styles. */ +table.draggable td.cell_of_moving_table { + padding-left: 14px !important; + padding-right: 0.6em !important; +} + +table.draggable td.hovered_column_td { + background-color: #cccccc; +} + +table.draggable td.second_through_last_col_headers_td { + padding-left: 0 !important; /* compensate handle images */ +} + +table.draggable td.cell_of_empty_space * { + visibility: hidden; +} + +table.draggable td.cell_of_empty_space { + border: none !important; + /*border-left: 1px solid #888888; + border-right: 1px solid #888888; + margin-right: -1px !important; + margin-left: -1px !important; */ +} + +/*table.draggable td.bottom_cell_of_empty_space { + border-bottom: 1px solid #888888 !important; +} + +table.draggable td.top_cell_of_empty_space { + border-top: 1px solid #888888 !important; + /*margin-top: -1px; +}*/ + +table.draggable td.top_cell_of_empty_space { +} + +table.draggable td.left_to_cell_of_empty_space { + /*outline-left: 1px solid #888888;*/ +} + +table.draggable td.right_to_cell_of_empty_space { + /*outline-right: 1px solid #888888;*/ +} + +/********/ +/* META */ +#main_ref_genome { + +} + +table#refgenome td.last_row { + border-top: 1px solid #ddd; +} + +/************/ +/* PLOTTING */ +.plot-switch { + margin-left: 10px; +} + +.plot-mis-type-switch { + margin-left: 23px; +} + +.plot-wrapper { + padding-right: 80px; +} + +.plot-header { + margin-left: 0; + font-weight: bold; + height: 1.5em; + display: block; +} + +.plots { + margin-left: -30px; + margin-right: 70px; + margin-top: 2px; + margin-bottom: 50px; + float: left; +} +.plots td { + vertical-align: top; + white-space: nowrap; +} + +.plots div#plots-switches, tr#plots-into-tr p { + padding-left: 30px; +} + +#legend-placeholder { + min-width: 80px; + margin-top: -2px; + margin-left: -5px; + position: relative; + z-index: 0; +} + +.legendColorBox div { + display: none; +} + +#legend-placeholder td { + vertical-align: top; + white-space: nowrap; +} + +#plot-placeholder { + width: 986px; + height: 600px; + + /* for auto sizing plots when resizing the page + min-width: 500px; + min-height: 500px; + width: 100%; + min-height: 400px; + height: 50%; */ + + margin-left: -55px; + margin-right: 20px; + float: left; + + z-index: 2; +} + +#change-assembly { + white-space: nowrap; + width: 0; +} + +/*************/ +/* Plot tips */ +#plot_tip { + position: absolute; + opacity: 1; + padding: 2px 5px 2px 5px; + + z-index: 1; +} + +#plot_tip_vertical_rule, #plot_tip_horizontal_rule { + position: absolute; + border: 1px solid #BBB; + z-index: -2; +} + +#plot_tip_vertical_rule { + border-left: 1px; +} + +#plot_tip_horizontal_rule { + border-top: 1px; +} + +.white_stroked { + color: black; + background-color: white; + text-shadow: + -3px -3px 0 white, + 3px -3px 0 white, + -3px 3px 0 white, + 3px 3px 0 white; +} + +img.icon_plot { + width: 14px; + height: 12px; + display: inline-block; + content: ''; + background: 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c=="object"?c[p.expando]?c:new p.Event(s,c):new p.Event(s),c.type=s,c.isTrigger=!0,c.exclusive=i,c.namespace=t.join("."),c.namespace_re=c.namespace?new RegExp("(^|\\.)"+t.join("\\.(?:.*\\.|)")+"(\\.|$)"):null,m=s.indexOf(":")<0?"on"+s:"";if(!f){h=p.cache;for(j in h)h[j].events&&h[j].events[s]&&p.event.trigger(c,d,h[j].handle.elem,!0);return}c.result=b,c.target||(c.target=f),d=d!=null?p.makeArray(d):[],d.unshift(c),n=p.event.special[s]||{};if(n.trigger&&n.trigger.apply(f,d)===!1)return;q=[[f,n.bindType||s]];if(!g&&!n.noBubble&&!p.isWindow(f)){r=n.delegateType||s,k=$.test(r+s)?f:f.parentNode;for(l=f;k;k=k.parentNode)q.push([k,r]),l=k;l===(f.ownerDocument||e)&&q.push([l.defaultView||l.parentWindow||a,r])}for(j=0;j<q.length&&!c.isPropagationStopped();j++)k=q[j][0],c.type=q[j][1],o=(p._data(k,"events")||{})[c.type]&&p._data(k,"handle"),o&&o.apply(k,d),o=m&&k[m],o&&p.acceptData(k)&&o.apply&&o.apply(k,d)===!1&&c.preventDefault();return c.type=s,!g&&!c.isDefaultPrevented()&&(!n._default||n._default.apply(f.ownerDocument,d)===!1)&&(s!=="click"||!p.nodeName(f,"a"))&&p.acceptData(f)&&m&&f[s]&&(s!=="focus"&&s!=="blur"||c.target.offsetWidth!==0)&&!p.isWindow(f)&&(l=f[m],l&&(f[m]=null),p.event.triggered=s,f[s](),p.event.triggered=b,l&&(f[m]=l)),c.result}return},dispatch:function(c){c=p.event.fix(c||a.event);var d,e,f,g,h,i,j,l,m,n,o=(p._data(this,"events")||{})[c.type]||[],q=o.delegateCount,r=k.call(arguments),s=!c.exclusive&&!c.namespace,t=p.event.special[c.type]||{},u=[];r[0]=c,c.delegateTarget=this;if(t.preDispatch&&t.preDispatch.call(this,c)===!1)return;if(q&&(!c.button||c.type!=="click"))for(f=c.target;f!=this;f=f.parentNode||this)if(f.disabled!==!0||c.type!=="click"){h={},j=[];for(d=0;d<q;d++)l=o[d],m=l.selector,h[m]===b&&(h[m]=l.needsContext?p(m,this).index(f)>=0:p.find(m,this,null,[f]).length),h[m]&&j.push(l);j.length&&u.push({elem:f,matches:j})}o.length>q&&u.push({elem:this,matches:o.slice(q)});for(d=0;d<u.length&&!c.isPropagationStopped();d++){i=u[d],c.currentTarget=i.elem;for(e=0;e<i.matches.length&&!c.isImmediatePropagationStopped();e++){l=i.matches[e];if(s||!c.namespace&&!l.namespace||c.namespace_re&&c.namespace_re.test(l.namespace))c.data=l.data,c.handleObj=l,g=((p.event.special[l.origType]||{}).handle||l.handler).apply(i.elem,r),g!==b&&(c.result=g,g===!1&&(c.preventDefault(),c.stopPropagation()))}}return 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+</script> + +<script type="text/javascript"> +/* + * jQuery.flot.dashes + * + * options = { + * series: { + * dashes: { + * + * // show + * // default: false + * // Whether to show dashes for the series. + * show: <boolean>, + * + * // lineWidth + * // default: 2 + * // The width of the dashed line in pixels. + * lineWidth: <number>, + * + * // dashLength + * // default: 10 + * // Controls the length of the individual dashes and the amount of + * // space between them. + * // If this is a number, the dashes and spaces will have that length. + * // If this is an array, it is read as [ dashLength, spaceLength ] + * dashLength: <number> or <array[2]> + * } + * } + * } + */ +(function($){ + + function init(plot) { + + plot.hooks.processDatapoints.push(function(plot, series, datapoints) { + + if (!series.dashes.show) return; + + plot.hooks.draw.push(function(plot, ctx) { + + var plotOffset = plot.getPlotOffset(), + axisx = series.xaxis, + axisy = series.yaxis; + + function plotDashes(xoffset, yoffset) { + + var points = datapoints.points, + ps = datapoints.pointsize, + prevx = null, + prevy = null, + dashRemainder = 0, + dashOn = true, + dashOnLength, + dashOffLength; + + if (series.dashes.dashLength[0]) { + dashOnLength = series.dashes.dashLength[0]; + if (series.dashes.dashLength[1]) { + dashOffLength = series.dashes.dashLength[1]; + } else { + dashOffLength = dashOnLength; + } + } else { + dashOffLength = dashOnLength = series.dashes.dashLength; + } + + ctx.beginPath(); + + for (var i = ps; i < points.length; i += ps) { + + var x1 = points[i - ps], + y1 = points[i - ps + 1], + x2 = points[i], + y2 = points[i + 1]; + + if (x1 == null || x2 == null) continue; + + // clip with ymin + if (y1 <= y2 && y1 < axisy.min) { + if (y2 < axisy.min) continue; // line segment is outside + // compute new intersection point + x1 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1; + y1 = axisy.min; + } else if (y2 <= y1 && y2 < axisy.min) { + if (y1 < axisy.min) continue; + x2 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1; + y2 = axisy.min; + } + + // clip with ymax + if (y1 >= y2 && y1 > axisy.max) { + if (y2 > axisy.max) continue; + x1 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1; + y1 = axisy.max; + } else if (y2 >= y1 && y2 > axisy.max) { + if (y1 > axisy.max) continue; + x2 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1; + y2 = axisy.max; + } + + // clip with xmin + if (x1 <= x2 && x1 < axisx.min) { + if (x2 < axisx.min) continue; + y1 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1; + x1 = axisx.min; + } else if (x2 <= x1 && x2 < axisx.min) { + if (x1 < axisx.min) continue; + y2 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1; + x2 = axisx.min; + } + + // clip with xmax + if (x1 >= x2 && x1 > axisx.max) { + if (x2 > axisx.max) continue; + y1 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1; + x1 = axisx.max; + } else if (x2 >= x1 && x2 > axisx.max) { + if (x1 > axisx.max) continue; + y2 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1; + x2 = axisx.max; + } + + if (x1 != prevx || y1 != prevy) { + ctx.moveTo(axisx.p2c(x1) + xoffset, axisy.p2c(y1) + yoffset); + } + + var ax1 = axisx.p2c(x1) + xoffset, + ay1 = axisy.p2c(y1) + yoffset, + ax2 = axisx.p2c(x2) + xoffset, + ay2 = axisy.p2c(y2) + yoffset, + dashOffset; + + function lineSegmentOffset(segmentLength) { + + var c = Math.sqrt(Math.pow(ax2 - ax1, 2) + Math.pow(ay2 - ay1, 2)); + + if (c <= segmentLength) { + return { + deltaX: ax2 - ax1, + deltaY: ay2 - ay1, + distance: c, + remainder: segmentLength - c + } + } else { + var xsign = ax2 > ax1 ? 1 : -1, + ysign = ay2 > ay1 ? 1 : -1; + return { + deltaX: xsign * Math.sqrt(Math.pow(segmentLength, 2) / (1 + Math.pow((ay2 - ay1)/(ax2 - ax1), 2))), + deltaY: ysign * Math.sqrt(Math.pow(segmentLength, 2) - Math.pow(segmentLength, 2) / (1 + Math.pow((ay2 - ay1)/(ax2 - ax1), 2))), + distance: segmentLength, + remainder: 0 + }; + } + } + //-end lineSegmentOffset + + do { + + dashOffset = lineSegmentOffset( + dashRemainder > 0 ? dashRemainder : + dashOn ? dashOnLength : dashOffLength); + + if (dashOffset.deltaX != 0 || dashOffset.deltaY != 0) { + if (dashOn) { + ctx.lineTo(ax1 + dashOffset.deltaX, ay1 + dashOffset.deltaY); + } else { + ctx.moveTo(ax1 + dashOffset.deltaX, ay1 + dashOffset.deltaY); + } + } + + dashOn = !dashOn; + dashRemainder = dashOffset.remainder; + ax1 += dashOffset.deltaX; + ay1 += dashOffset.deltaY; + + } while (dashOffset.distance > 0); + + prevx = x2; + prevy = y2; + } + + ctx.stroke(); + } + //-end plotDashes + + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + ctx.lineJoin = 'round'; + + var lw = series.dashes.lineWidth, + sw = series.shadowSize; + + // FIXME: consider another form of shadow when filling is turned on + if (lw > 0 && sw > 0) { + // draw shadow as a thick and thin line with transparency + ctx.lineWidth = sw; + ctx.strokeStyle = "rgba(0,0,0,0.1)"; + // position shadow at angle from the mid of line + var angle = Math.PI/18; + plotDashes(Math.sin(angle) * (lw/2 + sw/2), Math.cos(angle) * (lw/2 + sw/2)); + ctx.lineWidth = sw/2; + plotDashes(Math.sin(angle) * (lw/2 + sw/4), Math.cos(angle) * (lw/2 + sw/4)); + } + + ctx.lineWidth = lw; + ctx.strokeStyle = series.color; + + if (lw > 0) { + plotDashes(0, 0); + } + + ctx.restore(); + + }); + //-end draw hook + + }); + //-end processDatapoints hook + + } + //-end init + + $.plot.plugins.push({ + init: init, + options: { + series: { + dashes: { + show: false, + lineWidth: 2, + dashLength: 10 + } + } + }, + name: 'dashes', + version: '0.1' + }); + +})(jQuery) + + +</script> + +<script type="text/javascript"> + +var cumulative = { + isInitialized: false, + + maxX: 0, + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null, + colors: [], + + draw: function(name, title, colors, filenames, listsOfLengths, refLengths, tickX, + placeholder, legendPlaceholder, glossary, order, scalePlaceholder) { + + $(scalePlaceholder).empty(); + + if (!this.isInitialized) { + // div.html( + // "<span class='plot-header'>" + addTooltipIfDefinitionExists(glossary, title) + "</span>" + + // "<div class='plot-placeholder' id='cumulative-plot-placeholder'></div>" + // ); + cumulative.series = []; + var plotsN = filenames.length; + var refLength = 0; + if (refLengths) { + for (var i = 0, size = refLengths.length; i < size; i++) + refLength += refLengths[i]; + } + if (refLength) { + cumulative.maxY = refLength; + } + + cumulative.colors = colors; + + function addCumulativeLenData(label, index, color, lengths, isRef) { + if (!(lengths instanceof Array)) + lengths = [lengths]; + var size = lengths.length; + var points = { + data: new Array(size + 1), + label: label, + number: index, + color: color + }; + + points.data[0] = [0, 0]; + + var y = 0; + for (var j = 0; j < size; j++) { + y += lengths[j]; + points.data[j+1] = [j+1, y]; + if (y > cumulative.maxY) { + cumulative.maxY = y; + } + } + + if (size > cumulative.maxX) { + cumulative.maxX = size; + } + if (isRef){ + points.isReference = true; + points.dashes = {show: true, lineWidth: 1}; + if (size < cumulative.maxX) { + points.data[size + 1] = [cumulative.maxX, y]; + } + } + return points; + } + + for (var i = 0; i < plotsN; i++) { + var lengths = listsOfLengths[order[i]]; + var asm_name = filenames[order[i]]; + var color = colors[order[i]]; + cumulative.series[i] = addCumulativeLenData(asm_name, i, color, lengths); + } + +// var lineColors = []; +// +// for (i = 0; i < colors.length; i++) { +// lineColors.push(changeColor(colors[i], 0.9, false)); +// } + + for (i = 0; i < plotsN; i++) { + if (typeof broken_scaffolds_labels !== undefined && $.inArray(filenames[order[i]], broken_scaffolds_labels) != -1) { + cumulative.series[i].dashes = { + show: true, + lineWidth: 1 + }; + } + else { + cumulative.series[i].lines = { + show: true, + lineWidth: 1 + }; + } + } + + for (i = 0; i < plotsN; i++) { + cumulative.colors.push(cumulative.series[i].color); + } + + //cumulative.maxYTick = getMaxDecimalTick(cumulative.maxY); + + if (refLengths) { + size = refLengths.length; + var ref_label = 'reference, ' + toPrettyString(refLength, 'bp'); + cumulative.series.push(addCumulativeLenData(ref_label, i, '#000000', refLengths, true)); + cumulative.colors.push('#000000'); + } + + + // if (referenceLength) { + // yaxes.push({ + // ticks: [referenceLength], + // min: 0, + // max: maxYTick, + // position: 'right', + //// labelWidth: 50, + // reserveSpace: true, + // tickFormatter: function (val, axis) { + // return '<div style="">' + toPrettyStringWithDimension(referenceLength, 'bp') + + // ' <span style="margin-left: -0.2em;">(reference)</span></div>'; + // }, + // minTickSize: 1, + // }); + // } + var yaxis = { + min: 0, + //max: cumulative.maxYTick, + labelWidth: 120, + reserveSpace: true, + lineWidth: 0.5, + color: '#000000', + tickFormatter: getBpTickFormatter(cumulative.maxY), + minTickSize: 1 + }; + var yaxes = [yaxis]; + + cumulative.showWithData = function(series, colors) { + var plot = $.plot(placeholder, series, { + shadowSize: 0, + colors: cumulative.colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist'), + }, + // legend: { + // container: legendPlaceholder, + // position: 'se', + // labelBoxBorderColor: '#FFF', + // labelFormatter: labelFormatter, + // }, + grid: { + borderWidth: 1, + hoverable: true, + autoHighlight: false, + mouseActiveRadius: 1000 + }, + yaxes: yaxes, + xaxis: { + min: 0, + max: cumulative.maxX, + lineWidth: 0.5, + color: '#000', + tickFormatter: getContigNumberTickFormatter(cumulative.maxX, tickX), + minTickSize: tickX + } + }); + + bindTip(placeholder, series, plot, ordinalNumberToPrettyString, tickX, 'contig', 'bottom right'); + }; + + cumulative.isInitialized = true; + } + + addLegendClickEvents(cumulative, filenames.length, showPlotWithInfo, refLengths); + + showPlotWithInfo(cumulative); + + $('#contigs_are_ordered').show(); + }, +}; + +</script> + +<script type="text/javascript"> + +var nx = { + nx: { + isInitialized: false, + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null + }, + + nax: { + isInitialized: false, + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null + }, + + ngx: { + isInitialized: false, + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null + }, + + ngax: { + isInitialized: false, + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null + }, + + draw: function (name, title, colors, filenames, data, refPlotValue, tickX, + placeholder, legendPlaceholder, glossary, order, scalePlaceholder) { + + $(scalePlaceholder).empty(); + + var coordX = data.coord_x; + var coordY = data.coord_y; + + var cur_filenames = data.filenames; + var info = nx[name]; + + if (!info.isInitialized) { + var plotsN = cur_filenames.length; + info.series = new Array(plotsN); + + for (var i = 0; i < plotsN; i++) { + var index = $.inArray(cur_filenames[order[i]], filenames); + var plot_coordX = coordX[order[i]]; + var plot_coordY = coordY[order[i]]; + var size = plot_coordX.length; + + info.series[i] = { + data: [], + label: filenames[index], + number: index, + color: colors[index] + }; + info.series[i].data.push([0.0, plot_coordY[0]]); + var currentLen = 0; + var x = 0.0; + + for (var k = 0; k < size; k++) { + info.series[i].data.push([plot_coordX[k], plot_coordY[k]]); + } + + if (info.series[i].data[0][1] > info.maxY) { + info.maxY = info.series[i].data[0][1]; + } + + var lastPt = info.series[i].data[info.series[i].data.length-1]; + info.series[i].data.push([lastPt[0], 0]); + } + + for (i = 0; i < plotsN; i++) { + if (typeof broken_scaffolds_labels !== undefined && $.inArray(filenames[order[i]], broken_scaffolds_labels) != -1) { + info.series[i].dashes = { + show: true, + lineWidth: 1 + }; + } + else { + info.series[i].lines = { + show: true, + lineWidth: 1 + }; + } + } + + // for (i = 0; i < plotsN; i++) { + // plotsData[i].points = { + // show: true, + // radius: 1, + // fill: 1, + // fillColor: false, + // } + // } + + info.showWithData = function(series, colors) { + var plot = $.plot(placeholder, series, { + shadowSize: 0, + colors: colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist'), + }, + grid: { + borderWidth: 1, + hoverable: true, + autoHighlight: false, + mouseActiveRadius: 1000 + }, + yaxis: { + min: 0, +// max: info.maxY, + labelWidth: 120, + reserveSpace: true, + lineWidth: 0.5, + color: '#000', + tickFormatter: getBpTickFormatter(info.maxY), + minTickSize: 1 + }, + xaxis: { + min: 0, + max: 100, + lineWidth: 0.5, + color: '#000', + tickFormatter: function (val, axis) { + if (val == 100) { + return ' x<span class="rhs"> </span>=<span class="rhs"> </span>100%' + } else { + return val; + } + } + }, + minTickSize: tickX + } + ); + + var firstLabel = $('.yAxis .tickLabel').last(); + firstLabel.prepend(title + '<span class="rhs"> </span>=<span class="rhs"> </span>'); + + bindTip(placeholder, series, plot, toPrettyString, 1, '%', 'top right'); + + }; + + info.isInitialized = true; + } + + addLegendClickEvents(info, filenames.length, showPlotWithInfo); + showPlotWithInfo(info); + } +}; + + + +</script> + +<script type="text/javascript"> + +var normal_scale_span = + "<span class='selected-switch'>" + + 'Normal' + + "</span>"; +var normal_scale_a = + "<a class='dotted-link' onClick='setNormalScale()'>" + + 'Normal' + + "</a>"; +var log_scale_span = + "<span class='selected-switch'>" + + 'logarithmic' + + "</span>"; +var log_scale_a = + "<a class='dotted-link' onClick='setLogScale()'>" + + 'logarithmic' + + "</a>"; + +var show_all_span = + "<span class='selected-switch gc'>" + + 'Back to overview' + + "</span>"; +var show_all_a = + " <a class='dotted-link' onClick='showAll()'>" + + 'Back to overview' + + "</a>"; + +var gc = { + isInitialized: false, + + maxY: 0, + plot: null, + series: null, + showWithData: null, + minPow: 0, + ticks: null, + placeholder: null, + legendPlaceholder: null, + colors: null, + yAxisLabeled: false, + + show_all_el: show_all_span, + reference: false, + + normal_scale_el: null, + log_scale_el: null, + + draw: function(name, title, colors, filenames, gcInfos, reflen, tickX, + placeholder, legendPlaceholder, glossary, order, scalePlaceholder) { + gc.normal_scale_el = normal_scale_span; + gc.log_scale_el = log_scale_a; + $(scalePlaceholder).html( + "<div id='change-scale' style='margin-right: 3px; visibility: hidden;'>" + + "<span id='normal_scale_label'>" + + gc.normal_scale_el + + "</span> / " + + "<span id='log_scale_label'>" + + gc.log_scale_el + + "</span> scale" + + "</div>" + ); + + var refIndex = gcInfos.reference_index; + if (!gc.isInitialized) { + gc.legendPlaceholder = legendPlaceholder; + gc.placeholder = placeholder; + gc.colors = colors; + gc.filenames = filenames; + + var bin_size = 1.0; + var plotsN = filenames.length; + gc.series = new Array(plotsN + 1); + gc.series[0] = new Array(plotsN); + + gc.maxY = 0; + var minY = Number.MAX_VALUE; + + function updateMinY(y) { + if (y < minY && y != 0) { + minY = y; + } + } + function updateMaxY(y) { + if (y > gc.maxY) { + gc.maxY = y; + } + } + + for (var i = 0; i < plotsN; i++) { + gc.series[0][i] = { + data: [], + label: filenames[order[i]], + number: order[i], + color: colors[order[i]] + }; + } + + function makeSeriesFromDistributions(distributionsXandY, series_i, plot_i) { + var distributionsX = distributionsXandY[0]; + var distributionsY = distributionsXandY[1]; + + for (var j = 0; j < distributionsX.length; j++) { + var x = distributionsX[j]; + var y = distributionsY[j]; + gc.series[series_i][plot_i].data.push([x, y]); + updateMinY(y); + updateMaxY(y); + } + } + + function makeSeries(listsOfGCInfo, listOfGcDistributions, seriesIdx) { + for (var i = 0; i < plotsN; i++) { + if (listsOfGCInfo) { + makeSeriesFromInfo(listsOfGCInfo[order[i]], seriesIdx, i); + } else { + makeSeriesFromDistributions(listOfGcDistributions[order[i]], seriesIdx, i); + } + } + } + + var listsOfGCInfo = gcInfos.lists_of_gc_info; + var listOfGcDistributions = gcInfos.list_of_GC_distributions; + makeSeries(listsOfGCInfo, listOfGcDistributions, 0); + + function makeSeriesFromInfo(GC_info, series_i, i) { + var cur_bin = 0.0; + + var x = cur_bin; + var y = filterAndSumGcInfo(GC_info, function(GC_percent) { + return GC_percent == cur_bin; + }); + gc.series[series_i][i].data.push([x, y]); + + updateMinY(y); + updateMaxY(y); + + while (cur_bin < 100.0 - bin_size) { + cur_bin += bin_size; + + x = cur_bin; + y = filterAndSumGcInfo(GC_info, function(GC_percent) { + return GC_percent > (cur_bin - bin_size) && GC_percent <= cur_bin; + }); + gc.series[series_i][i].data.push([x, y]); + + updateMinY(y); + updateMaxY(y); + } + + x = 100.0; + y = filterAndSumGcInfo(GC_info, function(GC_percent) { + return GC_percent > cur_bin && GC_percent <= 100.0; + }); + + gc.series[series_i][i].data.push([x, y]); + + updateMinY(y); + updateMaxY(y); + } + + for (i = 0; i < plotsN; i++) { + if (typeof broken_scaffolds_labels !== undefined && $.inArray(filenames[order[i]], broken_scaffolds_labels) != -1) { + gc.series[0][i].dashes = { + show: true, + lineWidth: 1 + }; + } + else { + gc.series[0][i].lines = { + show: true, + lineWidth: 1 + }; + } + } + + if (refIndex) { + gc.reference = true; + gc.series[0].push({ + data: [], + label: 'reference', + isReference: true, + number: filenames.length, + lines: {}, + dashes: { + show: true, + lineWidth: 1 + }, + color: '#000000' + }); + if (listsOfGCInfo) { + makeSeriesFromInfo(listsOfGCInfo[refIndex], 0, refIndex); + } else { + makeSeriesFromDistributions(listOfGcDistributions[refIndex], 0, refIndex); + } + gc.colors.push('#000000') + } + + if (gcInfos.list_of_GC_contigs_distributions) { + listOfGcDistributions = gcInfos.list_of_GC_contigs_distributions; + var maxY = 0; + for (var file_n = 0; file_n < filenames.length; file_n++) { + gc.series[file_n + 1] = new Array(1); + gc.series[file_n + 1][0] = { + data: [], + label: filenames[order[file_n]], + number: order[file_n], + color: colors[order[file_n]], + bars: { + show: true, + lineWidth: 0.6, + fill: 0.6, + barWidth: 5 + } + }; + + var distributionsX = listOfGcDistributions[file_n][0]; + var distributionsY = listOfGcDistributions[file_n][1]; + + for (var j = 0; j < distributionsX.length; j++) { + var x = distributionsX[j]; + var y = distributionsY[j]; + gc.series[file_n + 1][0].data.push([x, y]); + maxY = Math.max(maxY, y); + } + } + for (var file_n = 0; file_n < filenames.length; file_n++) { + gc.series[file_n + 1][0].maxY = maxY; + } + } + // Calculate the minimum possible non-zero Y to clip useless bottoms + // of logarithmic plots. + var maxYTick = getMaxDecimalTick(gc.maxY); + gc.minPow = Math.round(Math.log(minY) / Math.log(10)); + gc.ticks = []; + for (var pow = gc.minPow; Math.pow(10, pow) < maxYTick; pow++) { + gc.ticks.push(Math.pow(10, pow)); + } + gc.ticks.push(Math.pow(10, pow)); + + gc.isInitialized = true; + } + + gc.showWithData = showInNormalScaleWithData; + if (gcInfos.list_of_GC_contigs_distributions) { + createLegend(gc.filenames, gc.colors, 0, gc.reference); + } + addLegendClickEvents(gc, filenames.length, showPlotWithInfo, false, 0); + + showPlotWithInfo(gc, 0); + + $('#change-scale').css('visibility', 'visible'); + $('#gc_info').show(); + } +}; + +function showAll() { + $('#change-scale').show(); + $('#gc_info').show(); + $('#gc_contigs_info').hide(); + createLegend(gc.filenames, gc.colors, 0, gc.reference); + + gc.show_all_el = show_all_span; + gc.showWithData = gc.log_scale_el == log_scale_a ? showInNormalScaleWithData : showInLogarithmicScaleWithData; + + $('#show_all_label').html(gc.show_all_el); + showPlotWithInfo(gc, 0); +} + +function showPlot(index) { + $('#change-scale').hide(); + $('#gc_info').hide(); + $('#gc_contigs_info').show(); + createLegend([gc.filenames[index - 1]], [gc.colors[index - 1]], index); + + gc.show_all_el = show_all_a; + gc.showWithData = showOneAssembly; + + $('#show_all_label').html(gc.show_all_el); + showPlotWithInfo(gc, index); +} + +function showOneAssembly(series, colors) { + if (series == null) { + return; + } + + gc.plot = $.plot(gc.placeholder, series, { + shadowSize: 0, + colors: colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist') + }, + grid: { + hoverable: true, + borderWidth: 1, + autoHighlight: false, + mouseActiveRadius: 1000 + }, + yaxis: { + min: 0, + max: series[0].maxY * 1.1, + labelWidth: 120, + reserveSpace: true, + lineWidth: 0.5, + color: '#000', + tickFormatter: getJustNumberTickFormatter(gc.maxY), + minTickSize: 1 + }, + xaxis: { + min: 0, + max: 100, + lineWidth: 0.5, + color: '#000', + tickFormatter: function (val, axis) { + if (val == 100) { + return ' 100% GC' + } else { + return val; + } + } + }, + minTickSize: 1 + } + ); + + var firstLabel = $('.yAxis .tickLabel').last(); + firstLabel.append(' contigs'); + unBindTips(gc.placeholder); + bindTip(gc.placeholder, series, gc.plot, getIntervalToPrettyString(5), 1, '%<span class="rhs"> </span>GC', 'top right'); +} + +function showInNormalScaleWithData(series, colors) { + if (series == null || gc.maxY == null) + return; + + gc.yAxisLabeled = false; + + gc.plot = $.plot(gc.placeholder, series, { + shadowSize: 0, + colors: colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist'), + }, + grid: { + borderWidth: 1, + hoverable: true, + autoHighlight: false, + mouseActiveRadius: 1000, + }, + yaxis: { + min: 0, +// max: gc.maxY + 0.1 * gc.maxY, + labelWidth: 120, + reserveSpace: true, + lineWidth: 0.5, + color: '#000', + tickFormatter: windowsTickFormatter, + minTickSize: 1 + }, + xaxis: { + min: 0, + max: 100, + lineWidth: 0.5, + color: '#000', + tickFormatter: function (val, axis) { + if (val == 100) { + return ' 100% GC' + } else { + return val; + } + } + }, + minTickSize: 1 + } + ); + + var firstLabel = $('.yAxis .tickLabel').last(); + firstLabel.append(' windows'); + bindTip(gc.placeholder, series, gc.plot, toPrettyString, 1, '%<span class="rhs"> </span>GC', 'top right'); +} + + +function showInLogarithmicScaleWithData(series, colors) { + if (series == null || gc.maxY == null || gc.minPow == null) { + return; + } + + gc.yAxisLabeled = false; + + gc.plot = $.plot(gc.placeholder, series, { + shadowSize: 0, + colors: colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist'), + }, + grid: { + hoverable: true, + borderWidth: 1, + autoHighlight: false, + mouseActiveRadius: 1000 + }, + yaxis: { + min: Math.pow(10, gc.minPow), +// max: gc.maxY, + labelWidth: 120, + reserveSpace: true, + lineWidth: 0.5, + color: '#000', + tickFormatter: windowsTickFormatter, + minTickSize: 1, + ticks: gc.ticks, + + transform: function(v) { + return Math.log(v + 0.0001)/*move away from zero*/ / Math.log(10); + }, + inverseTransform: function(v) { + return Math.pow(v, 10); + }, + tickDecimals: 3 + }, + xaxis: { + min: 0, + max: 100, + lineWidth: 0.5, + color: '#000', + tickFormatter: function (val, axis) { + if (val == 100) { + return ' 100%<span class="rhs"> </span>GC' + } else { + return val; + } + } + }, + minTickSize: 1 + } + ); + + var firstLabel = $('.yAxis .tickLabel').last(); + firstLabel.append(' windows'); + bindTip(gc.placeholder, series, gc.plot, toPrettyString, 1, '% GC', 'top right'); +} + + +function setLogScale() { + gc.normal_scale_el = normal_scale_a; + gc.log_scale_el = log_scale_span; + gc.showWithData = showInLogarithmicScaleWithData; + + $('#normal_scale_label').html(gc.normal_scale_el); + $('#log_scale_label').html(gc.log_scale_el); + showPlotWithInfo(gc, 0); +} + + +function setNormalScale() { + gc.normal_scale_el = normal_scale_span; + gc.log_scale_el = log_scale_a; + gc.showWithData = showInNormalScaleWithData; + + $('#normal_scale_label').html(gc.normal_scale_el); + $('#log_scale_label').html(gc.log_scale_el); + showPlotWithInfo(gc, 0); +} + + + +function filterAndSumGcInfo(GC_info, condition) { + var contigs_lengths_cur_bin = []; + for (var j = 0; j < GC_info.length; j++) { + var GC = GC_info[j]; + var contig_length = GC[0]; + var GC_percent = GC[1]; + + if (condition(GC_percent) == true) { + contigs_lengths_cur_bin.push(contig_length); + } + } + var val_bp = 0; + for (var j = 0; j < contigs_lengths_cur_bin.length; j++) { + val_bp += contigs_lengths_cur_bin[j]; + } + return val_bp; +} + +function createLegend(labels, colors, index, reference) { + var selectedAssemblies = getSelectedAssemblies(labels); + $('#legend-placeholder').empty(); + var selectors = ""; + + labels.forEach(function(label, i) { + var link = index ? '' : '<span id="' + labels[i] + '-switch"' + "class='plot-gc-type-switch dotted-link'>by contigs<br></span><br>"; + var assemblyIdx = gc.filenames.indexOf(label); + addLabelToLegend(assemblyIdx, label, selectedAssemblies, colors, link); + }); + if (reference) { + isChecked = (selectedAssemblies.length > 0 && selectedAssemblies.indexOf(gc.filenames.length.toString())) != -1 ? 'checked="checked"' : ""; + $('#legend-placeholder').append( + '<div id="reference-label">' + + '<label for="reference" style="color: #000000;">' + + '<input type="checkbox" name="' + gc.filenames.length + + '" checked="' + isChecked + '" id="reference"> ' + 'reference' + + '</label>' + + '</div>' + ); + } + if (index > 0) { + for (var filenames_n = 0; filenames_n < gc.filenames.length; filenames_n++){ + selectors += '<br><span id="' + gc.filenames[filenames_n] + '-switch" ' + + "class='plot-switch dotted-link'>" + + gc.filenames[filenames_n] + "</span>"; + } + $('#legend-placeholder').append( + "<br><br><div id='change-assembly' style='margin-right: 3px;'>" + + "<span id='show_all_label'>" + + gc.show_all_el + + "</span><br>" + selectors + + "</div>" + ); + } + addLinksToSwitches(index - 1); + addLegendClickEvents(gc, gc.series.length, showPlotWithInfo, false, index); +} + +function addLinksToSwitches(index) { + var filenames = gc.filenames; + for (filenames_n = 0; filenames_n < filenames.length; filenames_n++){ + var switchSpan = document.getElementById(filenames[filenames_n] + "-switch"); + $(switchSpan).click(getToggleSwitchFunction(filenames_n + 1)); + if (filenames_n == index) { + switchSpan.className = 'plot-switch selected-switch gc'; + } + } +} + +function getToggleSwitchFunction(index) { + return function() { + if (index > 0) { + showPlot(index); + } + else { + showAll(); + } + }; +} +</script> + +<script type="text/javascript"> + +var frc = { + genes: { + isInitialized: false, + + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null, + + yAxisLabeled: false + }, + + operons: { + isInitialized: false, + + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null, + + yAxisLabeled: false + }, + + misassemblies: { + isInitialized: false, + + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null, + + yAxisLabeled: false + }, + + draw: function (name, title, colors, filenames, data, refGenesNumber, tickX, + placeholder, legendPlaceholder, glossary, order, scalePlaceholder) { +// div.html( +// "<span class='plot-header'>" + kind[0].toUpperCase() + kind.slice(1) + "s covered</span>" + +// "<div class='plot-placeholder' id='" + kind + "s-plot-placeholder'></div>" +// ); + $(scalePlaceholder).empty(); + + var info = frc[name]; + var coordX = data.coord_x; + var coordY = data.coord_y; + + info.yAxisLabeled = false; + var cur_filenames = data.filenames; + if (!info.isInitialized) { + var plotsN = cur_filenames.length; + info.series = new Array(plotsN); + + info.maxY = 0; + info.maxX = 0; + + for (var i = 0; i < plotsN; i++) { + var index = $.inArray(cur_filenames[order[i]], filenames); + var plot_coordX = coordX[order[i]]; + var plot_coordY = coordY[order[i]]; + var featureSpace = plot_coordX[plot_coordX.length - 1]; + var maxY = plot_coordY[plot_coordY.length - 1]; + + info.series[i] = { + data: [], + label: filenames[index], + number: index, + color: colors[index] + }; + + info.series[i].data.push([0.0, plot_coordY[0]]); + + if (featureSpace > info.maxX) { + info.maxX = featureSpace; + } + for (var k = 0; k < plot_coordX.length; k++) { + info.series[i].data.push([plot_coordX[k], plot_coordY[k]]); + } + + if (maxY > info.maxY) { + info.maxY = maxY; + } + } + + for (i = 0; i < plotsN; i++) { + if (typeof broken_scaffolds_labels !== undefined && $.inArray(filenames[order[i]], broken_scaffolds_labels) != -1) { + info.series[i].dashes = { + show: true, + lineWidth: 1 + }; + } + else { + info.series[i].lines = { + show: true, + lineWidth: 1 + }; + } + } + + info.showWithData = function(series, colors) { + var plot = $.plot(placeholder, series, { + shadowSize: 0, + colors: colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist') + }, + grid: { + borderWidth: 1, + hoverable: true, + autoHighlight: false, + mouseActiveRadius: 1000, + }, + yaxis: { + min: 0, + max: Math.max(100, info.maxY), + labelWidth: 145, + reserveSpace: true, + lineWidth: 0.5, + color: '#000', + tickFormatter: getPercentTickFormatter(Math.max(100, info.maxY)), + minTickSize: 1 + }, + xaxis: { + min: 0, + max: info.maxX, + lineWidth: 0.5, + color: '#000', + tickFormatter: getJustNumberTickFormatter(info.maxX, ' ' + name), + minTickSize: tickX + } + }); + + var firstLabel = $('.yAxis .tickLabel').last(); + firstLabel.prepend('Genome coverage<span class="rhs"> </span>=<span class="rhs"> </span>'); + + bindTip(placeholder, series, plot, frcNumberToPrettyString, tickX, name, 'bottom right', false, '%'); + }; + + info.isInitialized = true; + } + + addLegendClickEvents(info, filenames.length, showPlotWithInfo, refGenesNumber); + showPlotWithInfo(info); + $('#frc_info').show(); + $('.frc_plot_name').html(name); + } +}; + + + +</script> + +<script type="text/javascript"> + +/**********/ +/* COLORS */ + +// var colors = ["#FF5900", "#008FFF", "#168A16", "#7C00FF", "#00B7FF", "#FF0080", "#7AE01B", "#782400", "#E01B6A"]; +var standard_colors = [ + '#FF0000', //red + '#0000FF', //blue + '#008000', //green + '#FFA500', //orange + '#FF00FF', //fushua + '#CCCC00', //yellow + '#800000', //maroon + '#00CCCC', //aqua + '#808080', //gray + '#800080', //purple + '#808000', //olive + '#000080', //navy + '#008080', //team + '#00FF00', //lime +]; + +function distinctColors(count) { + var colors = []; + for(var hue = 0; hue < 360; hue += 360 / count) { + var color = hsvToRgb(hue, 100, 100); + var colorStr = '#' + color[0].toString(16) + color[1].toString(16) + color[2].toString(16); + colors.push(); + } + return colors; +} + +/**************/ +/* FORMATTING */ +function isIntegral(num) { + return num % 1 === 0; +} + +function isFractional(num) { + return !isIntegral(num); +} + +function getIntervalToPrettyString(interval) { + return function(num, unit) { + return intervalToPrettyString(interval, num, unit); + } +} + +function intervalToPrettyString(interval, num, unit) { + if (typeof num === 'number') { + var str = toPrettyString(num); + str += '-' + toPrettyString(num + interval); + str += (unit ? '<span class="rhs"> </span>' + unit : ''); + return str; + } else { + return num; + } +} + +function toPrettyString(num, unit) { + if (typeof num === 'number') { + var str; + if (num <= 9999) { + if (isFractional(num)) { + if (isIntegral(num * 10)) { + str = num.toFixed(1); + } else if (isIntegral(num * 100) || num >= 100) { + str = num.toFixed(2); + } else { + str = num.toFixed(3); + if (str.slice(-1) == '0') + str = str.slice(0, -1); + } + } else { + str = num.toFixed(0); + } + } else { + str = num.toFixed(0).replace(/(\d)(?=(\d\d\d)+(?!\d))/g,'$1<span class="hs"></span>'); + } + str += (unit ? '<span class="rhs"> </span>' + unit : ''); + return str; + } else { + return num; + } +} + + //elif isinstance(value, float): + // if value == 0.0: + // return '0' + // if human_readable: + // if unit == '%': + // value *= 100 + // precision = 2 + // for i in range(10, 1, -1): + // if abs(value) < 1./(10**i): + // precision = i + 1 + // break + // return '{value:.{precision}f}{unit_str}'.format(**locals()) + // else: + // return str(value) + + +function refToPrettyString(num, refs) { + return refs[Math.round(num)-1]; +} + +function ordinalNumberToPrettyString(num, unit, tickX) { + num = num * tickX; + var numStr = num.toString(); + var lastDigit = numStr[numStr.length-1]; + var beforeLastDigit = numStr[numStr.length-2]; + + var res = toPrettyString(num); + + if (lastDigit == '1' && beforeLastDigit != '1') { + res += "st"; + } else if (lastDigit == '2' && beforeLastDigit != '1') { + res += "nd"; + } else if (lastDigit == '3' && beforeLastDigit != '1') { + res += "rd"; + } else { + res += 'th'; + } + + res += (unit ? '<span class="rhs"> </span>' + unit : ''); + + return res; +} + +function frcNumberToPrettyString(num, unit, tickX, index) { + if (index % 2 == 0 && num > 0) num--; + return toPrettyString(num) + ' ' + unit; +} + +function getMaxDecimalTick(maxY) { + var maxYTick = maxY; + if (maxY <= 100000000000) { + maxYTick = Math.ceil((maxY+1)/10000000000)*10000000000; + } if (maxY <= 10000000000) { + maxYTick = Math.ceil((maxY+1)/1000000000)*1000000000; + } if (maxY <= 1000000000) { + maxYTick = Math.ceil((maxY+1)/100000000)*100000000; + } if (maxY <= 100000000) { + maxYTick = Math.ceil((maxY+1)/10000000)*10000000; + } if (maxY <= 10000000) { + maxYTick = Math.ceil((maxY+1)/1000000)*1000000; + } if (maxY <= 1000000) { + maxYTick = Math.ceil((maxY+1)/100000)*100000; + } if (maxY <= 100000) { + maxYTick = Math.ceil((maxY+1)/10000)*10000; + } if (maxY <= 10000) { + maxYTick = Math.ceil((maxY+1)/1000)*1000; + } if (maxY <= 1000) { + maxYTick = Math.ceil((maxY+1)/100)*100. + } if (maxY <= 100) { + maxYTick = Math.ceil((maxY+1)/10)*10. + } + return maxYTick; +} + +function getBpTickFormatter(maxY, additionalText) { + additionalText = additionalText || ''; + + return function(val, axis) { + var res; + if (val == 0) { + res = 0; + + } else if (axis.max >= 1000000) { + res = val / 1000000; + + if (val > axis.max - 1 || val + axis.tickSize >= 1000000000) { + res = additionalText + toPrettyString(res, 'Mbp'); + } else { + res = toPrettyString(res); + } + } else if (axis.max >= 1000) { + res = val / 1000; + + if (val > axis.max - 1 || val + axis.tickSize >= 1000000) { + res = additionalText + toPrettyString(res, 'kbp'); + } else { + res = toPrettyString(res); + } + } else if (axis.max >= 1) { + res = val; + + if (val > axis.max - 1 || val + axis.tickSize >= 1000) { + res = additionalText + toPrettyString(res, 'bp'); + } else { + res = toPrettyString(res); + } + } + return res; + } +} + +function windowsTickFormatter(v, axis) { + return toPrettyString(v); +// var val = v.toFixed(0); +// if (!gc.yAxisLabeled && val > gc.maxY) { +// gc.yAxisLabeled = true; +// var res = val + ' window'; +// if (val > 1) { +// res += 's' +// } +// return res; +// } else { +// return val; +// } +} + +function getBpLogTickFormatter(maxY) { + return getBpTickFormatter(maxY); +} + +function getContigNumberTickFormatter(maxX, tickX) { + return function (val, axis) { + if (typeof axis.tickSize == 'number' && val > maxX - axis.tickSize) { + return " " + ordinalNumberToPrettyString(val, 'contig', tickX); + } else { + return val * tickX; + } + } +} + +function getJustNumberTickFormatter(maxY, additionalText) { + return function (val, axis) { + additionalText = additionalText || ''; + if (val > axis.max - axis.tickSize) { + res = toPrettyString(val) + additionalText; + } else { + res = toPrettyString(val); + } + return res; + } +} + +function getPercentTickFormatter(maxY, additionalText) { + return function (val, axis) { + additionalText = additionalText || ''; + if (val > maxY + 1 || val == 100) { + res = additionalText + toPrettyString(val, '%'); + } else { + res = toPrettyString(val); + } + return res; + } +} + +function trim(str) { + return str.replace(/^\s+/g, ''); +} + +function initial_spaces_to_nbsp(str, metricName) { + if (metricName.length > 0 && metricName[0] == ' ') { + str = ' ' + str; + } + return str; +} + +function containsObject(obj, list) { + var i; + for (i = 0; i < list.length; i++) { + if (list[i] === obj) { + return true; + } + } + + return false; +} + +function addLegendClickEvents(info, numLegendItems, showPlotWithInfo, showReference, index) { + if (showReference) numLegendItems++; + for (var i = 0; i < numLegendItems; i++) { + $('#legend-placeholder input[name=' + i + ']').click(function() { + showPlotWithInfo(info, index); + }); + } +} + +/*********************/ +/* GLOSSARY TOOLTIPS */ +function addTooltipIfDefinitionExists(glossary, metricName) { + metricName = trim(metricName); + + if (containsObject(metricName, Object.keys(glossary))) { + return '<a class="tooltip-link" rel="tooltip" title="' + + metricName + ' ' + glossary[metricName] + '">' + metricName + '</a>'; + } else { + return metricName; + } +} + +/*************/ +/* PLOT TIPS */ +function bindTip(placeholder, series, plot, xToPrettyStringFunction, tickX, xUnit, position, summaryPlots, unitY) { + var prevPoint = null; + var prevIndex = null; + + $(placeholder).bind("plothover", function(event, pos, item) { + if (dragTable && dragTable.isDragging) + return; + + if (item) { + if (prevPoint != item.dataIndex || (summaryPlots && item.seriesIndex != prevIndex)) { + prevPoint = item.dataIndex; + prevIndex = item.seriesIndex; + var x = item.datapoint[0]; + + showTip(item.pageX, item.pageY, plot.offset(), + plot.width(), plot.height(), + series, item.seriesIndex, x, item.dataIndex, + xToPrettyStringFunction(x, xUnit, tickX, item.dataIndex) + ':', + position, summaryPlots, unitY); + } + } else { + $('#plot_tip').hide(); + $('#plot_tip_vertical_rule').hide(); + $('#plot_tip_horizontal_rule').hide(); + prevPoint = null; + } + }); +} + +function unBindTips(placeholder) { + $(placeholder).unbind("plothover"); +} + +var tipElementExists = false; +function showTip(pageX, pageY, offset, plotWidth, plotHeight, + series, centralSeriesIndex, xPos, xIndex, xStr, position, summaryPlots, unitY) { + const LINE_HEIGHT = 16; // pixels + + position = ((position != null) ? position : 'bottom right'); +// pageY -= LINE_HEIGHT * (centralSeriesIndex + 1.5); + + var directions = position.split(' '); + + if (!tipElementExists) { + $('<div id="plot_tip" class="white_stroked"></div>').appendTo('body'); + + $('<div id="plot_tip_vertical_rule"></div>').css({ + height: plotHeight, + }).appendTo('body'); + + $('<div id="plot_tip_horizontal_rule"></div>').css({ + width: plotWidth, + }).appendTo('body'); + + tipElementExists = true; + } + + $('#plot_tip').html('').css({ + top: pageY + 5 - ((directions[0] == 'top') ? LINE_HEIGHT * (series.length + 2) : 0), + left: pageX + 10, + }).show(); + + $('#plot_tip_vertical_rule').html('').css({ + top: offset.top, + left: pageX, + }).show(); + + $('#plot_tip_horizontal_rule').html('').css({ + top: pageY, + left: offset.left, + }).show(); + + $('<div>' + xStr + '</div>').css({ + height: LINE_HEIGHT, + }).appendTo('#plot_tip'); + + var sortedYsAndColors = []; + for (var i = 0; i < series.length; i++) { + if (!summaryPlots || (summaryPlots && series[i].data[xIndex] != undefined && series[i].data[xIndex][1] != null)) { + sortedYsAndColors.push({ + y: summaryPlots ? series[i].data[xIndex][1] : (i == centralSeriesIndex ? (series[i].data[xIndex] || series[i].data[series[i].data.length - 1])[1] : + findNearestPoint(series[i].data, xPos)), + color: series[i].color, + label: (series[i].isReference ? 'Reference' : series[i].label), + isCurrent: i == centralSeriesIndex, + }); + } + } + sortedYsAndColors.sort(function(a, b) { return a.y < b.y;}); + + for (i = 0; i < sortedYsAndColors.length; i++) { + var item = sortedYsAndColors[i]; + + $('<div id="tip_line' + i + '">' + toPrettyString(item.y) + (unitY ? unitY : '') + + ', <span style="color: ' + item.color + ';">' + item.label + '</span></div>').css({ + height: LINE_HEIGHT, + "font-weight": item.isCurrent ? "bold" : "normal", + }).appendTo('#plot_tip'); + } +} + +function findNearestPoint(points, x) { + for (var i = 0; i < points.length; i++) { + if (points[i][0] >= x) return points[i][1]; + } + return points[points.length-1][1] +} + +function addLabelToLegend(idx, label, selectedLabels, colors, link) { + var isChecked = (selectedLabels.length > 0 && selectedLabels.indexOf(idx.toString())) != -1 ? 'checked="checked"' : ""; + $('#legend-placeholder').append('<div>' + + '<label for="' + label + '" style="color: ' + colors[idx] + '">' + + '<input type="checkbox" name="' + idx + '"' + isChecked + ' id="' + label + '"> ' + label + '</label>' + + (link ? '<br>' + link : '') + '</div>'); +} + +function getSelectedAssemblies(labels) { + var selectedAssemblies = []; + var labelsMatch = false; + var legendLabels = []; + $('#legend-placeholder input[type="checkbox"]').each(function() { + legendLabels.push($(this).attr('id')); + }); + if (labels.every(function(label, i) { return ($.inArray(label, legendLabels) != -1 || label == 'reference')}) ) { + labelsMatch = true; + } + if (labelsMatch) { + $('#legend-placeholder input:checked[type="checkbox"]').each(function() { + selectedAssemblies.push($(this).attr('name')); + }); + } + else { + selectedAssemblies = Array.apply(null, {length: labels}).map(Number.call, Number); + } + return selectedAssemblies; +} + +// Cookie functions based on http://www.quirksmode.org/js/cookies.html +// Cookies won't work for local files. + +var createCookie = function(name, value, days) { + var expires = ''; + if (days) { + var date = new Date(); + date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000)); + expires = '; expires=' + date.toGMTString(); + } + var path = document.location.pathname; + document.cookie = name + '=' + value + expires + '; path=' + path; +}; + +var readCookie = function(name) { + var nameEQ = name + '='; + var ca = document.cookie.split(';'); + for(var i = 0; i < ca.length; i++) { + var c = ca[i]; + while (c.charAt(0) == ' ') { + c = c.substring(1, c.length); + } + if (c.indexOf(nameEQ) == 0) { + return c.substring(nameEQ.length, c.length); + } + } + return null; +}; + +var eraseCookie = function(name) { + createCookie(name, '', -1); +}; + + +// Dean's forEach: http://dean.edwards.name/base/forEach.js +/*forEach, version 1.0 + Copyright 2006, Dean Edwards + License: http://www.opensource.org/licenses/mit-license.php */ + +// array-like enumeration +if (!Array.forEach) { // mozilla already supports this + Array.forEach = function(array, block, context) { + for (var i = 0; i < array.length; i++) { + block.call(context, array[i], i, array); + } + }; +} + +// generic enumeration +Function.prototype.forEach = function(object, block, context) { + for (var key in object) { + if (typeof this.prototype[key] == "undefined") { + block.call(context, object[key], key, object); + } + } +}; + +// character enumeration +String.forEach = function(string, block, context) { + Array.forEach(string.split(""), function(chr, index) { + block.call(context, chr, index, string); + }); +}; + +// globally resolve forEach enumeration +var forEach = function(object, block, context) { + if (object) { + if (object instanceof Function) { // functions have a "length" property + Function.forEach(object, block, context); + + } else if (object.each instanceof Function) { // jQuery + object.each(function(i, elt) { + block(elt); + }, context); + + } else if (object.forEach instanceof Function) { // the object implements a custom forEach method + object.forEach(block, context); + + } else if (typeof object == "string") { // a string + String.forEach(object, block, context); + + } else if (typeof object.length == "number") { // array-like object + Array.forEach(object, block, context); + + } else { + Object.forEach(object, block, context); + } + } +}; + + +jQuery.fn.exists = function(){ + return jQuery(this).length > 0; +}; + + +function Range(from, to) { + var r = []; + for (var i = from; i < to; i++) { + r.push(i); + } + return r; +} + + + +</script> + +<script type="text/javascript"> +/** + * HSV to RGB color conversion + * + * H runs from 0 to 360 degrees + * S and V run from 0 to 100 + * + * Ported from the excellent java algorithm by Eugene Vishnevsky at: + * http://www.cs.rit.edu/~ncs/color/t_convert.html + */ +function hsvToRgb(h, s, v) { + var r, g, b; + var i; + var f, p, q, t; + + // Make sure our arguments stay in-range + h = Math.max(0, Math.min(360, h)); + s = Math.max(0, Math.min(100, s)); + v = Math.max(0, Math.min(100, v)); + + // We accept saturation and value arguments from 0 to 100 because that's + // how Photoshop represents those values. Internally, however, the + // saturation and value are calculated from a range of 0 to 1. We make + // That conversion here. + s /= 100; + v /= 100; + + if(s == 0) { + // Achromatic (grey) + r = g = b = v; + return [Math.round(r * 255), Math.round(g * 255), Math.round(b * 255)]; + } + + h /= 60; // sector 0 to 5 + i = Math.floor(h); + f = h - i; // factorial part of h + p = v * (1 - s); + q = v * (1 - s * f); + t = v * (1 - s * (1 - f)); + + switch(i) { + case 0: + r = v; + g = t; + b = p; + break; + + case 1: + r = q; + g = v; + b = p; + break; + + case 2: + r = p; + g = v; + b = t; + break; + + case 3: + r = p; + g = q; + b = v; + break; + + case 4: + r = t; + g = p; + b = v; + break; + + default: // case 5: + r = v; + g = p; + b = q; + } + + return [Math.round(r * 255), Math.round(g * 255), Math.round(b * 255)]; +} + +function hslToRgb(h, s, l){ + var r, g, b; + + if(s == 0) { + r = g = b = l; // achromatic + } else { + function hue2rgb(p, q, t){ + if(t < 0) t += 1; + if(t > 1) t -= 1; + if(t < 1/6) return p + (q - p) * 6 * t; + if(t < 1/2) return q; + if(t < 2/3) return p + (q - p) * (2/3 - t) * 6; + return p; + } + + var q = l < 0.5 ? l * (1 + s) : l + s - l * s; + var p = 2 * l - q; + r = hue2rgb(p, q, h + 1/3); + g = hue2rgb(p, q, h); + b = hue2rgb(p, q, h - 1/3); + } + + return [Math.round(r * 255), Math.round(g * 255), Math.round(b * 255)]; +} +</script> + +<script type="text/javascript"> + +var gns = { + genes: { + isInitialized: false, + + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null, + + yAxisLabeled: false + }, + + operons: { + isInitialized: false, + + maxY: 0, + maxYTick: 0, + series: null, + showWithData: null, + + yAxisLabeled: false + }, + + draw: function (name, title, colors, filenames, data, refGenesNumber, tickX, + placeholder, legendPlaceholder, glossary, order, scalePlaceholder) { +// div.html( +// "<span class='plot-header'>" + kind[0].toUpperCase() + kind.slice(1) + "s covered</span>" + +// "<div class='plot-placeholder' id='" + kind + "s-plot-placeholder'></div>" +// ); + $(scalePlaceholder).empty(); + + var info = gns[name]; + + info.yAxisLabeled = false; + var cur_filenames = data.filenames; + if (!info.isInitialized) { + var filesFeatureInContigs = data.filesFeatureInContigs; + var kind = data.kind; + + var plotsN = cur_filenames.length; + info.series = new Array(plotsN); + + info.maxY = 0; + info.maxX = 0; + + if (refGenesNumber) { + info.maxY = refGenesNumber; + } + + for (var fi = 0; fi < plotsN; fi++) { + var index = $.inArray(cur_filenames[order[fi]], filenames); + var filename = filenames[index]; + var featureInContigs = filesFeatureInContigs[filename]; + + info.series[fi] = { + data: [[0, 0]], + label: filenames[index], + number: index, + color: colors[index] + }; + + var contigNo = 0; + var totalFull = 0; + + for (var k = 0; k < featureInContigs.length; k++) { + contigNo += 1; + totalFull += featureInContigs[k]; + + info.series[fi].data.push([contigNo, totalFull]); + + if (info.series[fi].data[k][1] > info.maxY) { + info.maxY = info.series[fi].data[k][1]; + } + } + + if (featureInContigs.length > info.maxX) { + info.maxX = featureInContigs.length; + } + } + + for (i = 0; i < plotsN; i++) { + if (typeof broken_scaffolds_labels !== undefined && $.inArray(filenames[order[i]], broken_scaffolds_labels) != -1) { + info.series[i].dashes = { + show: true, + lineWidth: 1 + }; + } + else { + info.series[i].lines = { + show: true, + lineWidth: 1 + }; + } + } + + // for (i = 0; i < plotsN; i++) { + // plotsData[i].points = { + // show: true, + // radius: 1, + // fill: 1, + // fillColor: false, + // } + // } + + if (refGenesNumber) { + info.series.push({ + data: [[0, refGenesNumber], [info.maxX, refGenesNumber]], + label: 'reference, ' + toPrettyString(refGenesNumber, 'genes'), + isReference: true, + dashes: { + show: true, + lineWidth: 1 + }, + yaxis: 1, + number: filenames.length, + color: '#000000' + }); + + colors.push('#000000'); + } + + info.showWithData = function(series, colors) { + var plot = $.plot(placeholder, series, { + shadowSize: 0, + colors: colors, + legend: { + container: $('useless-invisible-element-that-does-not-even-exist'), + }, + grid: { + borderWidth: 1, + hoverable: true, + autoHighlight: false, + mouseActiveRadius: 1000, + }, + yaxis: { + min: 0, +// max: info.maxY, + labelWidth: 120, + reserveSpace: true, + lineWidth: 0.5, + color: '#000', + tickFormatter: function (val, axis) { +// if (!info.yAxisLabeled && val > info.maxY) { +// info.yAxisLabeled = true; +// var res = val + ' ' + kind; +// if (val > 1) { +// res += 's' +// } +// return res; +// } else { + return val; +// } + }, + minTickSize: 1 + }, + xaxis: { + min: 0, + max: info.maxX, + lineWidth: 0.5, + color: '#000', + tickFormatter: getContigNumberTickFormatter(info.maxX, tickX), + minTickSize: tickX + }, + }); + + var firstLabel = $('.yAxis .tickLabel').last(); + firstLabel.append(' ' + name); + + bindTip(placeholder, series, plot, ordinalNumberToPrettyString, tickX, 'contig', 'bottom right'); + }; + + info.isInitialized = true; + } + + addLegendClickEvents(info, filenames.length, showPlotWithInfo, refGenesNumber); + + showPlotWithInfo(info); + + $('#contigs_are_ordered').show(); + } +}; + + + +</script> + +<script type="text/javascript"> +/* + DT v1.0 + June 26, 2008 + Dan Vanderkam, http://danvk.org/DT/ + http://code.google.com/p/DT/ + + This is code was based on: + - Stuart Langridge's SortTable (kryogenix.org/code/browser/sorttable) + - Mike Hall's draggable class (http://www.brainjar.com/dhtml/drag/) + - A discussion of permuting table columns on comp.lang.javascript + + Licensed under the MIT license. + */ + +// Here's the notice from Mike Hall's draggable script: +//***************************************************************************** +// Do not remove this notice. +// +// Copyright 2001 by Mike Hall. +// See http://www.brainjar.com for terms of use. +//***************************************************************************** + +var classes = { + cell_of_emptySpace: 'cell_of_empty_space', + cell_of_movingTable: 'cell_of_moving_table', + newTable: 'moving_table', + handle: 'drag_handle', + hoveredCell: 'hovered_column_td', + assemblyName: 'assembly_name', + + bottomCell_of_emptySpace: 'bottom_cell_of_empty_space', + topCell_of_emptySpace: 'top_cell_of_empty_space', + leftToCell_of_emptySpace: 'left_to_cell_of_empty_space', + rightToCell_of_emptySpace: 'right_to_cell_of_empty_space', + + mainReportTable_id: 'main_report_table', + totalReportJson_id: 'total-report-json', +}; + +var dragTable = { + isDragging: false, + + // How far should the mouse move before it's considered a drag, not a click? + dragRadius2: 0, // 100, + setMinDragDistance: function(x) { + DT.dragRadius2 = x * x; + }, + + // How long should cookies persist? (in days) + cookieDays: 365, + setCookieDays: function(x) { + DT.cookieDays = x; + }, + + // Determine browser and version. + // TODO: eliminate browser sniffing except where it's really necessary. + Browser: function() { + var ua, s, i; + + this.isIE = false; + this.isNS = false; + this.version = null; + ua = navigator.userAgent; + + s = "MSIE"; + if ((i = ua.indexOf(s)) >= 0) { + this.isIE = true; + this.version = parseFloat(ua.substr(i + s.length)); + return; + } + + s = "Netscape6/"; + if ((i = ua.indexOf(s)) >= 0) { + this.isNS = true; + this.version = parseFloat(ua.substr(i + s.length)); + return; + } + + // Treat any other "Gecko" browser as NS 6.1. + s = "Gecko"; + if ((i = ua.indexOf(s)) >= 0) { + this.isNS = true; + this.version = 6.1; + return; + } + }, + browser: null, + + // Detect all draggable tables and attach handlers to their headers. + init: function() { + // Don't initialize twice + if (arguments.callee.done) + return; + else + arguments.callee.done = true; + +// if (_dgtimer) +// clearInterval(_dgtimer); + + if (!document.createElement || !document.getElementsByTagName) + return; + + DT.dragObj.zIndex = 0; + DT.browser = new DT.Browser(); + forEach(document.getElementsByTagName('table'), function(table) { + if ($(table).hasClass('draggable')) { + DT.makeDraggable(table); + } + }); + }, + + // The thead business is taken straight from sorttable. + makeDraggable: function(table) { + DT.dragObj.table = table; + + if (table.getElementsByTagName('thead').length == 0) { + thead = document.createElement('thead'); + thead.appendChild(table.rows[0]); + table.insertBefore(thead, table.firstChild); + } + + // Safari doesn't support table.tHead, sigh + if (table.tHead == null) { + table.tHead = table.getElementsByTagName('thead')[0]; + } + + var handles = $('.' + classes.handle) || table.tHead.rows[0].cells; + + forEach(handles, function(handle) { + handle.onmousedown = DT.dragStart; + }); + }, + + // Global object to hold drag information. + dragObj: {}, + + getEventPosition: function(event) { + var x, y; + if (DT.browser.isIE) { + x = window.event.clientX + document.documentElement.scrollLeft + + document.body.scrollLeft; + y = window.event.clientY + document.documentElement.scrollTop + + document.body.scrollTop; + return {x: x, y: y}; + } + return {x: event.pageX, y: event.pageY}; + }, + + // Determine the position of this element on the page. Many thanks to Magnus + // Kristiansen for help making this work with "position: fixed" elements. + getPositionOnThePage: function(elt, stopAtRelative) { + var ex = 0, ey = 0; + do { + var curStyle = DT.browser.isIE ? elt.currentStyle + : window.getComputedStyle(elt, ''); + var supportFixed = !(DT.browser.isIE && + DT.browser.version < 7); + if (stopAtRelative && curStyle.position == 'relative') { + break; + } else if (supportFixed && curStyle.position == 'fixed') { + // Get the fixed el's offset + ex += parseInt(curStyle.left, 10); + ey += parseInt(curStyle.top, 10); + // Compensate for scrolling + ex += document.body.scrollLeft; + ey += document.body.scrollTop; + // End the loop + break; + } else { + ex += elt.offsetLeft; + ey += elt.offsetTop; + } + } while (elt = elt.offsetParent); + return {x: ex, y: ey}; + }, + + // MouseDown handler -- sets up the appropriate mousemove/mouseup handlers + // and fills in the global DT.dragObj object. + dragStart: function(event, id) { + DT.isDragging = true; + + var drag_obj = DT.dragObj; + + var browser = DT.browser; + var clicked_node = browser.isIE ? window.event.srcElement : event.target; + var pos = DT.getEventPosition(event); + + var table = $(clicked_node).closest('table')[0]; + var top_cell = $(clicked_node).closest('td, th')[0]; + drag_obj.topCell = top_cell; + drag_obj.table = table; + + var col_index = top_cell.cellIndex; + drag_obj.movingColIndex = drag_obj.startIndex = col_index; + drag_obj.movingColWidth = $(top_cell).width(); + + // Since a column header can't be dragged directly, duplicate its contents + // in a div and drag that instead. + var new_table = DT.fullCopy(table, false); + + // Copy the entire column + var forEachSection = function(table, func) { + if (table.tHead) { + func(table.tHead); + } + forEach(table.tBodies, function(tbody) { + func(tbody); + }); + if (table.tFoot) { + func(table.tFoot); + } + }; + + forEachSection(table, function(sec) { + var new_sec = DT.fullCopy(sec, false); + + forEach(sec.rows, function(row) { + var cell = row.cells[col_index]; + var new_tr = DT.fullCopy(row, false); + if (row.offsetHeight) new_tr.style.height = row.offsetHeight + "px"; + var new_td = DT.fullCopy(cell, true); + if (cell.offsetWidth) new_td.style.width = cell.offsetWidth + "px !important"; + new_tr.appendChild(new_td); + new_sec.appendChild(new_tr); + }); + + new_table.appendChild(new_sec); + }); + + var obj_pos = DT.getPositionOnThePage(top_cell, true); + new_table.style.position = "absolute"; + new_table.style.left = obj_pos.x + "px"; + new_table.style.top = obj_pos.y + "px"; + // new_table.style.width = dragObj.origNode.offsetWidth + "px"; + // new_table.style.height = dragObj.origNode.offsetHeight + "px"; + + // Hold off adding the element until this is clearly a drag. + drag_obj.addedNode = false; + + drag_obj.tableContainer = drag_obj.table.parentNode || document.body; + drag_obj.newTable = new_table; + + // Save starting positions of cursor and element. + drag_obj.startPos = pos; + drag_obj.prevPos = pos; + drag_obj.elStartLeft = parseInt(drag_obj.newTable.style.left, 10); + drag_obj.elStartTop = parseInt(drag_obj.newTable.style.top, 10); + + if (isNaN(drag_obj.elStartLeft)) drag_obj.elStartLeft = 0; + if (isNaN(drag_obj.elStartTop)) drag_obj.elStartTop = 0; + + // Update element's z-index. + drag_obj.newTable.style.zIndex = ++drag_obj.zIndex; + + // Capture mousemove and mouseup events on the page. + if (browser.isIE) { + document.attachEvent("onmousemove", DT.dragMove); + document.attachEvent("onmouseup", DT.dragEnd); + window.event.cancelBubble = true; + window.event.returnValue = false; + } else { + document.addEventListener("mousemove", DT.dragMove, true); + document.addEventListener("mouseup", DT.dragEnd, true); + event.preventDefault(); + } + }, + + // Move the floating column header with the mouse + // TODO: Reorder columns as the mouse moves for a more interactive feel. + dragMove: function(event) { + var x, y; + var drag_obj = DT.dragObj; + var col_index = drag_obj.movingColIndex; + + // Get cursor position with respect to the page. + var pos = DT.getEventPosition(event); + + var full_dx = drag_obj.startPos.x - pos.x; + var full_dy = drag_obj.startPos.y - pos.y; + + if (!drag_obj.addedNode && full_dx * full_dx + full_dy * full_dy > DT.dragRadius2) { + // Real dragging has began, the following block performs once + + // Attach a moving table + drag_obj.tableContainer.insertBefore(drag_obj.newTable, drag_obj.table); + drag_obj.addedNode = true; + + // Add classes for the dragged column (original and the clone) + $(drag_obj.newTable).addClass(classes.newTable); + $(DT.getColumn(drag_obj.newTable)).addClass(classes.cell_of_movingTable); + + $(DT.getColumn(drag_obj.table, col_index)).addClass(classes.cell_of_emptySpace); + $(DT.getColumn(drag_obj.table, col_index)[0]).addClass(classes.topCell_of_emptySpace); + var visibleCells = $(DT.getColumn(drag_obj.table, col_index)).filter(':visible'); + $(visibleCells[visibleCells.length - 1]).addClass(classes.bottomCell_of_emptySpace); + + DT.addStylesForAdjacentColumns(col_index); + } + + // Move drag element by the same amount the cursor has moved. + var style = drag_obj.newTable.style; + style.left = (drag_obj.elStartLeft + pos.x - drag_obj.startPos.x) + "px"; + style.top = (drag_obj.elStartTop + pos.y - drag_obj.startPos.y) + "px"; + + if (DT.browser.isIE) { + window.event.cancelBubble = true; + window.event.returnValue = false; + } else { + event.preventDefault(); + } + + // If moving over an adjacent column, do swapping, swapping with the adjacent column + var column_pos_x = DT.getPositionOnThePage(DT.getColumn(drag_obj.newTable)[0]).x; + var column_center_x = column_pos_x + drag_obj.movingColWidth / 2; + var hovered_col_index = DT.getColumnAtPosition(drag_obj.table, column_center_x); + + var dx = drag_obj.prevPos.x - pos.x; + + if (DT.isSuitableColumnToSwap(hovered_col_index, col_index)) { + if (dx < 0 && hovered_col_index > col_index || // moving right + dx > 0 && hovered_col_index < col_index) { // moving left + DT.removeStylesForAdjacentColumns(col_index); + DT.moveColumn(drag_obj.table, col_index, hovered_col_index); + DT.addStylesForAdjacentColumns(hovered_col_index); + drag_obj.movingColIndex = hovered_col_index; + } + } + drag_obj.prevPos = pos; + }, + + removeStylesForAdjacentColumns: function(oldIndex) { + var table = DT.dragObj.table; + var rows = table.rows; + var oldColumn = DT.getColumn(table, oldIndex); + $(DT.getColumn(table, oldIndex - 1)).removeClass(classes.leftToCell_of_emptySpace); + $(DT.getColumn(table, oldIndex + 1)).removeClass(classes.rightToCell_of_emptySpace); + }, + + addStylesForAdjacentColumns: function(index) { + var table = DT.dragObj.table; + var rows = table.rows; + var column = DT.getColumn(table, index); + $(DT.getColumn(table, index - 1)).addClass(classes.leftToCell_of_emptySpace); + $(DT.getColumn(table, index + 1)).addClass(classes.rightToCell_of_emptySpace); + }, + + // Stop capturing mousemove and mouseup events. + // Determine which (if any) column we're over and shuffle the table. + dragEnd: function(event) { + if (DT.browser.isIE) { + document.detachEvent("onmousemove", DT.dragMove); + document.detachEvent("onmouseup", DT.dragEnd); + } else { + document.removeEventListener("mousemove", DT.dragMove, true); + document.removeEventListener("mouseup", DT.dragEnd, true); + } + + var drag_obj = DT.dragObj; + var col_index = drag_obj.movingColIndex; + + // If the floating header wasn't added, the mouse didn't move far enough. + if (drag_obj.addedNode) { + // TODO: Move with animation + var final_pos = DT.getPositionOnThePage(DT.getColumn(drag_obj.table, col_index)[0]); + + $(drag_obj.newTable).animate({ + left: final_pos.x, + top: final_pos.y, + }, 'fast', function() { + $(drag_obj.newTable).remove(); + $(DT.getColumn(drag_obj.table, col_index)).removeClass(classes.cell_of_emptySpace); + $(DT.getColumn(drag_obj.table, col_index)[0]).removeClass(classes.topCell_of_emptySpace); + var visibleCells = $(DT.getColumn(drag_obj.table, col_index)).filter(':visible'); + $(visibleCells[visibleCells.length - 1]).removeClass(classes.bottomCell_of_emptySpace); + + DT.removeStylesForAdjacentColumns(col_index); + }); + + DT.storeDrag(drag_obj.table); + } + DT.isDragging = false; + }, + + moveColumn: function(table, index, nextIndex) { + forEach(table.rows, function(row) { + var startCell = $(row.cells[index]); + var finishCell = $(row.cells[nextIndex]); + + // startCell.animate({ + // left: finishCell.offset().left, + // }, 'slow', function() { + if (nextIndex > index) { + startCell.before(finishCell); + } else { + startCell.after(finishCell); + } + // }); + }); + }, + + // clone an element, copying its style and class. + fullCopy: function(elt, deep) { + if (!elt) { + return null; + } + var new_elt = elt.cloneNode(deep); + new_elt.className = elt.className; + $(new_elt).addClass('clone'); + forEach(elt.style, function(value, key, object) { + if (value == null) return; + if (typeof(value) == "string" && value.length == 0) return; + + new_elt.style[key] = elt.style[key]; + }); + return new_elt; + }, + + getColumn: function(table, index) { + index = typeof index !== 'undefined' ? index : 0; + + if (index < 0 || index >= table.rows[0].cells.length) { + return []; + + } else { + var column = []; + forEach(table.rows, function(row) { + column.push(row.cells[index]); + }); + return column; + } + }, + + isSuitableColumnToSwap: function(targetIndex, movingColIndex) { + if (targetIndex != -1) { + if (typeof movingColIndex === 'undefined' || targetIndex != movingColIndex) { // check if equals the moving one + var top_cell = $(DT.getColumn(DT.dragObj.table, targetIndex)[0]); + if (top_cell.find('.' + classes.handle).addBack('.' + classes.handle).exists()) { + return true; + } + } + } + return false; + }, + + // Which column does the x value fall inside of? x should include scrollLeft. + getColumnAtPosition: function(table, x) { + var header = table.tHead.rows[0].cells; + for (var i = 0; i < header.length; i++) { + //var left = header[i].offsetLeft; + var pos = DT.getPositionOnThePage(header[i]); + //if (left <= x && x <= left + header[i].offsetWidth) { + var px = pos.x; + var ow = header[i].offsetWidth; + var xpow = pos.x + header[i].offsetWidth; + if (pos.x <= x && x <= pos.x + header[i].offsetWidth) { + return i; + } + } + return -1; + }, + + // Store a column swap in a cookie for posterity. + storeDrag: function(table) { + var order = []; + forEach(table.rows[0].cells, function(cell) { + var pos = cell.getAttribute('position'); + if (pos) + order.push(pos); + }); + + var order_string = order[0]; + for (var i = 1; i < order.length; i++) + order_string += ' ' + order[i]; + + DT.storeInCookies(order_string); + DT.sendOrderToServer(order_string); + }, + + storeInCookies: function(string) { + if (navigator.cookieEnabled) { + var cookieName = 'order'; + createCookie(cookieName, string, DT.cookieDays); + } + }, + + sendOrderToServer: function(string) { + if (document.reportId) { + $.ajax({ + type: 'GET', + url: '/reorder-report-columns', + dataType: 'json', + data: { + reportId: document.reportId, + order: string, + }, + }); + } + }, +}; + +var DT = dragTable; + +/* ****************************************************************** + Supporting functions: bundled here to avoid depending on a library + ****************************************************************** */ + + +//// Dean Edwards/Matthias Miller/John Resig +//// has a hook for DT.init already been added? 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original jQuery.tipsy by Jason Frame + * =========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* TOOLTIP PUBLIC CLASS DEFINITION + * =============================== */ + + var Tooltip = function (element, options) { + this.init('tooltip', element, options) + }; + + Tooltip.prototype = { + + constructor: Tooltip + + , init: function (type, element, options) { + var eventIn + , eventOut; + + this.type = type; + this.$element = $(element); + this.options = this.getOptions(options); + this.enabled = true; + + if (this.options.trigger != 'manual') { + eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus'; + eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur'; + this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)); + this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)); + } + + this.options.selector ? + (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : + this.fixTitle(); + } + + , getOptions: function (options) { + options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) + + if (options.delay && typeof options.delay == 'number') { + options.delay = { + show: options.delay + , hide: options.delay + }; + } + + return options; + } + + , enter: function (e) { + if (dragTable && dragTable.isDragging) + return; + + var self = $(e.currentTarget)[this.type](this._options).data(this.type); + + if (!self.options.delay || !self.options.delay.show) self.show(); + + clearTimeout(this.timeout); + self.hoverState = 'in'; + this.timeout = setTimeout( + function() { if (self.hoverState == 'in') self.show(); }, + self.options.delay.show + ); + } + + , leave: function (e) { + var self = $(e.currentTarget)[this.type](this._options).data(this.type); + + if (this.timeout) clearTimeout(this.timeout); + if (!self.options.delay || !self.options.delay.hide) self.hide(); + + self.hoverState = 'out'; + this.timeout = setTimeout( + function() { if (self.hoverState == 'out') self.hide() }, + self.options.delay.hide + ); + } + + , show: function () { + var $tip + , inside + , pos + , actualWidth + , actualHeight + , placement + , tp; + + if (this.hasContent() && this.enabled) { + $tip = this.tip(); + this.setContent(); + + if (this.options.animation) { + $tip.addClass('fade'); + } + + placement = typeof this.options.placement == 'function' ? + this.options.placement.call(this, $tip[0], this.$element[0]) : + this.options.placement; + + inside = /in/.test(placement); + + $tip + .remove() + .css({ top: 0, left: 0, display: 'block' }) + .appendTo(inside ? this.$element : document.body); + + pos = this.getPosition(inside); + + actualWidth = $tip[0].offsetWidth; + actualHeight = $tip[0].offsetHeight; + + switch (inside ? placement.split(' ')[1] : placement) { + case 'bottom': + tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2}; + break; + case 'top': // modificated by Vlad Saveliev: +4px to top position + tp = {top: pos.top - actualHeight + 4, left: pos.left + pos.width / 2 - actualWidth / 2}; + break; + case 'left': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth}; + break; + case 'right': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width}; + break; + } + + $tip + .css(tp) + .addClass(placement) + .addClass('in'); + } + } + + , isHTML: function(text) { + // html string detection logic adapted from jQuery + return typeof text != 'string' + || ( text.charAt(0) === "<" + && text.charAt( text.length - 1 ) === ">" + && text.length >= 3 + ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text); + } + + , setContent: function () { + var $tip = this.tip() + , title = this.getTitle(); + + $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title); + $tip.removeClass('fade in top bottom left right'); + } + + , hide: function () { + var that = this + , $tip = this.tip(); + + $tip.removeClass('in'); + + function removeWithAnimation() { + var timeout = setTimeout(function () { + $tip.off($.support.transition.end).remove() + }, 500); + + $tip.one($.support.transition.end, function () { + clearTimeout(timeout); + $tip.remove(); + }) + } + + $.support.transition && this.$tip.hasClass('fade') ? + removeWithAnimation() : + $tip.remove() + } + + , fixTitle: function () { + var $e = this.$element; + if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { + $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title'); + } + } + + , hasContent: function () { + return this.getTitle(); + } + + , getPosition: function (inside) { + return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { + width: this.$element[0].offsetWidth + , height: this.$element[0].offsetHeight + }) + } + + , getTitle: function () { + var title + , $e = this.$element + , o = this.options; + + title = $e.attr('data-original-title') + || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title); + + return title; + } + + , tip: function () { + return this.$tip = this.$tip || $(this.options.template); + } + + , validate: function () { + if (!this.$element[0].parentNode) { + this.hide(); + this.$element = null; + this.options = null; + } + } + + , enable: function () { + this.enabled = true; + } + + , disable: function () { + this.enabled = false; + } + + , toggleEnabled: function () { + this.enabled = !this.enabled; + } + + , toggle: function () { + this[this.tip().hasClass('in') ? 'hide' : 'show'](); + } + + }; + + + /* TOOLTIP PLUGIN DEFINITION + * ========================= */ + + $.fn.tooltip = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('tooltip') + , options = typeof option == 'object' && option; + if (!data) $this.data('tooltip', (data = new Tooltip(this, options))); + if (typeof option == 'string') data[option](); + }) + }; + + $.fn.tooltip.Constructor = Tooltip; + + $.fn.tooltip.defaults = { + animation: true + , placement: 'top' + , selector: false + , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>' + , trigger: 'hover' + , title: '' + , delay: 0 + }; + +}(window.jQuery); + +</script> + +<script type="text/javascript"> +function showPlotWithInfo(info, index) { + var newSeries = []; + var newColors = []; + var oldSeries = info.series; + var usingSeries; + var sortOrder; + if ($("input[name=sortRefs]")[0]) + sortOrder = getSortOrder(); + if (index != undefined) { + oldSeries = info.series[index]; + } + if (sortOrder == 'alphabet') { + usingSeries = []; + sortedRefs = info.references.slice(0).sort(); + for(var i = 0; i < oldSeries.length; i++) { + usingSeries.push($.extend(true, {}, oldSeries[i])); + for(var j = 0; j < info.references.length; j++) { + usingSeries[i].data[j][1] = oldSeries[i].data[info.references.indexOf(sortedRefs[j])][1]; + } + } + } + else usingSeries = oldSeries; + $('#legend-placeholder').find('input[type="checkbox"]:checked').each(function() { + var number = $(this).attr('name'); + if (number && usingSeries && usingSeries.length > 0) { + var i = 0; + do { + var series = usingSeries[i]; + i++; + } while (i <= usingSeries.length && (series == null || series.number != number)); + // + if (i <= usingSeries.length) { + newSeries.push(series); + newColors.push(series.color); + } else { + console.log('no series with number ' + number); + } + } + }); + if (sortOrder) sortReferences(sortOrder, info); + + if (newSeries.length === 0) { + newSeries.push({ + data: [] + }); + newColors.push('#FFF'); + } + + info.showWithData(newSeries, newColors); +} + +function recoverOrderFromCookies() { + if (!navigator.cookieEnabled) + return null; + + var order_string = readCookie("order"); + if (!order_string) + return null; + + var order = []; + var fail = false; + forEach(order_string.split(' '), function(val) { + val = parseInt(val); + if (isNaN(val)) + fail = true; + else + order.push(val); + }); + + if (fail) + return null; + + return order; +} + + +function readJson(what) { + var result; + try { + result = JSON.parse($('#' + what + '-json').html()); + } catch (e) { + result = null; + } + return result; +} + + +function getToggleFunction(assembliesNames, order, name, title, drawPlot, data, refPlotValue, tickX) { + return function() { + this.parentNode.getElementsByClassName('selected-switch')[0].className = 'plot-switch dotted-link'; + this.className = 'plot-switch selected-switch'; + togglePlots(assembliesNames, order, name, title, drawPlot, data, refPlotValue, tickX) + }; +} + +function togglePlots(assembliesNames, order, name, title, drawPlot, data, refPlotValue, tickX) { + var plotPlaceholder = document.getElementById('plot-placeholder'); + var legendPlaceholder = document.getElementById('legend-placeholder'); + var scalePlaceholder = document.getElementById('scale-placeholder'); + + var glossary = JSON.parse($('#glossary-json').html()); + + if (name === 'cumulative') { + $(plotPlaceholder).addClass('cumulative-plot-placeholder'); + } else { + $(plotPlaceholder).removeClass('cumulative-plot-placeholder'); + } + + $('#contigs_are_ordered').hide(); + $('#gc_info').hide(); + $('#gc_contigs_info').hide(); + $('#frc_info').hide(); + + var selectedAssemblies = getSelectedAssemblies(assembliesNames); + var sortBtnClass; + if ($("input[name=sortRefs]")[0]) { + sortBtnClass = getSortRefsRule(); + } + $('#legend-placeholder').empty(); + assembliesNames.forEach(function(filename, i) { + addLabelToLegend(i, filename, selectedAssemblies, colors); + }); + if (refPlotValue) { + $('#legend-placeholder').append( + '<div id="reference-label">' + + '<label for="reference" style="color: #000000;">' + + '<input type="checkbox" name="' + assembliesNames.length + + '" checked="checked" id="reference"> ' + 'reference' + + '</label>' + + '</div>' + ); + } + if (sortBtnClass) { + addSortRefsBtn(sortBtnClass); + } + + drawPlot(name, title, colors, assembliesNames, data, refPlotValue, tickX, + plotPlaceholder, legendPlaceholder, glossary, order, scalePlaceholder); +} + +function makePlot(firstPlot, assembliesNames, order, name, title, drawPlot, data, refPlotValue, tickX) { + var switchSpan = document.createElement('span'); + switchSpan.id = name + '-switch'; + switchSpan.innerHTML = title; + var plotsSwitchesDiv = document.getElementById('plots-switches'); + plotsSwitchesDiv.appendChild(switchSpan); + + if (firstPlot) { + switchSpan.className = 'plot-switch selected-switch'; + togglePlots(assembliesNames, order, name, title, drawPlot, data, refPlotValue, tickX); + } else { + switchSpan.className = 'plot-switch dotted-link'; + } + + $(switchSpan).click(getToggleFunction(assembliesNames, order, name, title, drawPlot, data, refPlotValue, tickX)); +} +</script> + +<script type="text/javascript"> +String.prototype.trunc = + function(n){ + return this.substr(0, n-1) + (this.length > n ? '…' : ''); + }; + + +function getColor (hue, lightness) { + lightness = lightness ? lightness : 92; + var rgb = hslToRgb(hue / 360, 0.8, lightness / 100); + return '#' + rgb[0].toString(16) + rgb[1].toString(16) + rgb[2].toString(16); +} + +function getMedian (x) { + if (x.length == 0) return null; + if (x.length % 2 == 1) return x[(x.length - 1) / 2]; + else return (x[(x.length / 2) - 1] + x[(x.length / 2)]) / 2; +} + +function toggleSecondary(event, caller) { + event = event || window.event; + if(event.target.nodeName == "IMG") return; + if (!caller.hasClass('primary') || caller.hasClass('not_extend')) { + return; + } + var nextRow = caller.next('.content-row'); + $(caller).find('.metric-name').toggleClass('collapsed').toggleClass('expanded'); + + while (!nextRow.hasClass('primary') && (nextRow.length > 0)) { + nextRow.toggleClass('secondary_hidden'); + nextRow.find('.left_column_td').css('background-color', '#E8E8E8'); + nextRow = nextRow.next('.content-row'); + } +} + +function setUpHeatMap(table) { + + (function () { + $(function () { + $('tr.group_empty').removeClass('row_hidden'); + }); + })(); + + $('#main_report').append(table); + var rows = $('#main_report_table').find('.content-row'); + var showHeatmap = false; + for (var rows_n = 0; rows_n < rows.length; rows_n++) { + if ($(rows[rows_n]).find('td[number]').length > 1) { + showHeatmap = true; + break + } + } + + if (showHeatmap) { + var canvas = document.getElementById('gradientHeatmap'); + var context = canvas.getContext('2d'); + context.rect(0, 0, canvas.width, canvas.height); + + var gradient = context.createLinearGradient(0, 0, canvas.width, canvas.height); + gradient.addColorStop(0, getColor(0, 65)); + gradient.addColorStop(0.5, 'white'); + gradient.addColorStop(1, getColor(240, 65)); + canvas.style.border = "0px solid rgba(0, 0, 0, .1)"; + context.fillStyle = gradient; + context.fill(); + $('#heatmaps_chbox').change(function(){ + if($(this).is(':checked')) toggleHeatMap('on'); + else toggleHeatMap('off'); + }); + toggleHeatMap('on'); + $('#heatmap_header').show(); + } +} + +function toggleHeatMap(state){ + var rows = $('#main_report_table').find('.content-row'); + for (var rows_n = 0; rows_n < rows.length; rows_n++) { + var cells = $(rows[rows_n]).find('td[number]'); + if (state == 'on') { + var quality = $(rows[rows_n]).attr('quality'); + heatMapOneRow(cells, quality); + } + else cells.each(function (i) { + $(this).css('background', 'white'); + $(this).css('color', 'black'); + }); + } +} + +function heatMapOneRow (cells, quality) { + if (quality == 'Equal') + return; + var BLUE_HUE = 240; + var BLUE_OUTER_BRT = 55; + var BLUE_INNER_BRT = 65; + + var RED_HUE = 0; + var RED_OUTER_BRT = 50; + var RED_INNER_BRT = 60; + + var MIN_NORMAL_BRT = 80; + var MEDIAN_BRT = 100; + + var numbers = $.map(cells, function (cell) { + return parseFloat($(cell).attr('number')); + }); + + var min = Math.min.apply(null, numbers); + var max = Math.max.apply(null, numbers); + + var topHue = BLUE_HUE; + var lowHue = RED_HUE; + + var innerTopBrt = BLUE_INNER_BRT; + var outerTopBrt = BLUE_OUTER_BRT; + var innerLowBrt = RED_INNER_BRT; + var outerLowBrt = RED_OUTER_BRT; + + if (quality == 'Less is better') { + topHue = RED_HUE; + lowHue = BLUE_HUE; + + innerTopBrt = RED_INNER_BRT; + outerTopBrt = RED_OUTER_BRT; + innerLowBrt = BLUE_INNER_BRT; + outerLowBrt = BLUE_OUTER_BRT; + } + + var twoCols = cells.length == 2; + + if (max == min) { + $(cells).css('color', MEDIAN_BRT); + } else { + var sortedValues = numbers.slice().sort(function(a, b) { + return a - b; + }); + var median = getMedian(sortedValues); + var l = numbers.length; + var q1 = sortedValues[Math.floor((l - 1) / 4)]; + var q3 = sortedValues[Math.floor((l - 1) * 3 / 4)]; + + var d = q3 - q1; + var low_outer_fence = q1 - 3 * d; + var low_inner_fence = q1 - 1.5 * d; + var top_inner_fence = q3 + 1.5 * d; + var top_outer_fence = q3 + 3 * d; + cells.each(function (i) { + var number = numbers[i]; + if (number < low_outer_fence) { + $(this).css('background', getColor(lowHue, twoCols ? null : outerLowBrt)); + if (twoCols != true) $(this).css('color', 'white'); + } + else if (number < low_inner_fence) { + $(this).css('background', getColor(lowHue, twoCols ? null : innerLowBrt)); + } + else if (number < median) { + var k = (MEDIAN_BRT - MIN_NORMAL_BRT) / (median - low_inner_fence); + var brt = Math.round(MEDIAN_BRT - (median - number) * k); + $(this).css('background', getColor(lowHue, twoCols ? null : brt)); + } + else if (number > top_inner_fence) { + $(this).css('background', getColor(topHue, twoCols ? null : innerTopBrt)); + } + else if (number > top_outer_fence) { + $(this).css('background', getColor(topHue, twoCols ? null : outerTopBrt)); + if (twoCols != true) $(this).css('color', 'white'); + } + else if (number > median) { + var k = (MEDIAN_BRT - MIN_NORMAL_BRT) / (top_inner_fence - median); + var brt = Math.round(MEDIAN_BRT - (number - median) * k); + $(this).css('background', getColor(topHue, twoCols ? null : brt)); + } + }); + } +} +function extendedClick() { + $('.row_to_hide').toggleClass('row_hidden'); + + var link = $('#extended_report_link'); + if (link.html() == 'Extended report') { + link.html('Short report'); + } else { + link.html('Extended report'); + } +} + +function buildExtendedLinkClick() { + return '<p id="extended_link"><a class="dotted-link" id="extended_report_link" onclick="extendedClick($(this))">Extended report</a></p>'; +} + +function appendIcarusLinks() { + if (icarusLinks = readJson('icarus')) { + if (icarusLinks.links != undefined) { + var links = ''; + for (var link_n = 0; link_n < icarusLinks.links.length; link_n++) { + //links += '<a href="' + icarusLinks.links[link_n] + '">' + icarusLinks.links_names[link_n] + '</a><br>' + links += '<a class="btn btn-default btn-xs" role="button" href="' + icarusLinks.links[link_n] + '">' + icarusLinks.links_names[link_n] + '</a><br>' + } + $('#icarus').html(links); + } + } +} + +</script> + + + <script type="text/javascript"> + var colors = ["#FF0000","#0000FF"]; + var broken_scaffolds_labels = []; + </script> + <script type="text/javascript"> +function addRow(metric, mainMetrics, rowName, group_n, order, glossary, isExpandable, isPrimary) { + (function(group_n) { + var id_group = '#group_' + group_n; + $(function() { + $(id_group).removeClass('group_empty'); + }); + })(group_n); + + var table = ''; + metricName = metric.metricName; + var quality = metric.quality; + var values = metric.values; + + var trClass = 'content-row'; + if (metric.isMain || $.inArray(metricName, mainMetrics) > -1) { + (function(group_n) { + var id_group = '#group_' + group_n; + $(function() { + $(id_group).removeClass('row_hidden'); + $(id_group).removeClass('row_to_hide'); + }); + })(group_n); + } else { + trClass = 'content-row row_hidden row_to_hide'; + } + var tdClass = ''; + if (!isPrimary) { + trClass += ' secondary_hidden'; + tdClass = 'secondary_td'; + } + else { + trClass += ' primary'; + } + if (isExpandable) { + table += + '<tr class="' + trClass + '" quality="' + quality + '" onclick="toggleSecondary(event, $(this))">' + + '<td class="left_column_td ' + tdClass + '">' + + '<span class="metric-name expandable collapsed">' + + initial_spaces_to_nbsp(addTooltipIfDefinitionExists(glossary, rowName.trunc(55)), metricName) + + '</span></td>'; + } + else { + table += + '<tr class="' + trClass + '" quality="' + quality + '">' + + '<td class="left_column_td"><span class="metric-name">' + + initial_spaces_to_nbsp(addTooltipIfDefinitionExists(glossary, rowName.trunc(55)), metricName) + + '</span>' + + '</td>'; + } + for (var val_n = 0; val_n < values.length; val_n++) { + value = values[order[val_n]]; + + if (value === null || value === '') { + table += '<td><span>-</span></td>'; + } else { + if (typeof value === 'number') { + table += + '<td number="' + value + '"><span>' + + toPrettyString(value) + '</span></td>'; + } else { + var result = /([0-9\.]+)(.*)/.exec(value); + var num = parseFloat(result[1]); + var rest = result[2]; + // alert('value = ' + value + ' result = ' + result); + + // var num = parseFloat(value); + + if (num !== null) { + table += '<td number="' + num + '"><span>' + toPrettyString(num) + rest + '</span></td>'; + } else { + table += '<td><span>' + value + '</span></td>'; + } + } + } + } + return table; +} + +function getSubRows(subReports, groupName, metricName) { + rows = []; + if (subReports) { + for (var report_n = 0; report_n < subReports.length; report_n++) { + subReport = subReports[report_n]; + for (var group_n = 0; group_n < subReport.length; group_n++) { + if (subReport[group_n][0] != groupName) + continue; + metrics = subReport[group_n][1]; + for (var metric_n = 0; metric_n < metrics.length; metric_n++) { + if (metrics[metric_n].metricName == metricName) + rows.push(metrics[metric_n]) + } + } + } + } + return rows; +} + +function buildTotalReport(assembliesNames, totalReport, order, glossary, qualities, mainMetrics) { + var report = totalReport.report, + date = totalReport.date, + minContig = totalReport.minContig, + referenceName = totalReport.referenceName, + subReports = totalReport.subreports, + subReferences = totalReport.subreferences; + $('#report_date').html('<p>' + date + '</p>'); + var extraInfo = '<p>All statistics are based on contigs of size >= ' + minContig + + '<span class="rhs"> </span>bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).</p>'; + $('#extrainfo').html(extraInfo); + $('#plot-caption').show(); + + var table = ''; + table += '<table cellspacing="0" class="report_table draggable" id="main_report_table">'; + + if (referenceName) { + $('#reference_name').show().find('.val').html(referenceName); + } + + if (report[0][0] == 'Genome statistics') { // if first section is empty (no reference), swap it and w/o reference statistics + var genomeMetrics = report[0][1]; + var isSectionEmpty = true; + for (var index = 0; index < genomeMetrics.length; index++) { + if (genomeMetrics[index].isMain || $.inArray(genomeMetrics[index].metric_name, mainMetrics) > -1) + isSectionEmpty = false; + } + if (isSectionEmpty) { + for (var group_n = 0; group_n < report.length; group_n++) { + if (report[group_n][0] == 'Statistics without reference') { + report[0] = report.splice(group_n, 1, report[0])[0]; + } + } + } + } + + for (var group_n = 0; group_n < report.length; group_n++) { + var group = report[group_n]; + var groupName = group[0]; + var metrics = group[1]; + var width = assembliesNames.length + 1; + + if (groupName == 'Reference statistics') { + var referenceValues = {}; + for (var metric_n = 0; metric_n < metrics.length; metric_n++) { + var metric = metrics[metric_n]; + var metricName = metric.metricName; + var value = metric.values[0]; + referenceValues[metricName] = value; + } + var refLen = referenceValues['Reference length']; + var refFragments = referenceValues['Reference fragments']; + var refGC = referenceValues['Reference GC (%)']; + var refGenes = referenceValues['Reference genes']; + var refOperons = referenceValues['Reference operons']; + var refChr = referenceValues['Reference chromosomes']; + var totalReads = referenceValues['# total reads']; + var refMappedReads = referenceValues['Reference mapped (%)']; + var refPairedReads = referenceValues['Reference properly paired (%)']; + var estRefLen = referenceValues['Estimated reference length']; + + if (refLen) + $('#reference_length').show().find('.val').html(toPrettyString(refLen)); + else if (estRefLen) + $('#est_reference_length').show().find('.val').html(toPrettyString(estRefLen)); + if (refFragments) { + $('#reference_fragments').show().find('.val').html(refFragments); + if (refFragments > 1) + $('#reference_fragments').find('.plural_ending').show(); + } + if (refGC) + $('#reference_gc').show().find('.val').html(toPrettyString(refGC)); + if (refGenes) + $('#reference_genes').show().find('.val').html(toPrettyString(refGenes)); + if (refOperons) + $('#reference_operons').show().find('.val').html(toPrettyString(refOperons)); + if (refChr) { + $('#reference_chr').show().find('.val').html(refChr); + if (refChr > 1) + $('#reference_chr').find('.plural_ending').show(); + } + if (totalReads) + $('#total_reads').show().find('.val').html(toPrettyString(totalReads)); + if (refMappedReads !== undefined) + $('#reference_mapped_reads').show().find('.val').html(toPrettyString(refMappedReads)); + if (refPairedReads !== undefined) + $('#reference_paired_reads').show().find('.val').html(toPrettyString(refPairedReads)); + continue; + } + + if (group_n == 0) { + table += '<tr class="top_row_tr"><td id="top_left_td" class="left_column_td"><span>' + groupName + '</span></td>'; + + for (var assembly_n = 0; assembly_n < assembliesNames.length; assembly_n++) { + var assemblyName = assembliesNames[order[assembly_n]]; + if (assemblyName.length > 30) { + assemblyName = + '<span class="tooltip-link" rel="tooltip" title="' + assemblyName + '">' + + assemblyName.trunc(30) + + '</span>' + } + + table += '<td class="second_through_last_col_headers_td" position="' + order[assembly_n] + '">' + + '<span class="drag_handle"><span class="drag_image"></span></span>' + + '<span class="assembly_name">' + assemblyName + '</span>' + + '</td>'; + } + + } else { + table += + '<tr class="group_header row_to_hide row_hidden group_empty" id="group_' + group_n + '">' + + '<td class="left_column_td"><span>' + groupName + '</span></td>'; //colspan="' + width + '" + for (var i = 1; i < width; i++) { + table += '<td></td>'; + } + table += '</tr>'; + } + + for (metric_n = 0; metric_n < metrics.length; metric_n++) { + isExpandable = false; + isPrimary = true; + metricName = metrics[metric_n].metricName; + subRows = getSubRows(subReports, groupName, metricName); + if (subRows && subRows.length > 0) { + isExpandable = true; + table += addRow(metrics[metric_n], mainMetrics, metricName, group_n, order, glossary, isExpandable, isPrimary); + for (var rows_n = 0; rows_n < subRows.length; rows_n++) { + isExpandable = false; + isPrimary = false; + table += addRow(subRows[rows_n], mainMetrics, subReferences[rows_n], group_n, order, glossary, isExpandable, isPrimary); + } + } + else table += addRow(metrics[metric_n], mainMetrics, metricName, group_n, order, glossary, isExpandable, isPrimary); + } + table += '</tr>'; + } + table += '</table>'; + + table += buildExtendedLinkClick(); + + setUpHeatMap(table); +} + +</script> + + + <script type="text/javascript"> + +function buildReport() { + var assembliesNames; + var order; + + var totalReport = null; + var qualities = null; + var mainMetrics = null; + var contigsLens = null; + var coordNx = null; + var contigsLensNx = null; + var alignedContigsLens = null; + var refLengths = null; + var contigs = null; + var genesInContigs = null; + var operonsInContigs = null; + var gcInfos = null; + + var glossary = JSON.parse($('#glossary-json').html()); + + var plotsSwitchesDiv = document.getElementById('plots-switches'); + var toRemoveRefLabel = true; + var firstPlot = true; + + /****************/ + /* Total report */ + + if (!(totalReport = readJson('total-report'))) { + console.log("Error: cannot read #total-report-json"); + return 1; + } + + assembliesNames = totalReport.assembliesNames; + + order = recoverOrderFromCookies() || totalReport.order || Range(0, assembliesNames.length); + + buildTotalReport(assembliesNames, totalReport, order, glossary, qualities, mainMetrics); + + if (refLengths = readJson('reference-length')) + refLengths = refLengths.reflen; + + /****************/ + /* Plots */ + + while (assembliesNames.length > colors.length) { // colors is defined in utils.js + colors = colors.concat(colors); + } + + $(plotsSwitchesDiv).html('<b>Plots:</b>'); + + var selectedAssemblies = Array.apply(null, {length: assembliesNames}).map(Number.call, Number); + assembliesNames.forEach(function(filename, i) { + addLabelToLegend(i, filename, selectedAssemblies, colors) + }); + + var tickX = 1; + if (tickX = readJson('tick-x')) + tickX = tickX.tickX; + + if (contigsLens = readJson('contigs-lengths')) { + makePlot(firstPlot, assembliesNames, order, 'cumulative', 'Cumulative length', cumulative.draw, contigsLens.lists_of_lengths, refLengths, tickX); + firstPlot = false; + } + + if (coordNx = readJson('coord-nx')) { + makePlot(firstPlot, assembliesNames, order, 'nx', 'Nx', nx.draw, { + coord_x: coordNx.coord_x, + coord_y: coordNx.coord_y, + filenames: coordNx.filenames + }, + null, null + ); + firstPlot = false; + } + + if (coordNx = readJson('coord-nax')) { + makePlot(firstPlot, assembliesNames, order, 'nax', 'NAx', nx.draw, { + coord_x: coordNx.coord_x, + coord_y: coordNx.coord_y, + filenames: coordNx.filenames + }, + null, null + ); + firstPlot = false; + } + + if (coordNx = readJson('coord-ngx')) { + makePlot(firstPlot, assembliesNames, order, 'ngx', 'NGx', nx.draw, { + coord_x: coordNx.coord_x, + coord_y: coordNx.coord_y, + filenames: coordNx.filenames + }, + null, null + ); + firstPlot = false; + } + + if (coordNx = readJson('coord-ngax')) { + makePlot(firstPlot, assembliesNames, order, 'ngax', 'NGAx', nx.draw, { + coord_x: coordNx.coord_x, + coord_y: coordNx.coord_y, + filenames: coordNx.filenames + }, + null, null + ); + firstPlot = false; + } + + if (coordMisassemblies = readJson('coord-misassemblies')) { + makePlot(firstPlot, assembliesNames, order, 'misassemblies', 'Misassemblies', frc.draw, { + coord_x: coordMisassemblies.coord_x, + coord_y: coordMisassemblies.coord_y, + filenames: coordMisassemblies.filenames + }, + null, 1 + ); + firstPlot = false; + } + + genesInContigs = readJson('genes-in-contigs'); + operonsInContigs = readJson('operons-in-contigs'); +// if (genesInContigs || operonsInContigs) +// contigs = readJson('contigs'); + + if (genesInContigs) { + makePlot(firstPlot, assembliesNames, order, 'genes', 'Genes', gns.draw, { + filesFeatureInContigs: genesInContigs.genes_in_contigs, + kind: 'gene', + filenames: genesInContigs.filenames + }, + genesInContigs.ref_genes_number, tickX + ); + firstPlot = false; + } + if (operonsInContigs) { + makePlot(firstPlot, assembliesNames, order, 'operons', 'Operons', gns.draw, { + filesFeatureInContigs: operonsInContigs.operons_in_contigs, + kind: 'operon', + filenames: operonsInContigs.filenames + }, + operonsInContigs.ref_operons_number, tickX + ); + firstPlot = false; + } + gcInfos = readJson('gc'); + if (gcInfos && (gcInfos.lists_of_gc_info || gcInfos.list_of_GC_distributions)) { + makePlot(firstPlot, assembliesNames, order, 'gc', 'GC content', gc.draw, gcInfos, gcInfos.reference_index); + } + + var noReference = true; + var report = totalReport.report; + for (var group_n = 0; group_n < report.length; group_n++) { + var group = report[group_n]; + var groupName = group[0]; + if (groupName == 'Reference statistics' && group[1].length > 0) { + noReference = false; + } + } + if (noReference) extendAll(); + appendIcarusLinks(); + return 0; +} + +function extendAll() { + $('.row_to_hide').toggleClass('row_hidden'); + + var link = $('#extended_report_link'); + link.hide(); +} +</script> + + + <script type="text/javascript"> + $(function() { + + buildReport(); + + dragTable.init(); + + $("[rel=tooltip]").tooltip({ animation: false, }); + }); + </script> +</head> + +<body> +<div class="top-panel"> + <table class="layout-table"> + <tr> + <td class='layout-table-td'> + <div class="page_title"> + <h1> + QUAST + </h1> + <p class="page_subtitle"> + <b>Quality Assessment Tool for Genome Assemblies</b> + by <a href="http://cab.spbu.ru" class='dark_bg_link'>CAB</a> + </p> + </div> + </td> + </tr> + </table> +</div> +<div class="content"> + <div id='header'> + <p id='report_date'></p> + + <p id='icarus'></p> + <p id='extrainfo'>Loading...</p> + <p id='per_ref_msg'></p> + <p id='krona'></p> + + <p id="data_set_p"> + <span style="display: none;" id="reference_name">Aligned to + "<span class='val'></span>" + </span> + + <span style="display: none;" id="combined_reference_name"> + Combined reference + </span> + + <span style="display: none;" id="est_reference_length">Estimated reference size: + <span class='val'></span><span class='rhs'> </span>bp + </span> + + <span style="display: none;" id="reference_length">| + <span class='val'></span><span class='rhs'> </span>bp + </span> + + <span style="display: none;" id="combined_reference_files">| + <span class='val'></span><span class='rhs'> </span>reference<span style="display: none;" class='plural_ending'>s</span> + </span> + + <span style="display: none;" id="reference_fragments">| + <span class='val'></span><span class='rhs'> </span>fragment<span style="display: none;" class='plural_ending'>s</span> + </span> + + <span style="display: none;" id="reference_gc">| + <span class='val'></span><span class='rhs'> </span>% G+C + </span> + + <span style="display: none;" id="reference_chr">| + <span class='val'></span> chromosome<span style="display: none;" class='plural_ending'>s</span> + </span> + + <span style="display: none;" id="total_reads"><br> + <span class='val'></span> reads + </span> + + <span style="display: none;" id="reference_mapped_reads">| + <span class='val'></span>% mapped + </span> + + <span style="display: none;" id="reference_paired_reads">| + <span class='val'></span>% properly paired + </span> + + <span style="display: none;" id="reference_genes"><br> + <span class='val'></span> genes + </span> + + <span style="display: none;" id="reference_operons">| + <span class='val'></span> operons + </span> + </p> + </div> + + <noscript> + <div style="margin-left: 0;"> + Unfortunately, <span style="font-weight: bold">JavaScript</span> in your + browser <span style="font-weight: bold">is disabled</span> or is not supported.</br> + We need JavaScript to build report and plots. + </div> + </noscript> + + <div class='report-and-plots'> + <div class='report' id='main_report'> + <div id="heatmap_header" style='display: none; float: left;'> + <div style="padding-right: 10px; display: inline-block; vertical-align:top;"> + <canvas id="gradientHeatmap" width="150" height="6"></canvas> + <div style="margin-left: 0; text-align: justify;"> + <span class="heatmap_legend">Worst</span> + <span style="margin-left: -5px;" class="heatmap_legend">Median</span> + <span class="heatmap_legend">Best</span> + <span class="heatmap_legend" style='width: 100%; height: 0;'></span> + </div> + </div> + <label for="heatmaps_chbox"><input type="checkbox" checked="checked" id="heatmaps_chbox">Show heatmap</label> + </div> + <div style="clear: both;"></div> + </div> + <div class='plots'> + <table style='margin: -3px;'> + <tr id='all-switches'> + <td> + <div id='plots-switches'></div> + </td> + <td style='text-align: right; padding-right: 22px;'> + <span id='scale-placeholder'></span> + </td> + </tr> + <tr> + <td colspan="2"> + <div id='plot-placeholder' style=''></div> + </td> + <td> + <div id='legend-placeholder'></div> + </td> + </tr> + <tr> + <td colspan="3" id="plot-caption" style="display: none;"> + <p id="contigs_are_ordered">Contigs are ordered from largest (contig #1) to smallest.</p> + <p id="frc_info">FRCurve: + Y is the total number of aligned bases divided by the reference length, + in the contigs having the total number of <span class="frc_plot_name"></span> at most X.</p> + <p id="gc_info">Contigs are broken into nonoverlapping 100 bp windows. + Plot shows number of windows for each GC percentage.</p> + <p id="gc_contigs_info">Plot shows number of contigs with GC percentage in a certain range.</p> + </td> + </tr> + </table> + </div> + + <p> + <span id="main_ref_genome"></span> + </p> + + <div style="clear: left"></div> + <div style="clear: right"></div> + + <div class='json-code'> + <div id='total-report-json'> + {"date":"03 December 2018, Monday, 23:14:03","assembliesNames":["contigs2_fna","contigs1_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[1,3],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[1,3],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[1,3],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[6650,3980],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6650,6710],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6650,6710],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6650,6710],"isMain":true},{"metricName":"N50","quality":"More is better","values":[6650,3980],"isMain":false},{"metricName":"N75","quality":"More is better","values":[6650,1610],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[1,2],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["52.00","51.28"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500} + </div> + <div id='qualities-json'> + {{ qualities }} + </div> + <div id='main-metrics-json'> + {{ mainMetrics }} + </div> + + <div id="contigs-lengths-json"> + {"filenames":["contigs2_fna","contigs1_fna"],"lists_of_lengths":[[6650],[3980,1610,1120]]} + </div> + <div id='assemblies-lengths-json'> + {{ assembliesLengths }} + </div> + <div id='reference-length-json'> + {{ referenceLength }} + </div> + <div id='tick-x-json'> + {"tickX":1} + </div> + <div id='coord-nx-json'> + {"coord_x":[[0.0,1e-10,100.0,100.0000000001],[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001]],"coord_y":[[6650,6650,6650,0.0],[3980,3980,3980,1610,1610,1120,1120,0.0]],"filenames":["contigs2_fna","contigs1_fna"]} + </div> + <div id='coord-ngx-json'> + {{ coordNGx }} + </div> + <div id='coord-nax-json'> + {{ coordNAx }} + </div> + <div id='coord-ngax-json'> + {{ coordNGAx }} + </div> + <div id='coord-misassemblies-json'> + {{ coordmisassemblies }} + </div> + <div id='genes-in-contigs-json'> + {{ genesInContigs }} + </div> + <div id='operons-in-contigs-json'> + {{ operonsInContigs }} + </div> + <div id='summary-json'> + [{{ num_contigs }}, + {{ Largest_alignment }}, + {{ Total_aligned_length }}, + {{ num_misassemblies }}, + {{ Misassembled_contigs_length }}, + {{ num_mismatches_per_100_kbp }}, + {{ num_indels_per_100_kbp }}, + {{ num_N's_per_100_kbp }}, + {{ Genome_fraction }}, + {{ Duplication_ratio }}, + {{ NGA50 }}] + </div> + <div id='misassemblies-json'> + {{ allMisassemblies }} + </div> + <div id='krona-json'> + {{ krona }} + </div> + <div id='gc-json'> + {"filenames":["contigs2_fna","contigs1_fna"],"reference_index":null,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,3,2,1,0,0,5,3,4,4,7,3,5,2,4,7,0,10,1,1,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,3,1,0,1,2,1,5,5,5,2,5,4,4,7,1,6,2,5,1,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null} + </div> + <div id='icarus-json'> + {"links":["icarus_viewers/contig_size_viewer.html"],"links_names":["View in Icarus contig browser"]} + </div> + </div> + </div> + + <div class='json-code'> + <div id='glossary-json'> + { + "# contigs" : "<span>is the total number of contigs in the assembly.</span>", + "Largest contig" : "<span>is the length of the longest contig in the assembly.</span>", + "Total length" : "<span>is the total number of bases in the assembly.</span>", + "Reference length" : "<span>is the total number of bases in the reference.</span>", + + "# contigs (>= 0 bp)" : "<span>is the total number of contigs in the assembly that have size greater than or equal to 0 bp.</span>", + "Total length (>= 0 bp)" : "<span>is the total number of bases in the contigs having size greater than or equal to 0 bp.</span>", + + "N50" : "<span>is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly. Usually there is no value that produces exactly 50%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 50% of the total assembly length.</span>", + "NG50" : "<span>is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>", + "N75" : "<span>is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly. Usually there is no value that produces exactly 75%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 75% of the total assembly length.</span>", + "NG75" : "<span>is the contig length such that using longer or equal length contigs produces 75% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>", + + "L50" : "<span>is the minimum number of contigs that produce half (50%) of the bases of the assembly. In other words, it's the number of contigs of length at least N50.</span>", + "LG50" : "<span>is the minimum number of contigs that produce half (50%) of the bases of the reference genome. In other words, it's the number of contigs of length at least NG50. This metric is computed only if a reference genome is provided.</span>", + "L75" : "<span>is the minimum number of contigs that produce 75% of the bases of the assembly. In other words, it's the number of contigs of length at least N75.</span>", + "LG75" : "<span>is the minimum number of contigs that produce 75% of the bases of the reference genome. In other words, it's the number of contigs of length at least NG75. This metric is computed only if a reference genome is provided.</span>", + + "NA50" : "<span>is N50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.</span>", + "NGA50" : "<span>is NG50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.</span>", + "NA75" : "<span>is N75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.</span>", + "NGA75" : "<span>is NG75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.</span>", + + "LA50" : "<span>is L50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.</span>", + "LGA50" : "<span>is LG50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.</span>", + "LA75" : "<span>is L75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.</span>", + "LGA75" : "<span>is LG75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.</span>", + + "Average %IDY" : "<span>is the average of alignment identity percent (Nucmer measure of alignment accuracy) among all contigs.</span>", + "# misassemblies" : "<span>is the number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (<i>relocation</i>) or they overlap on more than 1 kbp (<i>relocation</i>) or flanking sequences align on different strands (<i>inversion</i>) or different chromosomes (<i>translocation</i>).</span>", + "# large block misassemblies" : "<span>is the number of misassemblies between alignments with length greater than or equal to 3 kbp and with the misassembly threshold equal to 5 kbp (instead of default 1 kbp for regular misassemblies).</span>", + "# misassembled contigs" : "<span>is the number of contigs that contain misassembly events.</span>", + "Misassembled contigs length" : "<span>is the number of total bases contained in all contigs that have one or more misassemblies.</span>", + + "# relocations" : "<span>is the number of relocation events among all misassembly events. Relocation is a misassembly where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference, or they overlap by more than 1 kbp and both flanking sequences align on the same chromosome.</span>", + "# translocations" : "<span>is the number of translocation events among all misassembly events. Translocation is a misassembly where the flanking sequences align on different chromosomes.</span>", + "# interspecies translocations" : "<span>is the number of interspecies translocation events among all misassembly events. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).</span>", + "# inversions" : "<span>is the number of inversion events among all misassembly events. Inversion is a misassembly where it is not a <i>relocation</i> and the flanking sequences align on opposite strands of the same chromosome.</span>", + "# large relocations" : "<span>is the number of relocation events among all large block misassemblies. Relocation is a misassembly where the left flanking sequence aligns over 5 kbp away from the right flanking sequence on the reference, or they overlap by more than 5 kbp and both flanking sequences align on the same chromosome.</span>", + "# large translocations" : "<span>is the number of translocation events among all large block misassemblies. Translocation is a misassembly where the flanking sequences align on different chromosomes.</span>", + "# large i/s translocations" : "<span>is the number of interspecies translocation events among all large block misassemblies. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).</span>", + "# large inversions" : "<span>is the number of inversion events among all large block misassemblies. Inversion is a misassembly where it is not a <i>relocation</i> and the flanking sequences align on opposite strands of the same chromosome.</span>", + "# local misassemblies" : "<span>is the number of local misassemblies. We define a local misassembly breakpoint as a breakpoint that satisfies these conditions: <ol> <li>Two or more distinct alignments cover the breakpoint.</li> <li>The gap between left and right flanking sequences is less than the misassembly threshold (1 kbp by default).</li> <li>The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.</li> </ol> </span>", + "# scaffold gap ext. mis." : "<span>is the number of scaffold gap size extensive misassemblies. We define a scaffold gap size misassembly as a breakpoint where the flanking sequences are combined in a scaffold on the wrong distance. These misassemblies are not included in the total number of misassemblies. </span>", + "# scaffold gap loc. mis." : "<span>is the number of scaffold gap size local misassemblies. Such breakpoints satisfy the local misassembly conditions but they occur inside scaffolds. These misassemblies are not included in the total number of local misassemblies. </span>", + "# possibly misassembled contigs": "<span>is the number of contigs that contain large unaligned fragment (default min length is 500 bp) and thus could possibly contain interspecies translocation with unknown reference.</span>", + "# possible misassemblies" : "<span>is the number of putative interspecies translocations in possibly misassembled contigs if each large unaligned fragment is supposed to be a fragment of unknown reference.</span>", + "# intergenomic misassemblies" : "<span>is the number of all found and putative (possible) interspecies translocations.</span>", + "# structural variations" : "<span>is the number of misassemblies matched with structural variations.</span>", + "# possible TEs" : "<span>is the number of misassemblies possibly caused by transposable elements (TEs). We define a possible TE as an event that satisfies these conditions: <ol> <li>There are two misassembly breakpoints of the same type around a short alignment (less than 7 kbp by default)</li> <li>The gap between two long flanking sequences on the sides of the short alignment is less than 7 kbp.</li> <li> The long flanking sequences both are on the same strand of the same chromosome of the reference genome.</li> </ol> </span>", + "# unaligned mis. contigs" : "<span>is the number of contigs that have the number of unaligned bases more than 50% of contig length and a misassembly event in their aligned fragment. Note that such misassemblies are not counted in <i># misassemblies</i> and other <i>misassemblies</i> statistics.</span>", + + "# fully unaligned contigs" : "<span>is the number of contigs that have no alignment to the reference sequence.</span>", + "Fully unaligned length" : "<span>is the total number of bases contained in all fully unaligned contigs. Uncalled bases (N's) are not counted.</span>", + "# partially unaligned contigs" : "<span>is the number of contigs that have at least one alignment to the reference sequence but also have at least one unaligned fragment of length ≥ <i>unaligned-part-size threshold</i>.</span>", + "Partially unaligned length" : "<span>is the total number of unaligned bases in all partially unaligned contigs. Uncalled bases (N's) are not counted.</span>", + + "# ambiguous contigs" : "<span>is the number of contigs that have reference alignments of equal quality in multiple locations on the reference.</span>", + "Ambiguous contigs length" : "<span>is the total number of bases contained in all ambiguous contigs.</span>", + + "Genome fraction (%)" : "<span>is the total number of aligned bases in the reference, divided by the genome size. A base in the reference genome is counted as aligned if there is at least one contig with at least one alignment to this base. Contigs from repeat regions may map to multiple places, and thus may be counted multiple times in this quantity.</span>", + "GC (%)" : "<span>is the total number of G and C nucleotides in the assembly, divided by the total length of the assembly.</span>", + "Reference GC (%)" : "<span>is the total number of G and C nucleotides in the reference, divided by the total length of the reference.</span>", + + "# mismatches per 100 kbp" : "<span>is the average number of mismatches per 100000 aligned bases.</span>", + "# mismatches" : "<span>is the number of mismatches in all aligned bases.</span>", + "# indels per 100 kbp" : "<span>is the average number of indels per 100000 aligned bases.</span>", + "# indels" : "<span>is the number of indels in all aligned bases</span>", + "# indels (<= 5 bp)" : "<span>is the number of indels of length less than or equal to 5 bp</span>", + "# indels (> 5 bp)" : "<span>is the number of indels of length greater than 5 bp</span>", + "Indels length" : "<span>is the number of total bases contained in all indels</span>", + + "# genomic features" : "<span>is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as 'partially covered' if the assembly contains at least 100 bp of this feature but not the whole feature.</span>", + "# operons" : "<span>is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as 'partially covered' if the assembly contains at least 100 bp of this operon but not the whole operon.</span>", + "# predicted genes (unique)" : "<span>is the number of unique genes in the assembly found by a gene prediction tool.</span>", + "# predicted genes (>= 0 bp)" : "<span>is the number of found genes having length greater than or equal to 0 bp.</span>", + + "Cumulative length" : "<span>plot shows the growth of assembly contig lengths. On the x-axis, contigs are ordered from largest (contig #1) to smallest. The y-axis gives the size of the x largest contigs in the assembly.</span>", + "Nx" : "<span>plot shows the Nx metric value as x varies from 0 to 100.</span> <span>Nx is the minimum contig length <b>y</b> such that using contigs of length at least <b>y</b> accounts for at least x% of the total assembly length.</span>", + "NGx" : "<span>plot shows the NGx metric value as x varies from 0 to 100.</span> <span>NGx is the minimum contig length <b>y</b> such that using contigs of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>", + "NAx" : "<span>plot shows the NAx metric value as x varies from 0 to 100.</span> <span>NAx is computed similarly to Nx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken into aligned blocks at misassembly breakpoints. NAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the assembly. This metric is computed only if a reference genome is provided.</span>", + "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>", + "GC content" : "<span>plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.</span>", + + "Duplication ratio" : "<span>is the total number of aligned bases in the assembly (i.e. <i>Total length</i> - <i>Fully unaligned length</i> - <i>Partially unaligned length</i>), divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>", + "Largest alignment" : "<span>is the length of the largest continuous alignment in the assembly. This metric is always equal to the <i>Largest contig</i> metric but it can be smaller if the largest contig of the assembly contains a misassembly event.</span>", + "Total aligned length" : "<span>is the total number of aligned bases in the assembly.</span>", + "Avg contig read support" : "<span>is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).</span>", + + "# N's" : "<span>is the total number of uncalled bases (N's) in the assembly.</span>", + "# N's per 100 kbp" : "<span>is the average number of uncalled bases (N's) per 100000 assembly bases.</span>", + + "# mapped" : "<span>is the number of reads that mapped to the assembly.</span>", + "Mapped (%)" : "<span>is the percent of reads that mapped to the assembly.</span>", + "# properly paired" : "<span>is the number of reads that mapped within expected range and orientation of each other to the assembly.</span>", + "Properly paired (%)" : "<span>is the percent of reads that mapped within expected range and orientation of each other to the assembly.</span>", + "# singletons" : "<span>is the number of reads which do not overlap any other reads.</span>", + "Singletons (%)" : "<span>is the percent of reads which do not overlap any other reads.</span>", + "# misjoint mates" : "<span>is the number of reads with mate mapped to a different contig.</span>", + "Misjoint mates (%)" : "<span>is the percent of reads with mate mapped to a different contig.</span>", + "Avg. coverage depth" : "<span>is the average depth of coverage.</span>", + "Coverage >= 1x (%)" : "<span>is the total number of bases with at least 1x coverage, divided by the total length of the assembly.</span>", + + "# similar correct contigs" : "<span>is the number of correct contigs similar among > 50% assemblies (see Icarus for visualization).</span>", + "# similar misassembled blocks" : "<span>is the number of misassembled blocks similar among > 50% assemblies (see Icarus for visualization).</span>" +} + + </div> + </div> +</div> +</body> +</html>