# HG changeset patch
# User qfab
# Date 1401855138 14400
# Node ID edf75201278569b59cd8c8c4bd67ac6168f45e91
# Parent  6a7d52777409fd310d6591c6dcaccef6e3f30664
Uploaded

diff -r 6a7d52777409 -r edf752012785 metagenomics_datatypes/datatypes_conf.xml
--- a/metagenomics_datatypes/datatypes_conf.xml	Tue Jun 03 23:25:25 2014 -0400
+++ b/metagenomics_datatypes/datatypes_conf.xml	Wed Jun 04 00:12:18 2014 -0400
@@ -12,9 +12,6 @@
         <datatype extension="shared" type="galaxy.datatypes.metagenomics:SharedRabund" display_in_upload="true"/>
         <datatype extension="relabund" type="galaxy.datatypes.metagenomics:RelAbund" display_in_upload="true"/>
         <datatype extension="accnos" type="galaxy.datatypes.metagenomics:AccNos" display_in_upload="true"/>
-        <datatype extension="tre" type="galaxy.datatypes.data:Newick" display_in_upload="true"/>
-        <datatype extension="nhx" type="galaxy.datatypes.metagenomics:Nhx" display_in_upload="true"/>
-        <datatype extension="nex" type="galaxy.datatypes.metagenomics:Nexus" display_in_upload="true"/>
     </registration>
     <sniffers>
         <sniffer type="galaxy.datatypes.metagenomics:Rabund"/>
@@ -23,7 +20,5 @@
         <sniffer type="galaxy.datatypes.metagenomics:GroupAbund"/>
         <sniffer type="galaxy.datatypes.metagenomics:SharedRabund"/>
         <sniffer type="galaxy.datatypes.metagenomics:RelAbund"/>
-        <sniffer type="galaxy.datatypes.metagenomics:Newick"/>
-        <sniffer type="galaxy.datatypes.metagenomics:Nexus"/>
     </sniffers>
 </datatypes>
diff -r 6a7d52777409 -r edf752012785 metagenomics_datatypes/metagenomics.py
--- a/metagenomics_datatypes/metagenomics.py	Tue Jun 03 23:25:25 2014 -0400
+++ b/metagenomics_datatypes/metagenomics.py	Wed Jun 04 00:12:18 2014 -0400
@@ -313,72 +313,3 @@
         Tabular.__init__( self, **kwd )
         self.column_names = ['name']
         self.columns = 1
-
-class Newick( Text ):
-    """
-    The Newick Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses.
-    http://evolution.genetics.washington.edu/phylip/newicktree.html
-    http://en.wikipedia.org/wiki/Newick_format
-    Example:
-    (B,(A,C,E),D);
-    or example with branch lengths:
-    (B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);
-    or an example with embedded comments but no branch lengths:
-    ((a [&&PRIME S=x], b [&&PRIME S=y]), c [&&PRIME S=z]);
-    Example with named interior noe:
-    (B:6.0,(A:5.0,C:3.0,E:4.0)Ancestor1:5.0,D:11.0);
-    """
-    file_ext = 'tre'
-
-    def __init__(self, **kwd):
-        Text.__init__( self, **kwd )
-
-    def sniff( self, filename ):   ## TODO
-        """
-        Determine whether the file is in Newick format
-        Note: Last non-space char of a tree should be a semicolon: ';'
-        Usually the first char will be a open parenthesis: '('
-        (,,(,));                               no nodes are named
-        (A,B,(C,D));                           leaf nodes are named
-        (A,B,(C,D)E)F;                         all nodes are named
-        (:0.1,:0.2,(:0.3,:0.4):0.5);           all but root node have a distance to parent
-        (:0.1,:0.2,(:0.3,:0.4):0.5):0.0;       all have a distance to parent
-        (A:0.1,B:0.2,(C:0.3,D:0.4):0.5);       distances and leaf names (popular)
-        (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;     distances and all names
-        ((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A;    a tree rooted on a leaf node (rare)
-        """
-        if not os.path.exists(filename):
-            return False
-        try:
-            ## For now, guess this is a Newick file if it starts with a '(' and ends with a ';'
-            flen = os.path.getsize(filename)
-            fh = open( filename )
-            len = min(flen,2000)
-            # check end of the file for a semicolon
-            fh.seek(-len,os.SEEK_END)
-            buf = fh.read(len).strip()
-            buf = buf.strip()
-            if not buf.endswith(';'):
-                return False
-            # See if this starts with a open parenthesis
-            if len < flen:
-                fh.seek(0)
-                buf = fh.read(len).strip()
-            if buf.startswith('('):
-                return True
-        except:
-            pass
-        finally:
-            close(fh)
-        return False
-
-class Nhx( Newick ):
-    """
-    New Hampshire eXtended  Newick with embedded
-    The Newick Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses.
-    http://evolution.genetics.washington.edu/phylip/newicktree.html
-    http://en.wikipedia.org/wiki/Newick_format
-    Example:
-    (gene1_Hu[&&NHX:S=Hu_Homo_sapiens], (gene2_Hu[&&NHX:S=Hu_Homo_sapiens], gene2_Mu[&&NHX:S=Mu_Mus_musculus]));
-    """
-    file_ext = 'nhx'