X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsupport_transfer.java;h=340bcf4833206fec1abebfbfb91991c4d2aa886b;hb=b528989f688291ba7615867e5322090ec42096d8;hp=927da4f14db5388a588c6bd671f61d7ed9c0b3f1;hpb=3d6a64e0371ffedf725bf8467211ed860f298550;p=jalview.git

diff --git a/forester/java/src/org/forester/application/support_transfer.java b/forester/java/src/org/forester/application/support_transfer.java
index 927da4f..340bcf4 100644
--- a/forester/java/src/org/forester/application/support_transfer.java
+++ b/forester/java/src/org/forester/application/support_transfer.java
@@ -48,7 +48,7 @@ public final class support_transfer {
      * Transfers branch length values from one Phylogeny to another. It is
      * mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )"
      * of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.
-     * 
+     *
      * @param args[0]
      *            Filename (String) for Phylogeny which has correct branch
      *            length values
@@ -60,8 +60,8 @@ public final class support_transfer {
      * @param args[2]
      *            String Filename (String) for outputfile
      * @param args[3]
-     *            String [number of tree with correct bl to use in case treefile contains more than one, default 0]            
-     
+     *            String [number of tree with correct bl to use in case treefile contains more than one, default 0]
+
      */
     public static void main( final String args[] ) {
         Phylogeny phylogeny_w_bl = null; // Has correct branch lengths
@@ -95,7 +95,7 @@ public final class support_transfer {
             final PhylogenyParser pp_bl = ParserUtils.createParserDependingOnFileType( infile_bl, true );
             final PhylogenyParser pp_s = ParserUtils.createParserDependingOnFileType( infile_support_vals, true );
             if ( pp_bl instanceof NHXParser ) {
-                ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
             }
             phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
             phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];
@@ -147,7 +147,7 @@ public final class support_transfer {
      * Important (but obvious): The topology of both trees needs to be the same.
      * The method is not robust, and might produce wrong results if the internal
      * topology differs or if the external node names are not unique.
-     * 
+     *
      * @param from
      *            the Phylogeny to copy the support values from
      * @param to