added AGRESSIVE tax extraction ^^

[jalview.git] / forester / java / src / org / forester / application / support_transfer.java

diff --git a/forester/java/src/org/forester/application/support_transfer.java b/forester/java/src/org/forester/application/support_transfer.java
index f6e2aed..927da4f 100644 (file)
--- a/forester/java/src/org/forester/application/support_transfer.java
+++ b/forester/java/src/org/forester/application/support_transfer.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.application;
 
@@ -31,15 +31,16 @@ import java.util.List;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
 
 public final class support_transfer {
 
@@ -91,10 +92,10 @@ public final class support_transfer {
                 System.exit( -1 );
             }
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp_bl = ForesterUtil.createParserDependingOnFileType( infile_bl, true );
-            final PhylogenyParser pp_s = ForesterUtil.createParserDependingOnFileType( infile_support_vals, true );
+            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( ForesterUtil.TAXONOMY_EXTRACTION.YES );
+                ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             }
             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 ];
@@ -137,7 +138,7 @@ public final class support_transfer {
             else {
                 PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
             }
-            node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+            node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
         }
     } // moveBranchLengthsToBootstrap()