big refactoring (moving of methods)

[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 12e0a41..82817e9 100644 (file)
--- a/forester/java/src/org/forester/application/support_transfer.java
+++ b/forester/java/src/org/forester/application/support_transfer.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -31,6 +31,7 @@ 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;
@@ -39,7 +40,6 @@ import org.forester.phylogeny.data.Confidence;
 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 +91,10 @@ 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( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
             }
             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 ];
@@ -162,8 +162,8 @@ public final class support_transfer {
                     final List<String> ext_children_from = node_from.getAllExternalDescendantsNames();
                     if ( ( ext_children_from.size() == ext_children_to.size() )
                             && ext_children_from.containsAll( ext_children_to ) ) {
-                        PhylogenyMethods.setBootstrapConfidence( node_to, PhylogenyMethods
-                                .getConfidenceValue( node_from ) );
+                        PhylogenyMethods.setBootstrapConfidence( node_to,
+                                                                 PhylogenyMethods.getConfidenceValue( node_from ) );
                         continue to;
                     }
                 }