X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurf_paup.java;h=eff34257d2a76270a67be74acbfad4c80e93b846;hb=d30f8d155dee1fbfa17946cf80a203cc886ffdd6;hp=297e16f2b4a5616e85556d8b6dda40079af48cef;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git

diff --git a/forester/java/src/org/forester/application/surf_paup.java b/forester/java/src/org/forester/application/surf_paup.java
index 297e16f..eff3425 100644
--- a/forester/java/src/org/forester/application/surf_paup.java
+++ b/forester/java/src/org/forester/application/surf_paup.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,7 +16,7 @@
 // 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
@@ -38,8 +38,10 @@ import org.forester.io.parsers.nexus.NexusCharactersParser;
 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
 import org.forester.io.parsers.nexus.PaupLogParser;
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.surfacing.DomainParsimonyCalculator;
 import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.CommandLineArguments;
@@ -101,8 +103,9 @@ public class surf_paup {
             phylogenies = factory.create( surfacing_nexus_outfile, phylogeny_parser );
         }
         catch ( final IOException e ) {
-            ForesterUtil.fatalError( PRG_NAME, "problem with parsing phylogeny [" + surfacing_nexus_outfile + "]: "
-                    + e.getMessage() );
+            ForesterUtil.fatalError( PRG_NAME,
+                                     "problem with parsing phylogeny [" + surfacing_nexus_outfile + "]: "
+                                             + e.getMessage() );
             e.printStackTrace();
         }
         if ( phylogenies.length != 1 ) {
@@ -113,7 +116,7 @@ public class surf_paup {
         if ( !phylogeny.isRooted() ) {
             ForesterUtil.fatalError( PRG_NAME, "phylogeny from [" + surfacing_nexus_outfile + "] is not rooted" );
         }
-        ForesterUtil.postOrderRelabelInternalNodes( phylogeny, phylogeny.getNumberOfExternalNodes() + 1 );
+        postOrderRelabelInternalNodes( phylogeny, phylogeny.getNumberOfExternalNodes() + 1 );
         CharacterStateMatrix<BinaryStates> matrix = null;
         final PaupLogParser paup_log_parser = new PaupLogParser();
         try {
@@ -121,11 +124,12 @@ public class surf_paup {
             matrix = paup_log_parser.parse();
         }
         catch ( final IOException e ) {
-            ForesterUtil.fatalError( PRG_NAME, "failed to parse matrix from  [" + paup_log_file + "]: "
-                    + e.getMessage() );
+            ForesterUtil.fatalError( PRG_NAME,
+                                     "failed to parse matrix from  [" + paup_log_file + "]: " + e.getMessage() );
         }
-        ForesterUtil.programMessage( PRG_NAME, "read in character state matrix of size "
-                + matrix.getNumberOfIdentifiers() + "x" + matrix.getNumberOfCharacters() );
+        ForesterUtil.programMessage( PRG_NAME,
+                                     "read in character state matrix of size " + matrix.getNumberOfIdentifiers() + "x"
+                                             + matrix.getNumberOfCharacters() );
         final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( phylogeny );
         domain_parsimony.executeOnGivenBinaryStatesMatrix( matrix, labels );
         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
@@ -156,6 +160,16 @@ public class surf_paup {
         ForesterUtil.programMessage( PRG_NAME, "OK" );
     }
 
+    final private static void postOrderRelabelInternalNodes( final Phylogeny phylogeny, final int starting_number ) {
+        int i = starting_number;
+        for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) {
+            final PhylogenyNode node = it.next();
+            if ( !node.isExternal() ) {
+                node.setName( String.valueOf( i++ ) );
+            }
+        }
+    }
+
     private static void printHelp() {
         System.out.println();
         System.out.println( "Usage:" );