From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 25 Oct 2013 02:16:34 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d8e62df9cac0a8e278873d32e78ff99394d64b61;p=jalview.git

inprogress
---

diff --git a/forester_applications/src/org/forester/applications/simple_node_processor.class b/forester_applications/src/org/forester/applications/simple_node_processor.class
index 9f0fe1a..ff02e21 100644
Binary files a/forester_applications/src/org/forester/applications/simple_node_processor.class and b/forester_applications/src/org/forester/applications/simple_node_processor.class differ
diff --git a/forester_applications/src/org/forester/applications/simple_node_processor.java b/forester_applications/src/org/forester/applications/simple_node_processor.java
index c2d832b..8ecbe86 100644
--- a/forester_applications/src/org/forester/applications/simple_node_processor.java
+++ b/forester_applications/src/org/forester/applications/simple_node_processor.java
@@ -48,12 +48,12 @@ public class simple_node_processor {
 
     public static void main( final String args[] ) {
         File in = null;
-        File out = null;
+        final File out = null;
         try {
             CommandLineArguments cla = null;
             cla = new CommandLineArguments( args );
             in = cla.getFile( 0 );
-            out = cla.getFile( 1 );
+            //out = cla.getFile( 1 );
             // if ( out.exists() ) {
             //      System.out.println( out + " already exists" );
             //      System.exit( -1 );
@@ -70,7 +70,7 @@ public class simple_node_processor {
                 i++;
             }
             final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toPhyloXML( out, phylogeny_0, 0 );
+            //writer.toPhyloXML( out, phylogeny_0, 0 );
         }
         catch ( final Exception e ) {
             System.out.println( e.getLocalizedMessage() );
@@ -107,6 +107,9 @@ public class simple_node_processor {
         //            }
         //        }
         if ( node.isExternal() ) {
+            //final Taxonomy t = node.getNodeData().getTaxonomy();
+            //System.out.println( t.getTaxonomyCode() + "\t" + t.getScientificName() + "\t" + t.getCommonName()
+            //        + "\t" + label );
             //            if ( node.getNodeData().isHasTaxonomy() ) {
             //                final Taxonomy t = node.getNodeData().getTaxonomy();
             //                if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) && ( t.getTaxonomyCode().length() == 5 ) ) {