From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 18 Nov 2013 05:31:27 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=350d69f48150a73b6ad4b0064acf9cd63c9cf9d1;p=jalview.git

in progress
---

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 8ecbe86..c3d7d28 100644
--- a/forester_applications/src/org/forester/applications/simple_node_processor.java
+++ b/forester_applications/src/org/forester/applications/simple_node_processor.java
@@ -53,6 +53,7 @@ public class simple_node_processor {
             CommandLineArguments cla = null;
             cla = new CommandLineArguments( args );
             in = cla.getFile( 0 );
+         //   in = new File( "");
             //out = cla.getFile( 1 );
             // if ( out.exists() ) {
             //      System.out.println( out + " already exists" );
@@ -121,7 +122,12 @@ public class simple_node_processor {
             if ( node.getNodeData().isHasTaxonomy() ) {
                 final Taxonomy t = node.getNodeData().getTaxonomy();
                 if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) ) {
-                    SurfacingUtil.obtainHexColorStringDependingOnTaxonomyGroup( t.getTaxonomyCode(), phy );
+                    final String c =  t.getTaxonomyCode();
+                    if ( c.indexOf( "XX" ) == 3 ) {
+                         System.out.println( "FAKE_CODE_TO_ID_MAP.put( \"" + c + "\", "+  t.getIdentifier().getValue()   + ");" );
+                    }
+                    
+                    //   SurfacingUtil.obtainHexColorStringDependingOnTaxonomyGroup( t.getTaxonomyCode(), phy );
                 }
             }
         }