From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 6 Dec 2012 00:10:57 +0000 (+0000)
Subject: "rio" work
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a6111a2153dc12fa437897cafd7e22d85962bc64;p=jalview.git

"rio" work
---

diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java
index 4515756..55c50ec 100644
--- a/forester/java/src/org/forester/sdi/RIO.java
+++ b/forester/java/src/org/forester/sdi/RIO.java
@@ -538,9 +538,11 @@ public final class RIO {
                 if ( nx == null ) {
                     throw new RioException( "node \"" + mx + "\" not present in gene tree #" + counter );
                 }
+                String my;
+                PhylogenyNode ny;
                 for( int y = 0; y < m.size(); ++y ) {
-                    final String my = m.getLabel( y );
-                    final PhylogenyNode ny = map.get( my );
+                    my = m.getLabel( y );
+                    ny = map.get( my );
                     if ( ny == null ) {
                         throw new RioException( "node \"" + my + "\" not present in gene tree #" + counter );
                     }
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index ce30298..b1bb3c6 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -3354,7 +3354,6 @@ public final class Test {
                 return false;
             }
             final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
-            System.out.println( p_c.toNewHampshireX() );
             PhylogenyMethods.preOrderReId( p_c );
             final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
                                                                                               p_c.getNode( "a" ) );
diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 71246dd..f87d66a 100644
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.007+";
-    public final static String  FORESTER_DATE               = "121130";
+    public final static String  FORESTER_VERSION            = "1.008";
+    public final static String  FORESTER_DATE               = "121205";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";