From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 20 Dec 2012 00:53:40 +0000 (+0000)
Subject: "rio" work
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e8c7440196e8fe798bd5dc2b83cc1e194c77f0d0;p=jalview.git

"rio" work
---

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index d1a317a..e47e31a 100644
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -328,11 +328,13 @@ public class rio {
         System.out.println( "                   disallowed, as are most options)" );
         System.out.println();
         System.out.println( " Formats" );
-        System.out.println( "  The species tree is expected to be in phyloXML format." );
         System.out
-                .println( "  The gene trees ideally are in phyloXML as well, but can also be in New Hamphshire (Newick)" );
-        System.out.println( "  or Nexus format as long as species information can be extracted from the gene names" );
-        System.out.println( "  (e.g. \"HUMAN\" from \"BCL2_HUMAN\")." );
+                .println( "  The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," );
+        System.out
+                .println( "  but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" );
+        System.out
+                .println( "  extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" );
+        System.out.println( "  in the species tree." );
         System.out.println();
         System.out.println( " Examples" );
         System.out.println( "  \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" );
diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 7b3f411..d566c75 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -2350,6 +2350,7 @@ public final class MainFrameApplication extends MainFrame {
 
     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
+        nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
     }
 
     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index bff716b..a096bf5 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            = "1.011";
-    public final static String  FORESTER_DATE               = "121214";
+    public final static String  FORESTER_VERSION            = "1.012";
+    public final static String  FORESTER_DATE               = "121219";
     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";