X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FRIO.java;h=1f4f3e6df9c95fa9db101a2be6627ebf80b2b5ae;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;hp=45d5633c1e8f3f5d075e1afacada4b7f880464e0;hpb=7a7a89b113566b2749f1e8e4fbb3064241145201;p=jalview.git

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index 45d5633..1f4f3e6 100644
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -273,7 +273,7 @@ public final class RIO {
             first = 0;
         }
         if ( log() ) {
-            postLog( species_tree, first, first + counter - 1 );
+            postLog( species_tree, first, ( first + counter ) - 1 );
         }
         if ( _verbose ) {
             System.out.println();
@@ -881,6 +881,10 @@ public final class RIO {
         else if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
             label = n.getNodeData().getSequence().getSymbol();
         }
+        else if ( n.getNodeData().isHasSequence()
+                && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+            label = n.getNodeData().getSequence().getGeneName();
+        }
         else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
             label = n.getName();
         }
@@ -901,13 +905,13 @@ public final class RIO {
             final NHXParser nhx = ( NHXParser ) p;
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
         }
         else if ( p instanceof NexusPhylogeniesParser ) {
             final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
             nex.setReplaceUnderscores( false );
             nex.setIgnoreQuotes( true );
-            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
         }
         return factory.create( gene_trees_file, p );
     }