fixing lining up of domains.

[jalview.git] / forester / java / src / org / forester / rio / RIO.java

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index b19d327..0de8e9a 100644 (file)
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -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.AGRESSIVE );
+            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.AGRESSIVE );
+            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
         }
         return factory.create( gene_trees_file, p );
     }