inprogress

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyMethods.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 9c83603..08fe7f0 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -1245,6 +1245,11 @@ public class PhylogenyMethods {
                         return n1.getNodeData().getSequence().getSymbol()
                                 .compareTo( n2.getNodeData().getSequence().getSymbol() );
                     }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                        return n1.getNodeData().getSequence().getGeneName()
+                                .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                    }
                     if ( ( n1.getNodeData().getSequence().getAccession() != null )
                             && ( n2.getNodeData().getSequence().getAccession() != null )
                             && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
@@ -1274,6 +1279,11 @@ public class PhylogenyMethods {
                         return n1.getNodeData().getSequence().getSymbol()
                                 .compareTo( n2.getNodeData().getSequence().getSymbol() );
                     }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                        return n1.getNodeData().getSequence().getGeneName()
+                                .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                    }
                     if ( ( n1.getNodeData().getSequence().getAccession() != null )
                             && ( n2.getNodeData().getSequence().getAccession() != null )
                             && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
@@ -1340,6 +1350,11 @@ public class PhylogenyMethods {
                         return n1.getNodeData().getSequence().getSymbol()
                                 .compareTo( n2.getNodeData().getSequence().getSymbol() );
                     }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                        return n1.getNodeData().getSequence().getGeneName()
+                                .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                    }
                     if ( ( n1.getNodeData().getSequence().getAccession() != null )
                             && ( n2.getNodeData().getSequence().getAccession() != null )
                             && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )