in progress

[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 0d404e8..7835d62 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -30,6 +30,7 @@ import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -45,6 +46,7 @@ import org.forester.phylogeny.data.BranchWidth;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.DomainArchitecture;
 import org.forester.phylogeny.data.Identifier;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
@@ -192,7 +194,7 @@ public class PhylogenyMethods {
         final PhylogenyNodeIterator it = phy.iteratorPostorder();
         while ( it.hasNext() ) {
             final PhylogenyNode n = it.next();
-            if ( !n.isRoot() && !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
+            if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
                 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
                     double d = -1.0;
                     try {
@@ -230,6 +232,21 @@ public class PhylogenyMethods {
             }
         }
     }
+    
+    
+    
+    final static public void sortNodeDescendents( PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getDescendants();
+       // Collections.sort( arg0, comparator );
+        Collections.sort( descs );
+        
+        int i = 0;
+        for( PhylogenyNode desc : descs ) {
+            node.setChildNode( i++, desc );
+        }
+        
+    }
+    
 
     final static public void transferNodeNameToField( final Phylogeny phy,
                                                       final PhylogenyMethods.PhylogenyNodeField field ) {
@@ -328,7 +345,7 @@ public class PhylogenyMethods {
         else if ( b >= 0.0 ) {
             return b;
         }
-        return PhylogenyNode.DISTANCE_DEFAULT;
+        return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
     }
 
     // Helper for getUltraParalogousNodes( PhylogenyNode ).