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 e8498c5..f14efd3 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -266,6 +266,18 @@ public class PhylogenyMethods {
         return stats;
     }
 
+    public final static void collapseSubtreeStructure( final PhylogenyNode n ) {
+        final List<PhylogenyNode> eds = n.getAllExternalDescendants();
+        final List<Double> d = new ArrayList<Double>();
+        for( final PhylogenyNode ed : eds ) {
+            d.add( calculateDistanceToAncestor( n, ed ) );
+        }
+        for( int i = 0; i < eds.size(); ++i ) {
+            n.setChildNode( i, eds.get( i ) );
+            eds.get( i ).setDistanceToParent( d.get( i ) );
+        }
+    }
+
     public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
         int count = 0;
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
@@ -1481,6 +1493,24 @@ public class PhylogenyMethods {
         return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
     }
 
+    static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {
+        double d = 0;
+        boolean all_default = true;
+        while ( anc != desc ) {
+            if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+                d += desc.getDistanceToParent();
+                if ( all_default ) {
+                    all_default = false;
+                }
+            }
+            desc = desc.getParent();
+        }
+        if ( all_default ) {
+            return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
+        }
+        return d;
+    }
+
     /**
      * Deep copies the phylogeny originating from this node.
      */