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..cc140e4 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(); ) {
@@ -297,9 +309,8 @@ public class PhylogenyMethods {
         return nodes;
     }
 
-    public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
-        phy.clearHashIdToNodeMap();
-        for( final Integer id : to_delete ) {
+    public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
+        for( final Long id : to_delete ) {
             phy.deleteSubtree( phy.getNode( id ), true );
         }
         phy.clearHashIdToNodeMap();
@@ -327,24 +338,6 @@ public class PhylogenyMethods {
         p.externalNodesHaveChanged();
     }
 
-    public static void deleteExternalNodesPositiveSelection( final Set<Taxonomy> species_to_keep, final Phylogeny phy ) {
-        //   final Set<Integer> to_delete = new HashSet<Integer>();
-        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
-            final PhylogenyNode n = it.next();
-            if ( n.getNodeData().isHasTaxonomy() ) {
-                if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
-                    //to_delete.add( n.getNodeId() );
-                    phy.deleteSubtree( n, true );
-                }
-            }
-            else {
-                throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
-            }
-        }
-        phy.clearHashIdToNodeMap();
-        phy.externalNodesHaveChanged();
-    }
-
     public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
                                                                      final Phylogeny p ) {
         final PhylogenyNodeIterator it = p.iteratorExternalForward();
@@ -367,6 +360,22 @@ public class PhylogenyMethods {
         return deleted;
     }
 
+    public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {
+        final Set<Long> to_delete = new HashSet<Long>();
+        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getNodeData().isHasTaxonomy() ) {
+                if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
+                    to_delete.add( n.getId() );
+                }
+            }
+            else {
+                throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
+            }
+        }
+        deleteExternalNodesNegativeSelection( to_delete, phy );
+    }
+
     final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
         final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
@@ -1481,6 +1490,24 @@ 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.
      */