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 01a4ab6..b154b48 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -598,6 +598,17 @@ public class PhylogenyMethods {
         return max;
     }
 
+    public static int countNumberOfPolytomies( final Phylogeny phy ) {
+        int count = 0;
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
+                count++;
+            }
+        }
+        return count;
+    }
+
     public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
@@ -740,11 +751,12 @@ public class PhylogenyMethods {
     }
 
     public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
-        phy.hashIDs();
+        phy.clearHashIdToNodeMap();
         for( final Integer id : to_delete ) {
             phy.deleteSubtree( phy.getNode( id ), true );
         }
-        phy.hashIDs();
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
     }
 
     public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
@@ -765,6 +777,8 @@ public class PhylogenyMethods {
                 p.deleteSubtree( n, true );
             }
         }
+        p.clearHashIdToNodeMap();
+        p.externalNodesHaveChanged();
     }
 
     public static void deleteExternalNodesPositiveSelection( final Set<Taxonomy> species_to_keep, final Phylogeny phy ) {
@@ -781,9 +795,8 @@ public class PhylogenyMethods {
                 throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
             }
         }
-        phy.hashIDs();
+        phy.clearHashIdToNodeMap();
         phy.externalNodesHaveChanged();
-        //  deleteExternalNodesNegativeSelection( to_delete, phy );
     }
 
     public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
@@ -1275,6 +1288,8 @@ public class PhylogenyMethods {
         }
         if ( remove_me.isExternal() ) {
             phylogeny.deleteSubtree( remove_me, false );
+            phylogeny.clearHashIdToNodeMap();
+            phylogeny.externalNodesHaveChanged();
         }
         else {
             final PhylogenyNode parent = remove_me.getParent();
@@ -1286,7 +1301,7 @@ public class PhylogenyMethods {
                                                                  desc.getDistanceToParent() ) );
             }
             remove_me.setParent( null );
-            phylogeny.setIdHash( null );
+            phylogeny.clearHashIdToNodeMap();
             phylogeny.externalNodesHaveChanged();
         }
     }
@@ -1602,6 +1617,8 @@ public class PhylogenyMethods {
         for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
             to_be_stripped.deleteSubtree( phylogenyNode, true );
         }
+        to_be_stripped.clearHashIdToNodeMap();
+        to_be_stripped.externalNodesHaveChanged();
         return nodes_to_delete.size();
     }