added AGRESSIVE tax extraction ^^

[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 d87188b..27f2a33 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -327,10 +327,14 @@ public class PhylogenyMethods {
 
     public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
         final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
-        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
-            final PhylogenyNode n = iter.next();
+        final List<PhylogenyNode> ext = phy.getExternalNodes();
+        for( final PhylogenyNode n : ext ) {
             nodes.put( n.getName(), n );
         }
+        // for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+        //     final PhylogenyNode n = iter.next();
+        //     nodes.put( n.getName(), n );
+        // }
         return nodes;
     }
 
@@ -439,7 +443,7 @@ public class PhylogenyMethods {
 
     public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
         final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
-        final Set<Integer> encountered = new HashSet<Integer>();
+        final Set<Long> encountered = new HashSet<Long>();
         if ( !node.isExternal() ) {
             final List<PhylogenyNode> exts = node.getAllExternalDescendants();
             for( PhylogenyNode current : exts ) {
@@ -764,25 +768,6 @@ public class PhylogenyMethods {
     }
 
     /**
-     * Returns the set of distinct taxonomies of
-     * all external nodes of node.
-     * If at least one the external nodes has no taxonomy,
-     * null is returned.
-     * 
-     */
-    public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
-        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
-        final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
-        for( final PhylogenyNode n : descs ) {
-            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
-                return null;
-            }
-            tax_set.add( n.getNodeData().getTaxonomy() );
-        }
-        return tax_set;
-    }
-
-    /**
      * Returns a map of distinct taxonomies of
      * all external nodes of node.
      * If at least one of the external nodes has no taxonomy,
@@ -882,7 +867,7 @@ public class PhylogenyMethods {
             return;
         }
         phy.setIdToNodeMap( null );
-        int i = PhylogenyNode.getNodeCount();
+        long i = PhylogenyNode.getNodeCount();
         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
             it.next().setId( i++ );
         }