X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=09db386ca18e72d7ec9111453503d29413611e08;hb=bfd17a215d89bce322b5d77163f0d1d6cedb390c;hp=052b23f7da9619c89e32596c59f9d9defc8f3882;hpb=841c7135a24076a444b2f6652cde00ef0cf60239;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 052b23f..09db386 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -32,6 +32,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -79,7 +80,7 @@ public class PhylogenyMethods {
      * @return distance between node1 and node2
      */
     public double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        final PhylogenyNode lca =calculateLCA( node1, node2 );
+        final PhylogenyNode lca = calculateLCA( node1, node2 );
         final PhylogenyNode n1 = node1;
         final PhylogenyNode n2 = node2;
         return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
@@ -114,10 +115,6 @@ public class PhylogenyMethods {
         return farthest_d;
     }
 
-    final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
-        return calculateLCA( n1, n2 ).getNodeData().getEvent();
-    }
-
     @Override
     public Object clone() throws CloneNotSupportedException {
         throw new CloneNotSupportedException();
@@ -131,22 +128,43 @@ public class PhylogenyMethods {
         return _farthest_2;
     }
 
-    final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
-        if ( n.isInternal() ) {
-            throw new IllegalArgumentException( "node is not external" );
-        }
-        final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
-        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
-            final PhylogenyNode i = it.next();
-            if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
-                to_delete.add( i );
+    public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
+                stats.addValue( n.getDistanceToParent() );
             }
         }
-        for( final PhylogenyNode d : to_delete ) {
-            phy.deleteSubtree( d, true );
+        return stats;
+    }
+
+    public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+        final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && !n.isRoot() ) {
+                if ( n.getBranchData().isHasConfidences() ) {
+                    for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
+                        final Confidence c = n.getBranchData().getConfidences().get( i );
+                        if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
+                            stats.add( i, new BasicDescriptiveStatistics() );
+                        }
+                        if ( !ForesterUtil.isEmpty( c.getType() ) ) {
+                            if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
+                                if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
+                                    throw new IllegalArgumentException( "support values in node [" + n.toString()
+                                            + "] appear inconsistently ordered" );
+                                }
+                            }
+                            stats.get( i ).setDescription( c.getType() );
+                        }
+                        stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
+                    }
+                }
+            }
         }
-        phy.clearHashIdToNodeMap();
-        phy.externalNodesHaveChanged();
+        return stats;
     }
 
     /**
@@ -158,14 +176,20 @@ public class PhylogenyMethods {
      * @return LCA of node1 and node2
      */
     public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == null ) {
+            throw new IllegalArgumentException( "first argument (node) is null" );
+        }
+        if ( node2 == null ) {
+            throw new IllegalArgumentException( "second argument (node) is null" );
+        }
         if ( node1 == node2 ) {
             return node1;
         }
-        if (( node1.getParent() == node2.getParent() ) /*&& node1.getParent() != null */ ) {
+        if ( ( node1.getParent() == node2.getParent() ) ) {
             return node1.getParent();
         }
-        int depth1 = node1.calculateDepth() ;
-        int depth2 = node2.calculateDepth() ;
+        int depth1 = node1.calculateDepth();
+        int depth2 = node2.calculateDepth();
         while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {
             if ( depth1 > depth2 ) {
                 node1 = node1.getParent();
@@ -189,604 +213,145 @@ public class PhylogenyMethods {
     }
 
     /**
-     * Returns all orthologs of the external PhylogenyNode n of this Phylogeny.
-     * Orthologs are returned as List of node references.
-     * <p>
-     * PRECONDITION: This tree must be binary and rooted, and speciation -
-     * duplication need to be assigned for each of its internal Nodes.
-     * <p>
-     * Returns null if this Phylogeny is empty or if n is internal.
-     * @param n
-     *            external PhylogenyNode whose orthologs are to be returned
-     * @return Vector of references to all orthologous Nodes of PhylogenyNode n
-     *         of this Phylogeny, null if this Phylogeny is empty or if n is
-     *         internal
+     * Returns the LCA of PhylogenyNodes node1 and node2.
+     * Precondition: ids are in pre-order (or level-order).
+     * 
+     * 
+     * @param node1
+     * @param node2
+     * @return LCA of node1 and node2
      */
-    public List<PhylogenyNode> getOrthologousNodes( final Phylogeny phy, final PhylogenyNode node ) {
-        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
-        final PhylogenyNodeIterator it = phy.iteratorExternalForward();
-        while ( it.hasNext() ) {
-            final PhylogenyNode temp_node = it.next();
-            if ( ( temp_node != node ) && isAreOrthologous( node, temp_node ) ) {
-                nodes.add( temp_node );
+    public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == null ) {
+            throw new IllegalArgumentException( "first argument (node) is null" );
+        }
+        if ( node2 == null ) {
+            throw new IllegalArgumentException( "second argument (node) is null" );
+        }
+        while ( node1 != node2 ) {
+            if ( node1.getId() > node2.getId() ) {
+                node1 = node1.getParent();
+            }
+            else {
+                node2 = node2.getParent();
             }
         }
-        return nodes;
+        return node1;
     }
 
-    public static boolean isAreOrthologous( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        return !calculateLCA( node1, node2 ).isDuplication();
+    public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
+        if ( node.isExternal() ) {
+            return 0;
+        }
+        short max = 0;
+        for( PhylogenyNode d : node.getAllExternalDescendants() ) {
+            short steps = 0;
+            while ( d != node ) {
+                if ( d.isCollapse() ) {
+                    steps = 0;
+                }
+                else {
+                    steps++;
+                }
+                d = d.getParent();
+            }
+            if ( max < steps ) {
+                max = steps;
+            }
+        }
+        return max;
     }
 
-    public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
-        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-        final Phylogeny[] trees = factory.create( file, parser );
-        if ( ( trees == null ) || ( trees.length == 0 ) ) {
-            throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+    public static int calculateMaxDepth( final Phylogeny phy ) {
+        int max = 0;
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            final int steps = node.calculateDepth();
+            if ( steps > max ) {
+                max = steps;
+            }
         }
-        return trees;
+        return max;
     }
 
-    public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
-            throws IOException {
-        final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
-        for( final File file : files ) {
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] trees = factory.create( file, parser );
-            if ( ( trees == null ) || ( trees.length == 0 ) ) {
-                throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+    public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
+        double max = 0.0;
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            final double d = node.calculateDistanceToRoot();
+            if ( d > max ) {
+                max = d;
             }
-            tree_list.addAll( Arrays.asList( trees ) );
         }
-        return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
+        return max;
     }
 
-    final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) {
-        final PhylogenyNodeIterator it = phy.iteratorPostorder();
-        while ( it.hasNext() ) {
-            final PhylogenyNode n = it.next();
-            if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
-                if ( !ForesterUtil.isEmpty( n.getName() ) ) {
-                    double d = -1.0;
-                    try {
-                        d = Double.parseDouble( n.getName() );
-                    }
-                    catch ( final Exception e ) {
-                        d = -1.0;
-                    }
-                    if ( d >= 0.0 ) {
-                        n.getBranchData().addConfidence( new Confidence( d, "" ) );
-                        n.setName( "" );
-                    }
-                }
+    public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        int x = 0;
+        for( final PhylogenyNode n : descs ) {
+            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+                x++;
             }
         }
+        return x;
     }
 
-    final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
-        final PhylogenyNodeIterator it = phy.iteratorPostorder();
-        while ( it.hasNext() ) {
-            final PhylogenyNode n = it.next();
-            if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
-                double value = -1;
-                try {
-                    value = Double.parseDouble( n.getName() );
-                }
-                catch ( final NumberFormatException e ) {
-                    throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
-                            + e.getLocalizedMessage() );
-                }
-                if ( value >= 0.0 ) {
-                    n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
-                    n.setName( "" );
-                }
+    public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() ) {
+                stats.addValue( n.getNumberOfDescendants() );
             }
         }
+        return stats;
     }
 
-    final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
-        class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
+    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;
+    }
 
-            @Override
-            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
-                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
-                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
-                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
-                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
-                    }
-                }
-                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
-                        return n1.getNodeData().getSequence().getName().toLowerCase()
-                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
-                        return n1.getNodeData().getSequence().getSymbol()
-                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
-                    }
-                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
-                            && ( n2.getNodeData().getSequence().getAccession() != null )
-                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
-                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
-                        return n1.getNodeData().getSequence().getAccession().getValue()
-                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
-                    }
-                }
-                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
-                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+    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();
+            nodes.put( n.getName(), n );
+        }
+        return nodes;
+    }
+
+    public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
+        phy.clearHashIdToNodeMap();
+        for( final Integer id : to_delete ) {
+            phy.deleteSubtree( phy.getNode( id ), true );
+        }
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
+    }
+
+    public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
+            throws IllegalArgumentException {
+        for( final String element : node_names_to_delete ) {
+            if ( ForesterUtil.isEmpty( element ) ) {
+                continue;
+            }
+            List<PhylogenyNode> nodes = null;
+            nodes = p.getNodes( element );
+            final Iterator<PhylogenyNode> it = nodes.iterator();
+            while ( it.hasNext() ) {
+                final PhylogenyNode n = it.next();
+                if ( !n.isExternal() ) {
+                    throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
                 }
-                return 0;
-            }
-        }
-        class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
-
-            @Override
-            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
-                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
-                        return n1.getNodeData().getSequence().getName().toLowerCase()
-                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
-                        return n1.getNodeData().getSequence().getSymbol()
-                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
-                    }
-                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
-                            && ( n2.getNodeData().getSequence().getAccession() != null )
-                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
-                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
-                        return n1.getNodeData().getSequence().getAccession().getValue()
-                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
-                    }
-                }
-                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
-                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
-                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
-                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
-                    }
-                }
-                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
-                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
-                }
-                return 0;
-            }
-        }
-        class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
-
-            @Override
-            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
-                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
-                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
-                }
-                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
-                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
-                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
-                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
-                    }
-                }
-                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
-                        return n1.getNodeData().getSequence().getName().toLowerCase()
-                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
-                    }
-                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
-                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
-                        return n1.getNodeData().getSequence().getSymbol()
-                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
-                    }
-                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
-                            && ( n2.getNodeData().getSequence().getAccession() != null )
-                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
-                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
-                        return n1.getNodeData().getSequence().getAccession().getValue()
-                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
-                    }
-                }
-                return 0;
-            }
-        }
-        Comparator<PhylogenyNode> c;
-        switch ( pri ) {
-            case SEQUENCE:
-                c = new PhylogenyNodeSortSequencePriority();
-                break;
-            case NODE_NAME:
-                c = new PhylogenyNodeSortNodeNamePriority();
-                break;
-            default:
-                c = new PhylogenyNodeSortTaxonomyPriority();
-        }
-        final List<PhylogenyNode> descs = node.getDescendants();
-        Collections.sort( descs, c );
-        int i = 0;
-        for( final PhylogenyNode desc : descs ) {
-            node.setChildNode( i++, desc );
-        }
-    }
-
-    final static public void transferNodeNameToField( final Phylogeny phy,
-                                                      final PhylogenyMethods.PhylogenyNodeField field,
-                                                      final boolean external_only ) throws PhyloXmlDataFormatException {
-        final PhylogenyNodeIterator it = phy.iteratorPostorder();
-        while ( it.hasNext() ) {
-            final PhylogenyNode n = it.next();
-            if ( external_only && n.isInternal() ) {
-                continue;
-            }
-            final String name = n.getName().trim();
-            if ( !ForesterUtil.isEmpty( name ) ) {
-                switch ( field ) {
-                    case TAXONOMY_CODE:
-                        n.setName( "" );
-                        setTaxonomyCode( n, name );
-                        break;
-                    case TAXONOMY_SCIENTIFIC_NAME:
-                        n.setName( "" );
-                        if ( !n.getNodeData().isHasTaxonomy() ) {
-                            n.getNodeData().setTaxonomy( new Taxonomy() );
-                        }
-                        n.getNodeData().getTaxonomy().setScientificName( name );
-                        break;
-                    case TAXONOMY_COMMON_NAME:
-                        n.setName( "" );
-                        if ( !n.getNodeData().isHasTaxonomy() ) {
-                            n.getNodeData().setTaxonomy( new Taxonomy() );
-                        }
-                        n.getNodeData().getTaxonomy().setCommonName( name );
-                        break;
-                    case SEQUENCE_SYMBOL:
-                        n.setName( "" );
-                        if ( !n.getNodeData().isHasSequence() ) {
-                            n.getNodeData().setSequence( new Sequence() );
-                        }
-                        n.getNodeData().getSequence().setSymbol( name );
-                        break;
-                    case SEQUENCE_NAME:
-                        n.setName( "" );
-                        if ( !n.getNodeData().isHasSequence() ) {
-                            n.getNodeData().setSequence( new Sequence() );
-                        }
-                        n.getNodeData().getSequence().setName( name );
-                        break;
-                    case TAXONOMY_ID_UNIPROT_1: {
-                        if ( !n.getNodeData().isHasTaxonomy() ) {
-                            n.getNodeData().setTaxonomy( new Taxonomy() );
-                        }
-                        String id = name;
-                        final int i = name.indexOf( '_' );
-                        if ( i > 0 ) {
-                            id = name.substring( 0, i );
-                        }
-                        else {
-                            n.setName( "" );
-                        }
-                        n.getNodeData().getTaxonomy()
-                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
-                        break;
-                    }
-                    case TAXONOMY_ID_UNIPROT_2: {
-                        if ( !n.getNodeData().isHasTaxonomy() ) {
-                            n.getNodeData().setTaxonomy( new Taxonomy() );
-                        }
-                        String id = name;
-                        final int i = name.indexOf( '_' );
-                        if ( i > 0 ) {
-                            id = name.substring( i + 1, name.length() );
-                        }
-                        else {
-                            n.setName( "" );
-                        }
-                        n.getNodeData().getTaxonomy()
-                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
-                        break;
-                    }
-                    case TAXONOMY_ID: {
-                        if ( !n.getNodeData().isHasTaxonomy() ) {
-                            n.getNodeData().setTaxonomy( new Taxonomy() );
-                        }
-                        n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
-                        break;
-                    }
-                }
-            }
-        }
-    }
-
-    static double addPhylogenyDistances( final double a, final double b ) {
-        if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
-            return a + b;
-        }
-        else if ( a >= 0.0 ) {
-            return a;
-        }
-        else if ( b >= 0.0 ) {
-            return b;
-        }
-        return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
-    }
-
-    // Helper for getUltraParalogousNodes( PhylogenyNode ).
-    public static boolean areAllChildrenDuplications( final PhylogenyNode n ) {
-        if ( n.isExternal() ) {
-            return false;
-        }
-        else {
-            if ( n.isDuplication() ) {
-                //FIXME test me!
-                for( final PhylogenyNode desc : n.getDescendants() ) {
-                    if ( !areAllChildrenDuplications( desc ) ) {
-                        return false;
-                    }
-                }
-                return true;
-            }
-            else {
-                return false;
-            }
-        }
-    }
-
-    public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
-        if ( node.isExternal() ) {
-            return 0;
-        }
-        short max = 0;
-        for( PhylogenyNode d : node.getAllExternalDescendants() ) {
-            short steps = 0;
-            while ( d != node ) {
-                if ( d.isCollapse() ) {
-                    steps = 0;
-                }
-                else {
-                    steps++;
-                }
-                d = d.getParent();
-            }
-            if ( max < steps ) {
-                max = steps;
-            }
-        }
-        return max;
-    }
-
-    public static int calculateMaxDepth( final Phylogeny phy ) {
-        int max = 0;
-        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
-            final PhylogenyNode node = iter.next();
-            final int steps = node.calculateDepth();
-            if ( steps > max ) {
-                max = steps;
-            }
-        }
-        return max;
-    }
-
-    public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
-        double max = 0.0;
-        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
-            final PhylogenyNode node = iter.next();
-            final double d = node.calculateDistanceToRoot();
-            if ( d > max ) {
-                max = d;
-            }
-        }
-        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(); ) {
-            final PhylogenyNode n = iter.next();
-            if ( !n.isExternal() ) {
-                stats.addValue( n.getNumberOfDescendants() );
-            }
-        }
-        return stats;
-    }
-
-    public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
-        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
-        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
-            final PhylogenyNode n = iter.next();
-            if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
-                stats.addValue( n.getDistanceToParent() );
-            }
-        }
-        return stats;
-    }
-
-    public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
-        final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
-        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
-            final PhylogenyNode n = iter.next();
-            if ( !n.isExternal() && !n.isRoot() ) {
-                if ( n.getBranchData().isHasConfidences() ) {
-                    for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
-                        final Confidence c = n.getBranchData().getConfidences().get( i );
-                        if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
-                            stats.add( i, new BasicDescriptiveStatistics() );
-                        }
-                        if ( !ForesterUtil.isEmpty( c.getType() ) ) {
-                            if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
-                                if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
-                                    throw new IllegalArgumentException( "support values in node [" + n.toString()
-                                            + "] appear inconsistently ordered" );
-                                }
-                            }
-                            stats.get( i ).setDescription( c.getType() );
-                        }
-                        stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
-                    }
-                }
-            }
-        }
-        return stats;
-    }
-
-    /**
-     * 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,
-     * null is returned.
-     * 
-     */
-    public static SortedMap<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
-        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
-        final SortedMap<Taxonomy, Integer> tax_map = new TreeMap<Taxonomy, Integer>();
-        for( final PhylogenyNode n : descs ) {
-            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
-                return null;
-            }
-            final Taxonomy t = n.getNodeData().getTaxonomy();
-            if ( tax_map.containsKey( t ) ) {
-                tax_map.put( t, tax_map.get( t ) + 1 );
-            }
-            else {
-                tax_map.put( t, 1 );
-            }
-        }
-        return tax_map;
-    }
-
-    public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
-        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
-        int x = 0;
-        for( final PhylogenyNode n : descs ) {
-            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
-                x++;
-            }
-        }
-        return x;
-    }
-
-    /**
-     * Deep copies the phylogeny originating from this node.
-     */
-    static PhylogenyNode copySubTree( final PhylogenyNode source ) {
-        if ( source == null ) {
-            return null;
-        }
-        else {
-            final PhylogenyNode newnode = source.copyNodeData();
-            if ( !source.isExternal() ) {
-                for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
-                    newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
-                }
-            }
-            return newnode;
-        }
-    }
-
-    /**
-     * Shallow copies the phylogeny originating from this node.
-     */
-    static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
-        if ( source == null ) {
-            return null;
-        }
-        else {
-            final PhylogenyNode newnode = source.copyNodeDataShallow();
-            if ( !source.isExternal() ) {
-                for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
-                    newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
-                }
-            }
-            return newnode;
-        }
-    }
-
-    public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
-        phy.clearHashIdToNodeMap();
-        for( final Integer id : to_delete ) {
-            phy.deleteSubtree( phy.getNode( id ), true );
-        }
-        phy.clearHashIdToNodeMap();
-        phy.externalNodesHaveChanged();
-    }
-
-    public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
-            throws IllegalArgumentException {
-        for( final String element : node_names_to_delete ) {
-            if ( ForesterUtil.isEmpty( element ) ) {
-                continue;
-            }
-            List<PhylogenyNode> nodes = null;
-            nodes = p.getNodes( element );
-            final Iterator<PhylogenyNode> it = nodes.iterator();
-            while ( it.hasNext() ) {
-                final PhylogenyNode n = it.next();
-                if ( !n.isExternal() ) {
-                    throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
-                }
-                p.deleteSubtree( n, true );
+                p.deleteSubtree( n, true );
             }
         }
         p.clearHashIdToNodeMap();
@@ -833,6 +398,24 @@ public class PhylogenyMethods {
         return deleted;
     }
 
+    final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
+        if ( n.isInternal() ) {
+            throw new IllegalArgumentException( "node is not external" );
+        }
+        final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            final PhylogenyNode i = it.next();
+            if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
+                to_delete.add( i );
+            }
+        }
+        for( final PhylogenyNode d : to_delete ) {
+            phy.deleteSubtree( d, true );
+        }
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
+    }
+
     public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
         final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
         final Set<Integer> encountered = new HashSet<Integer>();
@@ -902,24 +485,8 @@ public class PhylogenyMethods {
         return values;
     }
 
-    /**
-     * Calculates the distance between PhylogenyNodes n1 and n2.
-     * PRECONDITION: n1 is a descendant of n2.
-     * 
-     * @param n1
-     *            a descendant of n2
-     * @param n2
-     * @return distance between n1 and n2
-     */
-    private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
-        double d = 0.0;
-        while ( n1 != n2 ) {
-            if ( n1.getDistanceToParent() > 0.0 ) {
-                d += n1.getDistanceToParent();
-            }
-            n1 = n1.getParent();
-        }
-        return d;
+    final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+        return calculateLCA( n1, n2 ).getNodeData().getEvent();
     }
 
     /**
@@ -1014,67 +581,6 @@ public class PhylogenyMethods {
     }
 
     /**
-     * Returns all Nodes which are connected to external PhylogenyNode n of this
-     * Phylogeny by a path containing only speciation events. We call these
-     * "super orthologs". Nodes are returned as Vector of references to Nodes.
-     * <p>
-     * PRECONDITION: This tree must be binary and rooted, and speciation -
-     * duplication need to be assigned for each of its internal Nodes.
-     * <p>
-     * Returns null if this Phylogeny is empty or if n is internal.
-     * @param n
-     *            external PhylogenyNode whose strictly speciation related Nodes
-     *            are to be returned
-     * @return Vector of references to all strictly speciation related Nodes of
-     *         PhylogenyNode n of this Phylogeny, null if this Phylogeny is
-     *         empty or if n is internal
-     */
-    public static List<PhylogenyNode> getSuperOrthologousNodes( final PhylogenyNode n ) {
-        // FIXME
-        PhylogenyNode node = n, deepest = null;
-        final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
-        if ( !node.isExternal() ) {
-            return null;
-        }
-        while ( !node.isRoot() && !node.getParent().isDuplication() ) {
-            node = node.getParent();
-        }
-        deepest = node;
-        deepest.setIndicatorsToZero();
-        do {
-            if ( !node.isExternal() ) {
-                if ( node.getIndicator() == 0 ) {
-                    node.setIndicator( ( byte ) 1 );
-                    if ( !node.isDuplication() ) {
-                        node = node.getChildNode1();
-                    }
-                }
-                if ( node.getIndicator() == 1 ) {
-                    node.setIndicator( ( byte ) 2 );
-                    if ( !node.isDuplication() ) {
-                        node = node.getChildNode2();
-                    }
-                }
-                if ( ( node != deepest ) && ( node.getIndicator() == 2 ) ) {
-                    node = node.getParent();
-                }
-            }
-            else {
-                if ( node != n ) {
-                    v.add( node );
-                }
-                if ( node != deepest ) {
-                    node = node.getParent();
-                }
-                else {
-                    node.setIndicator( ( byte ) 2 );
-                }
-            }
-        } while ( ( node != deepest ) || ( deepest.getIndicator() != 2 ) );
-        return v;
-    }
-
-    /**
      * Convenience method for display purposes.
      * Not intended for algorithms.
      */
@@ -1085,73 +591,23 @@ public class PhylogenyMethods {
         return node.getNodeData().getTaxonomy().getIdentifier().getValue();
     }
 
-    /**
-     * Returns all Nodes which are connected to external PhylogenyNode n of this
-     * Phylogeny by a path containing, and leading to, only duplication events.
-     * We call these "ultra paralogs". Nodes are returned as Vector of
-     * references to Nodes.
-     * <p>
-     * PRECONDITION: This tree must be binary and rooted, and speciation -
-     * duplication need to be assigned for each of its internal Nodes.
-     * <p>
-     * Returns null if this Phylogeny is empty or if n is internal.
-     * <p>
-     * (Last modified: 10/06/01)
-     * 
-     * @param n
-     *            external PhylogenyNode whose ultra paralogs are to be returned
-     * @return Vector of references to all ultra paralogs of PhylogenyNode n of
-     *         this Phylogeny, null if this Phylogeny is empty or if n is
-     *         internal
-     */
-    public static List<PhylogenyNode> getUltraParalogousNodes( final PhylogenyNode n ) {
-        // FIXME test me
-        PhylogenyNode node = n;
-        if ( !node.isExternal() ) {
-            return null;
-        }
-        while ( !node.isRoot() && node.getParent().isDuplication() && areAllChildrenDuplications( node.getParent() ) ) {
-            node = node.getParent();
+    public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
+        if ( n.isExternal() ) {
+            return true;
         }
-        final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
-        nodes.remove( n );
-        return nodes;
-    }
-
-    public static String inferCommonPartOfScientificNameOfDescendants( final PhylogenyNode node ) {
-        final List<PhylogenyNode> descs = node.getDescendants();
-        String sn = null;
-        for( final PhylogenyNode n : descs ) {
-            if ( !n.getNodeData().isHasTaxonomy()
-                    || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
-                return null;
-            }
-            else if ( sn == null ) {
-                sn = n.getNodeData().getTaxonomy().getScientificName().trim();
-            }
-            else {
-                String sn_current = n.getNodeData().getTaxonomy().getScientificName().trim();
-                if ( !sn.equals( sn_current ) ) {
-                    boolean overlap = false;
-                    while ( ( sn.indexOf( ' ' ) >= 0 ) || ( sn_current.indexOf( ' ' ) >= 0 ) ) {
-                        if ( ForesterUtil.countChars( sn, ' ' ) > ForesterUtil.countChars( sn_current, ' ' ) ) {
-                            sn = sn.substring( 0, sn.lastIndexOf( ' ' ) ).trim();
-                        }
-                        else {
-                            sn_current = sn_current.substring( 0, sn_current.lastIndexOf( ' ' ) ).trim();
-                        }
-                        if ( sn.equals( sn_current ) ) {
-                            overlap = true;
-                            break;
-                        }
-                    }
-                    if ( !overlap ) {
-                        return null;
+        else {
+            if ( n.isDuplication() ) {
+                for( final PhylogenyNode desc : n.getDescendants() ) {
+                    if ( !isAllDecendentsAreDuplications( desc ) ) {
+                        return false;
                     }
                 }
+                return true;
+            }
+            else {
+                return false;
             }
         }
-        return sn;
     }
 
     public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
@@ -1183,27 +639,6 @@ public class PhylogenyMethods {
         }
     }
 
-    private static boolean match( final String s,
-                                  final String query,
-                                  final boolean case_sensitive,
-                                  final boolean partial ) {
-        if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
-            return false;
-        }
-        String my_s = s.trim();
-        String my_query = query.trim();
-        if ( !case_sensitive ) {
-            my_s = my_s.toLowerCase();
-            my_query = my_query.toLowerCase();
-        }
-        if ( partial ) {
-            return my_s.indexOf( my_query ) >= 0;
-        }
-        else {
-            return my_s.equals( my_query );
-        }
-    }
-
     public static void midpointRoot( final Phylogeny phylogeny ) {
         if ( phylogeny.getNumberOfExternalNodes() < 2 ) {
             return;
@@ -1237,36 +672,123 @@ public class PhylogenyMethods {
         }
     }
 
-    public static void normalizeBootstrapValues( final Phylogeny phylogeny,
-                                                 final double max_bootstrap_value,
-                                                 final double max_normalized_value ) {
-        for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
-            final PhylogenyNode node = iter.next();
-            if ( node.isInternal() ) {
-                final double confidence = getConfidenceValue( node );
-                if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
-                    if ( confidence >= max_bootstrap_value ) {
-                        setBootstrapConfidence( node, max_normalized_value );
-                    }
-                    else {
-                        setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
+    public static void normalizeBootstrapValues( final Phylogeny phylogeny,
+                                                 final double max_bootstrap_value,
+                                                 final double max_normalized_value ) {
+        for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            if ( node.isInternal() ) {
+                final double confidence = getConfidenceValue( node );
+                if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+                    if ( confidence >= max_bootstrap_value ) {
+                        setBootstrapConfidence( node, max_normalized_value );
+                    }
+                    else {
+                        setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
+                    }
+                }
+            }
+        }
+    }
+
+    public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+        if ( phy.isEmpty() ) {
+            return nodes;
+        }
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            nodes.add( iter.next() );
+        }
+        return nodes;
+    }
+
+    /**
+     * 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,
+     * null is returned.
+     * 
+     */
+    public static SortedMap<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        final SortedMap<Taxonomy, Integer> tax_map = new TreeMap<Taxonomy, Integer>();
+        for( final PhylogenyNode n : descs ) {
+            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+                return null;
+            }
+            final Taxonomy t = n.getNodeData().getTaxonomy();
+            if ( tax_map.containsKey( t ) ) {
+                tax_map.put( t, tax_map.get( t ) + 1 );
+            }
+            else {
+                tax_map.put( t, 1 );
+            }
+        }
+        return tax_map;
+    }
+
+    /**
+     * Arranges the order of childern for each node of this Phylogeny in such a
+     * way that either the branch with more children is on top (right) or on
+     * bottom (left), dependent on the value of boolean order.
+     * 
+     * @param order
+     *            decides in which direction to order
+     * @param pri 
+     */
+    public static void orderAppearance( final PhylogenyNode n,
+                                        final boolean order,
+                                        final boolean order_ext_alphabetically,
+                                        final DESCENDANT_SORT_PRIORITY pri ) {
+        if ( n.isExternal() ) {
+            return;
+        }
+        else {
+            PhylogenyNode temp = null;
+            if ( ( n.getNumberOfDescendants() == 2 )
+                    && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
+                    && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
+                temp = n.getChildNode1();
+                n.setChild1( n.getChildNode2() );
+                n.setChild2( temp );
+            }
+            else if ( order_ext_alphabetically ) {
+                boolean all_ext = true;
+                for( final PhylogenyNode i : n.getDescendants() ) {
+                    if ( !i.isExternal() ) {
+                        all_ext = false;
+                        break;
                     }
                 }
+                if ( all_ext ) {
+                    PhylogenyMethods.sortNodeDescendents( n, pri );
+                }
+            }
+            for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+                orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
             }
         }
     }
 
-    public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
-        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
-        if ( phy.isEmpty() ) {
-            return nodes;
-        }
-        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
-            nodes.add( iter.next() );
-        }
-        return nodes;
-    }
-
     public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
         for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
@@ -1294,6 +816,41 @@ public class PhylogenyMethods {
         }
     }
 
+    public static final void preOrderReId( final Phylogeny phy ) {
+        if ( phy.isEmpty() ) {
+            return;
+        }
+        phy.setIdToNodeMap( null );
+        int i = PhylogenyNode.getNodeCount();
+        for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+            it.next().setId( i++ );
+        }
+        PhylogenyNode.setNodeCount( i );
+    }
+
+    public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
+        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+        final Phylogeny[] trees = factory.create( file, parser );
+        if ( ( trees == null ) || ( trees.length == 0 ) ) {
+            throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+        }
+        return trees;
+    }
+
+    public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
+            throws IOException {
+        final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
+        for( final File file : files ) {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final Phylogeny[] trees = factory.create( file, parser );
+            if ( ( trees == null ) || ( trees.length == 0 ) ) {
+                throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+            }
+            tree_list.addAll( Arrays.asList( trees ) );
+        }
+        return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
+    }
+
     public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
         if ( remove_me.isRoot() ) {
             throw new IllegalArgumentException( "ill advised attempt to remove root node" );
@@ -1587,7 +1144,165 @@ public class PhylogenyMethods {
         if ( !node.getNodeData().isHasTaxonomy() ) {
             node.getNodeData().setTaxonomy( new Taxonomy() );
         }
-        node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
+        node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
+    }
+
+    final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
+        class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                return 0;
+            }
+        }
+        class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                return 0;
+            }
+        }
+        class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                return 0;
+            }
+        }
+        Comparator<PhylogenyNode> c;
+        switch ( pri ) {
+            case SEQUENCE:
+                c = new PhylogenyNodeSortSequencePriority();
+                break;
+            case NODE_NAME:
+                c = new PhylogenyNodeSortNodeNamePriority();
+                break;
+            default:
+                c = new PhylogenyNodeSortTaxonomyPriority();
+        }
+        final List<PhylogenyNode> descs = node.getDescendants();
+        Collections.sort( descs, c );
+        int i = 0;
+        for( final PhylogenyNode desc : descs ) {
+            node.setChildNode( i++, desc );
+        }
     }
 
     /**
@@ -1598,9 +1313,10 @@ public class PhylogenyMethods {
      *            a reference Phylogeny
      * @param to_be_stripped
      *            Phylogeny to be stripped
-     * @return number of external nodes removed from to_be_stripped
+     * @return nodes removed from to_be_stripped
      */
-    public static int taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference, final Phylogeny to_be_stripped ) {
+    public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
+                                                                            final Phylogeny to_be_stripped ) {
         final Set<String> ref_ext_taxo = new HashSet<String>();
         for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
@@ -1615,10 +1331,6 @@ public class PhylogenyMethods {
                 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
             }
         }
-        System.out.println( "  ref_ext_tax:" );
-        for( final String string : ref_ext_taxo ) {
-            System.out.println( string );
-        }
         final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
@@ -1630,59 +1342,237 @@ public class PhylogenyMethods {
                 nodes_to_delete.add( n );
             }
         }
-        System.out.println( "  to delete:" );
-        for( final PhylogenyNode string : nodes_to_delete ) {
-            System.out.println( string.getNodeData().getTaxonomy().getTaxonomyCode() );
-        }
-        for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
-            to_be_stripped.deleteSubtree( phylogenyNode, true );
+        for( final PhylogenyNode n : nodes_to_delete ) {
+            to_be_stripped.deleteSubtree( n, true );
         }
         to_be_stripped.clearHashIdToNodeMap();
         to_be_stripped.externalNodesHaveChanged();
-        return nodes_to_delete.size();
+        return nodes_to_delete;
     }
 
-    /**
-     * Arranges the order of childern for each node of this Phylogeny in such a
-     * way that either the branch with more children is on top (right) or on
-     * bottom (left), dependent on the value of boolean order.
-     * 
-     * @param order
-     *            decides in which direction to order
-     * @param pri 
-     */
-    public static void orderAppearance( final PhylogenyNode n,
-                                        final boolean order,
-                                        final boolean order_ext_alphabetically,
-                                        final DESCENDANT_SORT_PRIORITY pri ) {
-        if ( n.isExternal() ) {
-            return;
+    final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
+                double value = -1;
+                try {
+                    value = Double.parseDouble( n.getName() );
+                }
+                catch ( final NumberFormatException e ) {
+                    throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
+                            + e.getLocalizedMessage() );
+                }
+                if ( value >= 0.0 ) {
+                    n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
+                    n.setName( "" );
+                }
+            }
         }
-        else {
-            PhylogenyNode temp = null;
-            if ( ( n.getNumberOfDescendants() == 2 )
-                    && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
-                    && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
-                temp = n.getChildNode1();
-                n.setChild1( n.getChildNode2() );
-                n.setChild2( temp );
+    }
+
+    final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
+                if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+                    double d = -1.0;
+                    try {
+                        d = Double.parseDouble( n.getName() );
+                    }
+                    catch ( final Exception e ) {
+                        d = -1.0;
+                    }
+                    if ( d >= 0.0 ) {
+                        n.getBranchData().addConfidence( new Confidence( d, "" ) );
+                        n.setName( "" );
+                    }
+                }
             }
-            else if ( order_ext_alphabetically ) {
-                boolean all_ext = true;
-                for( final PhylogenyNode i : n.getDescendants() ) {
-                    if ( !i.isExternal() ) {
-                        all_ext = false;
+        }
+    }
+
+    final static public void transferNodeNameToField( final Phylogeny phy,
+                                                      final PhylogenyNodeField field,
+                                                      final boolean external_only ) throws PhyloXmlDataFormatException {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( external_only && n.isInternal() ) {
+                continue;
+            }
+            final String name = n.getName().trim();
+            if ( !ForesterUtil.isEmpty( name ) ) {
+                switch ( field ) {
+                    case TAXONOMY_CODE:
+                        n.setName( "" );
+                        setTaxonomyCode( n, name );
+                        break;
+                    case TAXONOMY_SCIENTIFIC_NAME:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        n.getNodeData().getTaxonomy().setScientificName( name );
+                        break;
+                    case TAXONOMY_COMMON_NAME:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        n.getNodeData().getTaxonomy().setCommonName( name );
+                        break;
+                    case SEQUENCE_SYMBOL:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasSequence() ) {
+                            n.getNodeData().setSequence( new Sequence() );
+                        }
+                        n.getNodeData().getSequence().setSymbol( name );
+                        break;
+                    case SEQUENCE_NAME:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasSequence() ) {
+                            n.getNodeData().setSequence( new Sequence() );
+                        }
+                        n.getNodeData().getSequence().setName( name );
+                        break;
+                    case TAXONOMY_ID_UNIPROT_1: {
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        String id = name;
+                        final int i = name.indexOf( '_' );
+                        if ( i > 0 ) {
+                            id = name.substring( 0, i );
+                        }
+                        else {
+                            n.setName( "" );
+                        }
+                        n.getNodeData().getTaxonomy()
+                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+                        break;
+                    }
+                    case TAXONOMY_ID_UNIPROT_2: {
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        String id = name;
+                        final int i = name.indexOf( '_' );
+                        if ( i > 0 ) {
+                            id = name.substring( i + 1, name.length() );
+                        }
+                        else {
+                            n.setName( "" );
+                        }
+                        n.getNodeData().getTaxonomy()
+                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+                        break;
+                    }
+                    case TAXONOMY_ID: {
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
                         break;
                     }
                 }
-                if ( all_ext ) {
-                    PhylogenyMethods.sortNodeDescendents( n, pri );
+            }
+        }
+    }
+
+    static double addPhylogenyDistances( final double a, final double b ) {
+        if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
+            return a + b;
+        }
+        else if ( a >= 0.0 ) {
+            return a;
+        }
+        else if ( b >= 0.0 ) {
+            return b;
+        }
+        return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
+    }
+
+    /**
+     * Deep copies the phylogeny originating from this node.
+     */
+    static PhylogenyNode copySubTree( final PhylogenyNode source ) {
+        if ( source == null ) {
+            return null;
+        }
+        else {
+            final PhylogenyNode newnode = source.copyNodeData();
+            if ( !source.isExternal() ) {
+                for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
+                    newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
                 }
             }
-            for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
-                orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
+            return newnode;
+        }
+    }
+
+    /**
+     * Shallow copies the phylogeny originating from this node.
+     */
+    static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
+        if ( source == null ) {
+            return null;
+        }
+        else {
+            final PhylogenyNode newnode = source.copyNodeDataShallow();
+            if ( !source.isExternal() ) {
+                for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
+                    newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
+                }
+            }
+            return newnode;
+        }
+    }
+
+    /**
+     * Calculates the distance between PhylogenyNodes n1 and n2.
+     * PRECONDITION: n1 is a descendant of n2.
+     * 
+     * @param n1
+     *            a descendant of n2
+     * @param n2
+     * @return distance between n1 and n2
+     */
+    private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
+        double d = 0.0;
+        while ( n1 != n2 ) {
+            if ( n1.getDistanceToParent() > 0.0 ) {
+                d += n1.getDistanceToParent();
             }
+            n1 = n1.getParent();
         }
+        return d;
+    }
+
+    private static boolean match( final String s,
+                                  final String query,
+                                  final boolean case_sensitive,
+                                  final boolean partial ) {
+        if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
+            return false;
+        }
+        String my_s = s.trim();
+        String my_query = query.trim();
+        if ( !case_sensitive ) {
+            my_s = my_s.toLowerCase();
+            my_query = my_query.toLowerCase();
+        }
+        if ( partial ) {
+            return my_s.indexOf( my_query ) >= 0;
+        }
+        else {
+            return my_s.equals( my_query );
+        }
+    }
+
+    public static enum DESCENDANT_SORT_PRIORITY {
+        TAXONOMY, SEQUENCE, NODE_NAME;
     }
 
     public static enum PhylogenyNodeField {
@@ -1696,12 +1586,4 @@ public class PhylogenyMethods {
         TAXONOMY_ID_UNIPROT_2,
         TAXONOMY_ID;
     }
-
-    public static enum TAXONOMY_EXTRACTION {
-        NO, YES, PFAM_STYLE_ONLY;
-    }
-
-    public static enum DESCENDANT_SORT_PRIORITY {
-        TAXONOMY, SEQUENCE, NODE_NAME;
-    }
 }