X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=97eba29cd3af458cc6b0e9f00100cd02329bbba1;hb=f507bf348ffed906d04bc76a614d6778d4cb5d64;hp=2d238a2fa9df628e5afa2ecdc2b726a035d1635e;hpb=619edf1dd8026422bf60d9d746947559cad4be28;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 2d238a2..97eba29 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -21,209 +21,222 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.phylogeny;
 
 import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
 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;
+import java.util.Map;
 import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+import org.forester.archaeopteryx.TreePanelUtil;
+import org.forester.io.parsers.FastaParser;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.msa.Msa;
+import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.BranchWidth;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.DomainArchitecture;
+import org.forester.phylogeny.data.Event;
+import org.forester.phylogeny.data.Identifier;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
+import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 import org.forester.util.FailedConditionCheckException;
 import org.forester.util.ForesterUtil;
+import org.forester.util.TaxonomyUtil;
 
 public class PhylogenyMethods {
 
-    private static PhylogenyMethods _instance      = null;
-    private final Set<Integer>      _temp_hash_set = new HashSet<Integer>();
-    private PhylogenyNode           _farthest_1    = null;
-    private PhylogenyNode           _farthest_2    = null;
+    private static boolean _order_changed;
 
     private PhylogenyMethods() {
         // Hidden constructor.
     }
 
-    /**
-     * Calculates the distance between PhylogenyNodes node1 and node2.
-     * 
-     * 
-     * @param node1
-     * @param node2
-     * @return distance between node1 and node2
-     */
-    public double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        final PhylogenyNode lca = obtainLCA( node1, node2 );
-        final PhylogenyNode n1 = node1;
-        final PhylogenyNode n2 = node2;
-        return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
+    @Override
+    public Object clone() throws CloneNotSupportedException {
+        throw new CloneNotSupportedException();
     }
 
-    public double calculateFurthestDistance( final Phylogeny phylogeny ) {
-        if ( phylogeny.getNumberOfExternalNodes() < 2 ) {
-            return 0.0;
-        }
-        _farthest_1 = null;
-        _farthest_2 = null;
-        PhylogenyNode node_1 = null;
-        PhylogenyNode node_2 = null;
-        double farthest_d = -Double.MAX_VALUE;
-        final PhylogenyMethods methods = PhylogenyMethods.getInstance();
-        final List<PhylogenyNode> ext_nodes = phylogeny.getRoot().getAllExternalDescendants();
-        for( int i = 1; i < ext_nodes.size(); ++i ) {
-            for( int j = 0; j < i; ++j ) {
-                final double d = methods.calculateDistance( ext_nodes.get( i ), ext_nodes.get( j ) );
-                if ( d < 0.0 ) {
-                    throw new RuntimeException( "distance cannot be negative" );
-                }
-                if ( d > farthest_d ) {
-                    farthest_d = d;
-                    node_1 = ext_nodes.get( i );
-                    node_2 = ext_nodes.get( j );
+    public static boolean extractFastaInformation( final Phylogeny phy ) {
+        boolean could_extract = false;
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            if ( !ForesterUtil.isEmpty( node.getName() ) ) {
+                final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
+                if ( name_m.lookingAt() ) {
+                    could_extract = true;
+                    final String acc_source = name_m.group( 1 );
+                    final String acc = name_m.group( 2 );
+                    final String seq_name = name_m.group( 3 );
+                    final String tax_sn = name_m.group( 4 );
+                    if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
+                        ForesterUtil.ensurePresenceOfSequence( node );
+                        node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
+                    }
+                    if ( !ForesterUtil.isEmpty( seq_name ) ) {
+                        ForesterUtil.ensurePresenceOfSequence( node );
+                        node.getNodeData().getSequence( 0 ).setName( seq_name );
+                    }
+                    if ( !ForesterUtil.isEmpty( tax_sn ) ) {
+                        ForesterUtil.ensurePresenceOfTaxonomy( node );
+                        node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
+                    }
                 }
             }
         }
-        _farthest_1 = node_1;
-        _farthest_2 = node_2;
-        return farthest_d;
-    }
-
-    @Override
-    public Object clone() throws CloneNotSupportedException {
-        throw new CloneNotSupportedException();
+        return could_extract;
     }
 
-    public PhylogenyNode getFarthestNode1() {
-        return _farthest_1;
+    public static DescriptiveStatistics calculateBranchLengthStatistics( 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 PhylogenyNode getFarthestNode2() {
-        return _farthest_2;
+    public static List<DescriptiveStatistics> calculateConfidenceStatistics( 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 LCA of PhylogenyNodes node1 and node2.
-     * 
-     * 
+     * Calculates the distance between PhylogenyNodes node1 and node2.
+     *
+     *
      * @param node1
      * @param node2
-     * @return LCA of node1 and node2
+     * @return distance between node1 and node2
      */
-    public PhylogenyNode obtainLCA( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        _temp_hash_set.clear();
-        PhylogenyNode n1 = node1;
-        PhylogenyNode n2 = node2;
-        _temp_hash_set.add( n1.getId() );
-        while ( !n1.isRoot() ) {
-            n1 = n1.getParent();
-            _temp_hash_set.add( n1.getId() );
-        }
-        while ( !_temp_hash_set.contains( n2.getId() ) && !n2.isRoot() ) {
-            n2 = n2.getParent();
-        }
-        if ( !_temp_hash_set.contains( n2.getId() ) ) {
-            throw new IllegalArgumentException( "attempt to get LCA of two nodes which do not share a common root" );
-        }
-        return n2;
+    public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
+        final PhylogenyNode lca = calculateLCA( node1, node2 );
+        final PhylogenyNode n1 = node1;
+        final PhylogenyNode n2 = node2;
+        return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
     }
 
     /**
-     * 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.
+     *
+     *
+     * @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 );
-            }
-        }
-        return nodes;
-    }
-
-    public boolean isAreOrthologous( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        return !obtainLCA( node1, node2 ).isDuplication();
-    }
-
-    static double addPhylogenyDistances( final double a, final double b ) {
-        if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
-            return a + b;
+    public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == null ) {
+            throw new IllegalArgumentException( "first argument (node) is null" );
         }
-        else if ( a >= 0.0 ) {
-            return a;
+        if ( node2 == null ) {
+            throw new IllegalArgumentException( "second argument (node) is null" );
         }
-        else if ( b >= 0.0 ) {
-            return b;
+        if ( node1 == node2 ) {
+            return node1;
         }
-        return PhylogenyNode.DISTANCE_DEFAULT;
-    }
-
-    // Helper for getUltraParalogousNodes( PhylogenyNode ).
-    public static boolean areAllChildrenDuplications( final PhylogenyNode n ) {
-        if ( n.isExternal() ) {
-            return false;
+        if ( ( node1.getParent() == node2.getParent() ) ) {
+            return node1.getParent();
         }
-        else {
-            if ( n.isDuplication() ) {
-                //FIXME test me!
-                for( final PhylogenyNode desc : n.getDescendants() ) {
-                    if ( !areAllChildrenDuplications( desc ) ) {
-                        return false;
-                    }
-                }
-                return true;
+        int depth1 = node1.calculateDepth();
+        int depth2 = node2.calculateDepth();
+        while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {
+            if ( depth1 > depth2 ) {
+                node1 = node1.getParent();
+                depth1--;
+            }
+            else if ( depth2 > depth1 ) {
+                node2 = node2.getParent();
+                depth2--;
             }
             else {
-                return false;
+                if ( node1 == node2 ) {
+                    return node1;
+                }
+                node1 = node1.getParent();
+                node2 = node2.getParent();
+                depth1--;
+                depth2--;
             }
         }
+        throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
     }
 
-    public static int calculateDepth( final PhylogenyNode node ) {
-        PhylogenyNode n = node;
-        int steps = 0;
-        while ( !n.isRoot() ) {
-            steps++;
-            n = n.getParent();
+    /**
+     * 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 final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == null ) {
+            throw new IllegalArgumentException( "first argument (node) is null" );
         }
-        return steps;
-    }
-
-    public static double calculateDistanceToRoot( final PhylogenyNode node ) {
-        PhylogenyNode n = node;
-        double d = 0.0;
-        while ( !n.isRoot() ) {
-            if ( n.getDistanceToParent() > 0.0 ) {
-                d += n.getDistanceToParent();
+        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();
             }
-            n = n.getParent();
         }
-        return d;
+        return node1;
     }
 
     public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
@@ -253,7 +266,48 @@ public class PhylogenyMethods {
         int max = 0;
         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
-            final int steps = calculateDepth( node );
+            final int steps = node.calculateDepth();
+            if ( steps > max ) {
+                max = steps;
+            }
+        }
+        return max;
+    }
+    
+    public static String[] obtainPresentRanksSorted( final Phylogeny phy ) {
+        final Set<String> present_ranks = new HashSet<String>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            if ( !node.isExternal() && !node.isRoot() && ( node.getNodeData().getTaxonomy() != null )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getRank() ) ) {
+                final String current_rank = node.getNodeData().getTaxonomy().getRank();
+                if ( TaxonomyUtil.RANK_TO_INT.containsKey( current_rank ) ) {
+                    present_ranks.add( current_rank );
+                }
+            }
+        }
+        final String ordered_ranks[] = new String[present_ranks.size() + 1];
+        int c = 0;
+        for( final String rank : TaxonomyUtil.RANKS ) {
+             if ( present_ranks.contains( rank ) ) {
+                 ordered_ranks[ c++ ] = rank;
+             }
+        }
+        ordered_ranks[ c ] = "off";
+        return ordered_ranks;
+    }
+
+    public static int calculateMaxDepthConsiderCollapsed( final Phylogeny phy ) {
+        int max = 0;
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            PhylogenyNode n = iter.next();
+            int steps = 0;
+            while ( n.getParent() != null ) {
+                if ( !n.isCollapse() ) {
+                    steps++;
+                }
+                n = n.getParent();
+            }
             if ( steps > max ) {
                 max = steps;
             }
@@ -265,7 +319,7 @@ public class PhylogenyMethods {
         double max = 0.0;
         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
-            final double d = calculateDistanceToRoot( node );
+            final double d = node.calculateDistanceToRoot();
             if ( d > max ) {
                 max = d;
             }
@@ -273,166 +327,112 @@ public class PhylogenyMethods {
         return max;
     }
 
-    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() );
+    public static PhylogenyNode calculateNodeWithMaxDistanceToRoot( final Phylogeny phy ) {
+        double max = 0.0;
+        PhylogenyNode max_node = phy.getFirstExternalNode();
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            final double d = node.calculateDistanceToRoot();
+            if ( d > max ) {
+                max = d;
+                max_node = node;
             }
         }
-        return stats;
+        return max_node;
+    }
+
+    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;
     }
 
-    public static DescriptiveStatistics calculatConfidenceStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculateNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( !n.isExternal() ) {
-                if ( n.getBranchData().isHasConfidences() ) {
-                    stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
-                }
+                stats.addValue( n.getNumberOfDescendants() );
             }
         }
         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() );
+    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 ) );
         }
-        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 );
-            }
+        for( int i = 0; i < eds.size(); ++i ) {
+            n.setChildNode( i, eds.get( i ) );
+            eds.get( i ).setDistanceToParent( d.get( i ) );
         }
-        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++;
+    public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
+        int count = 0;
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {
+                count++;
             }
         }
-        return x;
+        return count;
     }
 
-    /**
-     * 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 ) ) );
-                }
+    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 newnode;
         }
+        return count;
     }
 
-    /**
-     * 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 final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
+        final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
+        final List<PhylogenyNode> ext = phy.getExternalNodes();
+        for( final PhylogenyNode n : ext ) {
+            nodes.put( n.getName(), n );
         }
+        return nodes;
     }
 
-    public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
-        phy.hashIDs();
-        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.hashIDs();
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
     }
 
     public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
             throws IllegalArgumentException {
-        for( int i = 0; i < node_names_to_delete.length; ++i ) {
-            if ( ForesterUtil.isEmpty( node_names_to_delete[ i ] ) ) {
+        for( final String element : node_names_to_delete ) {
+            if ( ForesterUtil.isEmpty( element ) ) {
                 continue;
             }
             List<PhylogenyNode> nodes = null;
-            nodes = p.getNodes( node_names_to_delete[ i ] );
+            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 \""
-                            + node_names_to_delete[ i ] + "\"" );
+                    throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
                 }
                 p.deleteSubtree( n, true );
             }
         }
-    }
-
-    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.hashIDs();
-        phy.externalNodesHaveChanged();
-        //  deleteExternalNodesNegativeSelection( to_delete, phy );
+        p.clearHashIdToNodeMap();
+        p.externalNodesHaveChanged();
     }
 
     public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
@@ -457,31 +457,101 @@ public class PhylogenyMethods {
         return deleted;
     }
 
-    public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
-        final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
-        final Set<Integer> encountered = new HashSet<Integer>();
-        if ( !node.isExternal() ) {
-            final List<PhylogenyNode> exts = node.getAllExternalDescendants();
-            for( PhylogenyNode current : exts ) {
-                descs.add( current );
-                while ( current != node ) {
-                    current = current.getParent();
-                    if ( encountered.contains( current.getId() ) ) {
-                        continue;
-                    }
-                    descs.add( current );
-                    encountered.add( current.getId() );
+    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" );
+            }
         }
-        return descs;
+        deleteExternalNodesNegativeSelection( to_delete, phy );
     }
 
-    /**
-     * 
-     * Convenience method
-     * 
-     * @param node
+    final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
+        final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {
+                to_delete.add( n );
+            }
+        }
+        for( final PhylogenyNode d : to_delete ) {
+            PhylogenyMethods.removeNode( d, phy );
+        }
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
+    }
+
+    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 final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,
+                                                                      final double min_distance_to_root ) {
+        if ( min_distance_to_root <= 0 ) {
+            throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );
+        }
+        final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();
+        setAllIndicatorsToZero( phy );
+        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getIndicator() != 0 ) {
+                continue;
+            }
+            l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
+            if ( l.isEmpty() ) {
+                throw new RuntimeException( "this should not have happened" );
+            }
+        }
+        return l;
+    }
+
+    public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
+        final Set<Long> encountered = new HashSet<Long>();
+        if ( !node.isExternal() ) {
+            final List<PhylogenyNode> exts = node.getAllExternalDescendants();
+            for( PhylogenyNode current : exts ) {
+                descs.add( current );
+                while ( current != node ) {
+                    current = current.getParent();
+                    if ( encountered.contains( current.getId() ) ) {
+                        continue;
+                    }
+                    descs.add( current );
+                    encountered.add( current.getId() );
+                }
+            }
+        }
+        return descs;
+    }
+
+    /**
+     *
+     * Convenience method
+     *
+     * @param node
      * @return
      */
     public static Color getBranchColorValue( final PhylogenyNode node ) {
@@ -526,30 +596,14 @@ 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();
     }
 
     /**
-     * Returns taxonomy t if all external descendants have 
+     * Returns taxonomy t if all external descendants have
      * the same taxonomy t, null otherwise.
-     * 
+     *
      */
     public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {
         final List<PhylogenyNode> descs = node.getAllExternalDescendants();
@@ -581,13 +635,12 @@ public class PhylogenyMethods {
         return farthest;
     }
 
-    public static PhylogenyMethods getInstance() {
-        if ( PhylogenyMethods._instance == null ) {
-            PhylogenyMethods._instance = new PhylogenyMethods();
-        }
-        return PhylogenyMethods._instance;
-    }
-
+    // public static PhylogenyMethods getInstance() {
+    //     if ( PhylogenyMethods._instance == null ) {
+    //         PhylogenyMethods._instance = new PhylogenyMethods();
+    //    }
+    //    return PhylogenyMethods._instance;
+    //  }
     /**
      * Returns the largest confidence value found on phy.
      */
@@ -626,79 +679,18 @@ public class PhylogenyMethods {
         if ( !node.getNodeData().isHasTaxonomy() ) {
             return "";
         }
-        if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
-            return node.getNodeData().getTaxonomy().getTaxonomyCode();
-        }
         else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
             return node.getNodeData().getTaxonomy().getScientificName();
         }
+        if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+            return node.getNodeData().getTaxonomy().getTaxonomyCode();
+        }
         else {
             return node.getNodeData().getTaxonomy().getCommonName();
         }
     }
 
     /**
-     * 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.
      */
@@ -709,73 +701,23 @@ 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 ) {
@@ -789,7 +731,7 @@ public class PhylogenyMethods {
 
     /*
      * This is case insensitive.
-     * 
+     *
      */
     public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
                                                                                final String[] providers ) {
@@ -807,58 +749,45 @@ 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;
-        }
-        final PhylogenyMethods methods = getInstance();
-        final double farthest_d = methods.calculateFurthestDistance( phylogeny );
-        final PhylogenyNode f1 = methods.getFarthestNode1();
-        final PhylogenyNode f2 = methods.getFarthestNode2();
-        if ( farthest_d <= 0.0 ) {
+        if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {
             return;
         }
-        double x = farthest_d / 2.0;
-        PhylogenyNode n = f1;
-        if ( PhylogenyMethods.getDistance( f1, phylogeny.getRoot() ) < PhylogenyMethods.getDistance( f2, phylogeny
-                .getRoot() ) ) {
-            n = f2;
-        }
-        while ( ( x > n.getDistanceToParent() ) && !n.isRoot() ) {
-            x -= ( n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0 );
-            n = n.getParent();
+        int counter = 0;
+        final int total_nodes = phylogeny.getNodeCount();
+        while ( true ) {
+            if ( ++counter > total_nodes ) {
+                throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );
+            }
+            PhylogenyNode a = null;
+            double da = 0;
+            double db = 0;
+            for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {
+                final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );
+                final double df = getDistance( f, phylogeny.getRoot() );
+                if ( df > 0 ) {
+                    if ( df > da ) {
+                        db = da;
+                        da = df;
+                        a = f;
+                    }
+                    else if ( df > db ) {
+                        db = df;
+                    }
+                }
+            }
+            final double diff = da - db;
+            if ( diff < 0.000001 ) {
+                break;
+            }
+            double x = da - ( diff / 2.0 );
+            while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {
+                x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );
+                a = a.getParent();
+            }
+            phylogeny.reRoot( a, x );
         }
-        phylogeny.reRoot( n, x );
         phylogeny.recalculateNumberOfExternalDescendants( true );
-        final PhylogenyNode a = getFurthestDescendant( phylogeny.getRoot().getChildNode1() );
-        final PhylogenyNode b = getFurthestDescendant( phylogeny.getRoot().getChildNode2() );
-        final double da = getDistance( a, phylogeny.getRoot() );
-        final double db = getDistance( b, phylogeny.getRoot() );
-        if ( Math.abs( da - db ) > 0.000001 ) {
-            throw new FailedConditionCheckException( "this should not have happened: midpoint rooting failed:  da="
-                    + da + ",  db=" + db + ",  diff=" + Math.abs( da - db ) );
-        }
     }
 
     public static void normalizeBootstrapValues( final Phylogeny phylogeny,
@@ -891,6 +820,90 @@ public class PhylogenyMethods {
         return nodes;
     }
 
+    /**
+     * 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 Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        final Map<Taxonomy, Integer> tax_map = new HashMap<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 {
+            if ( ( n.getNumberOfDescendants() == 2 )
+                    && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
+                    && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2()
+                            .getNumberOfExternalNodes() ) == order ) ) {
+                final PhylogenyNode temp = n.getChildNode1();
+                n.setChild1( n.getChildNode2() );
+                n.setChild2( temp );
+                _order_changed = true;
+            }
+            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 synchronized static void orderAppearanceX( final PhylogenyNode n,
+                                                      final boolean order_ext_alphabetically,
+                                                      final DESCENDANT_SORT_PRIORITY pri ) {
+        if ( n.isExternal() ) {
+            return;
+        }
+        else {
+            _order_changed = false;
+            orderAppearance( n, true, order_ext_alphabetically, pri );
+            if ( !_order_changed ) {
+                orderAppearance( n, false, order_ext_alphabetically, pri );
+            }
+        }
+    }
+
     public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
         for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
@@ -899,8 +912,9 @@ public class PhylogenyMethods {
             double blue = 0.0;
             int n = 0;
             if ( node.isInternal() ) {
-                for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
-                    final PhylogenyNode child_node = iterator.next();
+                //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
+                for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+                    final PhylogenyNode child_node = node.getChildNode( i );
                     final Color child_color = getBranchColorValue( child_node );
                     if ( child_color != null ) {
                         ++n;
@@ -917,12 +931,60 @@ public class PhylogenyMethods {
         }
     }
 
+    public static final void preOrderReId( final Phylogeny phy ) {
+        if ( phy.isEmpty() ) {
+            return;
+        }
+        phy.setIdToNodeMap( null );
+        long 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" );
+            if ( remove_me.getNumberOfDescendants() == 1 ) {
+                final PhylogenyNode desc = remove_me.getDescendants().get( 0 );
+                desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
+                                                                 desc.getDistanceToParent() ) );
+                desc.setParent( null );
+                phylogeny.setRoot( desc );
+                phylogeny.clearHashIdToNodeMap();
+            }
+            else {
+                throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );
+            }
         }
-        if ( remove_me.isExternal() ) {
+        else if ( remove_me.isExternal() ) {
             phylogeny.deleteSubtree( remove_me, false );
+            phylogeny.clearHashIdToNodeMap();
+            phylogeny.externalNodesHaveChanged();
         }
         else {
             final PhylogenyNode parent = remove_me.getParent();
@@ -934,216 +996,418 @@ public class PhylogenyMethods {
                                                                  desc.getDistanceToParent() ) );
             }
             remove_me.setParent( null );
-            phylogeny.setIdHash( null );
+            phylogeny.clearHashIdToNodeMap();
             phylogeny.externalNodesHaveChanged();
         }
     }
 
-    public static List<PhylogenyNode> searchData( final String query,
-                                                  final Phylogeny phy,
-                                                  final boolean case_sensitive,
-                                                  final boolean partial ) {
-        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+    private static enum NDF {
+                             NodeName( "NN" ),
+                             TaxonomyCode( "TC" ),
+                             TaxonomyCommonName( "CN" ),
+                             TaxonomyScientificName( "TS" ),
+                             TaxonomyIdentifier( "TI" ),
+                             TaxonomySynonym( "SY" ),
+                             SequenceName( "SN" ),
+                             GeneName( "GN" ),
+                             SequenceSymbol( "SS" ),
+                             SequenceAccession( "SA" ),
+                             Domain( "DO" ),
+                             Annotation( "AN" ),
+                             CrossRef( "XR" ),
+                             BinaryCharacter( "BC" ),
+                             MolecularSequence( "MS" );
+
+        private final String _text;
+
+        NDF( final String text ) {
+            _text = text;
+        }
+
+        public static NDF fromString( final String text ) {
+            for( final NDF n : NDF.values() ) {
+                if ( text.startsWith( n._text ) ) {
+                    return n;
+                }
+            }
+            return null;
+        }
+    }
+
+    public static List<Long> searchData( final String query,
+                                         final Phylogeny phy,
+                                         final boolean case_sensitive,
+                                         final boolean partial,
+                                         final boolean regex,
+                                         final boolean search_domains,
+                                         final double domains_confidence_threshold ) {
+        final List<Long> nodes = new ArrayList<Long>();
         if ( phy.isEmpty() || ( query == null ) ) {
             return nodes;
         }
         if ( ForesterUtil.isEmpty( query ) ) {
             return nodes;
         }
+        String my_query = query;
+        NDF ndf = null;
+        if ( ( my_query.length() > 2 ) && ( my_query.indexOf( ":" ) == 2 ) ) {
+            ndf = NDF.fromString( my_query );
+            if ( ndf != null ) {
+                my_query = my_query.substring( 3 );
+            }
+        }
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             boolean match = false;
-            if ( match( node.getName(), query, case_sensitive, partial ) ) {
+            if ( ( ( ndf == null ) || ( ndf == NDF.NodeName ) )
+                    && match( node.getName(), my_query, case_sensitive, partial, regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
-                    && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCode ) ) && node.getNodeData().isHasTaxonomy()
+                    && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
-                    && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCommonName ) ) && node.getNodeData().isHasTaxonomy()
+                    && match( node.getNodeData().getTaxonomy().getCommonName(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
-                    && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyScientificName ) ) && node.getNodeData().isHasTaxonomy()
+                    && match( node.getNodeData().getTaxonomy().getScientificName(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyIdentifier ) ) && node.getNodeData().isHasTaxonomy()
                     && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
                     && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
-                              query,
+                              my_query,
                               case_sensitive,
-                              partial ) ) {
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomySynonym ) ) && node.getNodeData().isHasTaxonomy()
+                    && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
                 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
                 I: for( final String syn : syns ) {
-                    if ( match( syn, query, case_sensitive, partial ) ) {
+                    if ( match( syn, my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break I;
                     }
                 }
             }
-            if ( !match && node.getNodeData().isHasSequence()
-                    && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceName ) ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getName(), my_query, case_sensitive, partial, regex ) ) {
                 match = true;
             }
-            if ( !match && node.getNodeData().isHasSequence()
-                    && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.GeneName ) ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getGeneName(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            if ( !match
-                    && node.getNodeData().isHasSequence()
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceSymbol ) ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getSymbol(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
+                match = true;
+            }
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceAccession ) ) && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getAccession() != null )
                     && match( node.getNodeData().getSequence().getAccession().getValue(),
-                              query,
+                              my_query,
                               case_sensitive,
-                              partial ) ) {
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            if ( !match && node.getNodeData().isHasSequence()
+            if ( !match && ( ( ( ndf == null ) && search_domains ) || ( ndf == NDF.Domain ) )
+                    && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
                 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
-                    if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
+                    if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold )
+                            && ( match( da.getDomain( i ).getName(), my_query, case_sensitive, partial, regex ) ) ) {
                         match = true;
                         break I;
                     }
                 }
             }
-            if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
-                final String[] bcp_ary = node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringArray();
-                I: for( final String bc : bcp_ary ) {
-                    if ( match( bc, query, case_sensitive, partial ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.Annotation ) ) && node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+                for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+                    if ( match( ann.getDesc(), my_query, case_sensitive, partial, regex ) ) {
+                        match = true;
+                        break;
+                    }
+                    if ( match( ann.getRef(), my_query, case_sensitive, partial, regex ) ) {
+                        match = true;
+                        break;
+                    }
+                }
+            }
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.CrossRef ) ) && node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+                for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+                    if ( match( x.getComment(), my_query, case_sensitive, partial, regex ) ) {
+                        match = true;
+                        break;
+                    }
+                    if ( match( x.getSource(), my_query, case_sensitive, partial, regex ) ) {
+                        match = true;
+                        break;
+                    }
+                    if ( match( x.getValue(), my_query, case_sensitive, partial, regex ) ) {
+                        match = true;
+                        break;
+                    }
+                }
+            }
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.BinaryCharacter ) )
+                    && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+                Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+                I: while ( it.hasNext() ) {
+                    if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break I;
                     }
                 }
-                final String[] bcg_ary = node.getNodeData().getBinaryCharacters().getGainedCharactersAsStringArray();
-                I: for( final String bc : bcg_ary ) {
-                    if ( match( bc, query, case_sensitive, partial ) ) {
+                it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+                I: while ( it.hasNext() ) {
+                    if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break I;
                     }
                 }
             }
+            if ( !match && ( ndf == NDF.MolecularSequence ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getMolecularSequence(),
+                              my_query,
+                              case_sensitive,
+                              true,
+                              regex ) ) {
+                match = true;
+            }
             if ( match ) {
-                nodes.add( node );
+                nodes.add( node.getId() );
             }
         }
         return nodes;
     }
 
-    public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
-                                                            final Phylogeny phy,
-                                                            final boolean case_sensitive,
-                                                            final boolean partial ) {
-        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+    public static List<Long> searchDataLogicalAnd( final String[] queries,
+                                                   final Phylogeny phy,
+                                                   final boolean case_sensitive,
+                                                   final boolean partial,
+                                                   final boolean search_domains,
+                                                   final double domains_confidence_threshold ) {
+        final List<Long> nodes = new ArrayList<Long>();
         if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
             return nodes;
         }
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             boolean all_matched = true;
-            for( final String query : queries ) {
+            for( String query : queries ) {
+                if ( query == null ) {
+                    continue;
+                }
+                query = query.trim();
+                NDF ndf = null;
+                if ( ( query.length() > 2 ) && ( query.indexOf( ":" ) == 2 ) ) {
+                    ndf = NDF.fromString( query );
+                    if ( ndf != null ) {
+                        query = query.substring( 3 );
+                    }
+                }
                 boolean match = false;
                 if ( ForesterUtil.isEmpty( query ) ) {
                     continue;
                 }
-                if ( match( node.getName(), query, case_sensitive, partial ) ) {
+                if ( ( ( ndf == null ) || ( ndf == NDF.NodeName ) )
+                        && match( node.getName(), query, case_sensitive, partial, false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
-                        && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCode ) ) && node.getNodeData().isHasTaxonomy()
+                        && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
+                                  query,
+                                  case_sensitive,
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
-                        && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCommonName ) ) && node.getNodeData().isHasTaxonomy()
+                        && match( node.getNodeData().getTaxonomy().getCommonName(),
+                                  query,
+                                  case_sensitive,
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
-                        && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyScientificName ) )
+                        && node.getNodeData().isHasTaxonomy()
+                        && match( node.getNodeData().getTaxonomy().getScientificName(),
+                                  query,
+                                  case_sensitive,
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyIdentifier ) ) && node.getNodeData().isHasTaxonomy()
                         && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
                         && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
                                   query,
                                   case_sensitive,
-                                  partial ) ) {
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomySynonym ) ) && node.getNodeData().isHasTaxonomy()
                         && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
                     final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
                     I: for( final String syn : syns ) {
-                        if ( match( syn, query, case_sensitive, partial ) ) {
+                        if ( match( syn, query, case_sensitive, partial, false ) ) {
                             match = true;
                             break I;
                         }
                     }
                 }
-                if ( !match && node.getNodeData().isHasSequence()
-                        && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceName ) ) && node.getNodeData().isHasSequence()
+                        && match( node.getNodeData().getSequence().getName(),
+                                  query,
+                                  case_sensitive,
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                if ( !match && node.getNodeData().isHasSequence()
-                        && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.GeneName ) ) && node.getNodeData().isHasSequence()
+                        && match( node.getNodeData().getSequence().getGeneName(),
+                                  query,
+                                  case_sensitive,
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                if ( !match
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceSymbol ) )
+                        && node.getNodeData().isHasSequence() && match( node.getNodeData().getSequence().getSymbol(),
+                                                                        query,
+                                                                        case_sensitive,
+                                                                        partial,
+                                                                        false ) ) {
+                    match = true;
+                }
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceAccession ) )
                         && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getAccession() != null )
                         && match( node.getNodeData().getSequence().getAccession().getValue(),
                                   query,
                                   case_sensitive,
-                                  partial ) ) {
+                                  partial,
+                                  false ) ) {
                     match = true;
                 }
-                if ( !match && node.getNodeData().isHasSequence()
+                if ( !match && ( ( ( ndf == null ) && search_domains ) || ( ndf == NDF.Domain ) )
+                        && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                     final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
                     I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
-                        if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
+                        if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold )
+                                && match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) {
                             match = true;
                             break I;
                         }
                     }
                 }
-                if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
-                    final String[] bcp_ary = node.getNodeData().getBinaryCharacters()
-                            .getPresentCharactersAsStringArray();
-                    I: for( final String bc : bcp_ary ) {
-                        if ( match( bc, query, case_sensitive, partial ) ) {
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.Annotation ) ) && node.getNodeData().isHasSequence()
+                        && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+                    for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+                        if ( match( ann.getDesc(), query, case_sensitive, partial, false ) ) {
+                            match = true;
+                            break;
+                        }
+                        if ( match( ann.getRef(), query, case_sensitive, partial, false ) ) {
+                            match = true;
+                            break;
+                        }
+                    }
+                }
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.CrossRef ) ) && node.getNodeData().isHasSequence()
+                        && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+                    for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+                        if ( match( x.getComment(), query, case_sensitive, partial, false ) ) {
+                            match = true;
+                            break;
+                        }
+                        if ( match( x.getSource(), query, case_sensitive, partial, false ) ) {
+                            match = true;
+                            break;
+                        }
+                        if ( match( x.getValue(), query, case_sensitive, partial, false ) ) {
+                            match = true;
+                            break;
+                        }
+                    }
+                }
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.BinaryCharacter ) )
+                        && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+                    Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+                    I: while ( it.hasNext() ) {
+                        if ( match( it.next(), query, case_sensitive, partial, false ) ) {
                             match = true;
                             break I;
                         }
                     }
-                    final String[] bcg_ary = node.getNodeData().getBinaryCharacters()
-                            .getGainedCharactersAsStringArray();
-                    I: for( final String bc : bcg_ary ) {
-                        if ( match( bc, query, case_sensitive, partial ) ) {
+                    it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+                    I: while ( it.hasNext() ) {
+                        if ( match( it.next(), query, case_sensitive, partial, false ) ) {
                             match = true;
                             break I;
                         }
                     }
                 }
+                if ( !match && ( ndf == NDF.MolecularSequence ) && node.getNodeData().isHasSequence()
+                        && match( node.getNodeData().getSequence().getMolecularSequence(),
+                                  query,
+                                  case_sensitive,
+                                  true,
+                                  false ) ) {
+                    match = true;
+                }
                 if ( !match ) {
                     all_matched = false;
                     break;
                 }
             }
             if ( all_matched ) {
-                nodes.add( node );
+                nodes.add( node.getId() );
             }
         }
         return nodes;
     }
 
+    public static void setAllIndicatorsToZero( final Phylogeny phy ) {
+        for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+            it.next().setIndicator( ( byte ) 0 );
+        }
+    }
+
     /**
      * Convenience method.
-     * Sets value for the first confidence value (created if not present, values overwritten otherwise). 
+     * Sets value for the first confidence value (created if not present, values overwritten otherwise).
      */
     public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {
         setConfidence( node, bootstrap_confidence_value, "bootstrap" );
@@ -1165,7 +1429,7 @@ public class PhylogenyMethods {
 
     /**
      * Convenience method.
-     * Sets value for the first confidence value (created if not present, values overwritten otherwise). 
+     * Sets value for the first confidence value (created if not present, values overwritten otherwise).
      */
     public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {
         setConfidence( node, confidence_value, "" );
@@ -1173,7 +1437,7 @@ public class PhylogenyMethods {
 
     /**
      * Convenience method.
-     * Sets value for the first confidence value (created if not present, values overwritten otherwise). 
+     * Sets value for the first confidence value (created if not present, values overwritten otherwise).
      */
     public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {
         Confidence c = null;
@@ -1197,43 +1461,686 @@ public class PhylogenyMethods {
 
     /**
      * Convenience method to set the taxonomy code of a phylogeny node.
-     * 
-     * 
+     *
+     *
      * @param node
      * @param taxonomy_code
+     * @throws PhyloXmlDataFormatException
      */
-    public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code ) {
+    public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )
+            throws PhyloXmlDataFormatException {
         if ( !node.getNodeData().isHasTaxonomy() ) {
             node.getNodeData().setTaxonomy( new Taxonomy() );
         }
         node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
     }
 
+    final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
+        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 );
+        }
+    }
+
     /**
      * Removes from Phylogeny to_be_stripped all external Nodes which are
      * associated with a species NOT found in Phylogeny reference.
-     * 
+     *
      * @param reference
      *            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>();
-        final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
-            ref_ext_taxo.add( getSpecies( it.next() ) );
+            final PhylogenyNode n = it.next();
+            if ( !n.getNodeData().isHasTaxonomy() ) {
+                throw new IllegalArgumentException( "no taxonomic data in node: " + n );
+            }
+            if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );
+            }
+            if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+                ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+            }
+            if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )
+                    && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
+                ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );
+            }
         }
+        final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
-            if ( !ref_ext_taxo.contains( getSpecies( n ) ) ) {
+            if ( !n.getNodeData().isHasTaxonomy() ) {
+                nodes_to_delete.add( n );
+            }
+            else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
+                    && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                    && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo
+                            .contains( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
                 nodes_to_delete.add( n );
             }
         }
-        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;
+    }
+
+    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( "" );
+                }
+            }
+        }
+    }
+
+    final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( !n.isExternal() && !n.isRoot() ) {
+                if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+                    double value = -1;
+                    try {
+                        value = Double.parseDouble( n.getName() );
+                    }
+                    catch ( final NumberFormatException e ) {
+                        return false;
+                    }
+                    if ( ( value < 0.0 ) || ( value > 100 ) ) {
+                        return false;
+                    }
+                }
+            }
+        }
+        return true;
+    }
+
+    final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy,
+                                                                    final String confidence_type ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            transferInternalNodeNameToConfidence( confidence_type, it.next() );
+        }
+    }
+
+    private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {
+        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, confidence_type ) );
+                    n.setName( "" );
+                }
+            }
+        }
+    }
+
+    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;
+                    }
+                    default: {
+                        throw new IllegalArgumentException( "don't know what to do with " + field );
+                    }
+                }
+            }
+        }
+    }
+
+    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;
+    }
+
+    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;
+    }
+
+    public static double calculateAverageTreeHeight( final PhylogenyNode node ) {
+        final List<PhylogenyNode> ext = node.getAllExternalDescendants();
+        double s = 0;
+        for( PhylogenyNode n : ext ) {
+            while ( n != node ) {
+                if ( n.getDistanceToParent() > 0 ) {
+                    s += n.getDistanceToParent();
+                }
+                n = n.getParent();
+            }
+        }
+        return s / ext.size();
+    }
+
+    /**
+     * 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;
+        }
+    }
+
+    private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,
+                                                                       final double min_distance_to_root ) {
+        final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();
+        final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );
+        for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {
+            if ( ext.getIndicator() != 0 ) {
+                throw new RuntimeException( "this should not have happened" );
+            }
+            ext.setIndicator( ( byte ) 1 );
+            l.add( ext );
+        }
+        return l;
+    }
+
+    /**
+     * 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,
+                                  final boolean regex ) {
+        if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
+            return false;
+        }
+        String my_s = s.trim();
+        String my_query = query.trim();
+        if ( !case_sensitive && !regex ) {
+            my_s = my_s.toLowerCase();
+            my_query = my_query.toLowerCase();
+        }
+        if ( regex ) {
+            Pattern p = null;
+            try {
+                if ( case_sensitive ) {
+                    p = Pattern.compile( my_query );
+                }
+                else {
+                    p = Pattern.compile( my_query, Pattern.CASE_INSENSITIVE );
+                }
+            }
+            catch ( final PatternSyntaxException e ) {
+                return false;
+            }
+            if ( p != null ) {
+                return p.matcher( my_s ).find();
+            }
+            else {
+                return false;
+            }
+        }
+        else if ( partial ) {
+            return my_s.indexOf( my_query ) >= 0;
+        }
+        else {
+            Pattern p = null;
+            try {
+                p = Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" );
+            }
+            catch ( final PatternSyntaxException e ) {
+                return false;
+            }
+            if ( p != null ) {
+                return p.matcher( my_s ).find();
+            }
+            else {
+                return false;
+            }
+        }
+    }
+
+    private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {
+        PhylogenyNode n = node;
+        PhylogenyNode prev = node;
+        while ( min_distance_to_root < n.calculateDistanceToRoot() ) {
+            prev = n;
+            n = n.getParent();
+        }
+        return prev;
+    }
+
+    public static enum DESCENDANT_SORT_PRIORITY {
+                                                 NODE_NAME,
+                                                 SEQUENCE,
+                                                 TAXONOMY;
+    }
+
+    public static enum PhylogenyNodeField {
+                                           CLADE_NAME,
+                                           SEQUENCE_NAME,
+                                           SEQUENCE_SYMBOL,
+                                           TAXONOMY_CODE,
+                                           TAXONOMY_COMMON_NAME,
+                                           TAXONOMY_ID,
+                                           TAXONOMY_ID_UNIPROT_1,
+                                           TAXONOMY_ID_UNIPROT_2,
+                                           TAXONOMY_SCIENTIFIC_NAME;
+    }
+
+    public static void addMolecularSeqsToTree( final Phylogeny phy, final Msa msa ) {
+        for( int s = 0; s < msa.getNumberOfSequences(); ++s ) {
+            final org.forester.sequence.MolecularSequence seq = msa.getSequence( s );
+            final PhylogenyNode node = phy.getNode( seq.getIdentifier() );
+            final org.forester.phylogeny.data.Sequence new_seq = new Sequence();
+            new_seq.setMolecularSequenceAligned( true );
+            new_seq.setMolecularSequence( seq.getMolecularSequenceAsString() );
+            new_seq.setName( seq.getIdentifier() );
+            try {
+                new_seq.setType( PhyloXmlUtil.SEQ_TYPE_PROTEIN );
+            }
+            catch ( final PhyloXmlDataFormatException ignore ) {
+                // do nothing
+            }
+            node.getNodeData().addSequence( new_seq );
+        }
+    }
+
+    final private static 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 ( 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().getGeneName() ) )
+                        && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                    return n1.getNodeData().getSequence().getGeneName()
+                            .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                        && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                    return n1.getNodeData().getSequence().getSymbol()
+                            .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                }
+            }
+            if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+            }
+            return 0;
+        }
+    }
+
+    final private static 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().getGeneName() ) )
+                        && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                    return n1.getNodeData().getSequence().getGeneName()
+                            .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                }
+                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().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.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+            }
+            return 0;
+        }
+    }
+
+    final private static 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 ( 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().getGeneName() ) )
+                        && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+                    return n1.getNodeData().getSequence().getGeneName()
+                            .compareTo( n2.getNodeData().getSequence().getGeneName() );
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                        && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                    return n1.getNodeData().getSequence().getSymbol()
+                            .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                }
+            }
+            return 0;
+        }
+    }
+
+    public final static Map<Long, Integer> calculateDepths( final Phylogeny phy ) {
+        final Map<Long, Integer> depths = new HashMap<Long, Integer>();
+        calculateDepthsHelper( phy.getRoot(), 0, depths );
+        return depths;
+    }
+
+    private final static void calculateDepthsHelper( final PhylogenyNode n, int d, final Map<Long, Integer> depths ) {
+        depths.put( n.getId(), d );
+        ++d;
+        final List<PhylogenyNode> descs = n.getDescendants();
+        for( final PhylogenyNode desc : descs ) {
+            calculateDepthsHelper( desc, d, depths );
+        }
+    }
+
+    public final static void collapseToDepth( final Phylogeny phy, final int depth ) {
+         if ( phy.getNumberOfExternalNodes() < 3 ) {
+            return;
+        }
+        collapseToDepthHelper( phy.getRoot(), 0, depth );
+    }
+
+    private final static void collapseToDepthHelper( final PhylogenyNode n, int d, final int depth ) {
+        if ( n.isExternal() ) {
+            n.setCollapse( false );
+            return;
+        }
+        if ( d >= depth ) {
+            n.setCollapse( true );
+            final PhylogenyNodeIterator it = new PreorderTreeIterator( n );
+            while ( it.hasNext() ) {
+                it.next().setCollapse( true );
+            }
+        }
+        else {
+            n.setCollapse( false );
+            ++d;
+            final List<PhylogenyNode> descs = n.getDescendants();
+            for( final PhylogenyNode desc : descs ) {
+                collapseToDepthHelper( desc, d, depth );
+            }
+        }
+    }
+
+   
+    
+    public final static void collapseToRank( final Phylogeny phy, final int rank ) {
+        if ( phy.getNumberOfExternalNodes() < 3 ) {
+            return;
+        }
+        if ( rank < 0 || rank >= TaxonomyUtil.RANKS.length ) {
+            throw new IllegalArgumentException( "Rank " + rank + " is out of range" );
+        }
+        collapseToRankHelper( phy.getRoot(), rank );
+    }
+
+    private final static void collapseToRankHelper( final PhylogenyNode n, final int target_rank ) {
+        if ( n.isExternal() ) {
+            n.setCollapse( false );
+            return;
+        }
+        if ( ( n.getNodeData().getTaxonomy() != null )
+                && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
+            final String current_rank = n.getNodeData().getTaxonomy().getRank();
+            if ( !TaxonomyUtil.RANK_TO_INT.containsKey( current_rank ) ) {
+                System.out.println( "Don't know rank \"" + current_rank + "\", ignoring." );
+            }
+            else {
+                if ( TaxonomyUtil.RANK_TO_INT.get( current_rank ) >= target_rank ) {
+                    n.setCollapse( true );
+                    
+                    final PhylogenyNodeIterator it = new PreorderTreeIterator( n );
+                    while ( it.hasNext() ) {
+                        it.next().setCollapse( true );
+                    }
+                    return;
+                }
+            }
+        }
+        n.setCollapse( false );
+        final List<PhylogenyNode> descs = n.getDescendants();
+        for( final PhylogenyNode desc : descs ) {
+            collapseToRankHelper( desc, target_rank );
+        }
+    }
+    
+    public final static PhylogenyNode getFirstExternalNode( final PhylogenyNode node ) {
+        PhylogenyNode n = node;
+        while ( n.isInternal() ) {
+            n = n.getFirstChildNode();
+        }
+        return n;
+    }
+    
+    public final static PhylogenyNode getLastExternalNode( final PhylogenyNode node ) {
+        PhylogenyNode n = node;
+        while ( n.isInternal() ) {
+            n = n.getLastChildNode();
         }
-        return nodes_to_delete.size();
+        return n;
     }
+    
 }