X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=64c7965fb42f6e1efeeb1d92c18b3b1f17cc78b1;hb=5309073b8da93adc2ece844bb84ff2735805b38c;hp=2b7fd29cec240e418fe463a7d441d0fb6d73d25f;hpb=bb78bbf463fdbb67cfa123c94ddaa1e8f1d3c356;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 2b7fd29..64c7965 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -26,8 +26,13 @@
 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;
@@ -35,11 +40,21 @@ import java.util.Set;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
+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.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.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
@@ -48,10 +63,9 @@ import org.forester.util.ForesterUtil;
 
 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 PhylogenyMethods _instance   = null;
+    private PhylogenyNode           _farthest_1 = null;
+    private PhylogenyNode           _farthest_2 = null;
 
     private PhylogenyMethods() {
         // Hidden constructor.
@@ -66,7 +80,7 @@ public class PhylogenyMethods {
      * @return distance between node1 and node2
      */
     public double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        final PhylogenyNode lca = obtainLCA( node1, node2 );
+        final PhylogenyNode lca = calculateLCA( node1, node2 );
         final PhylogenyNode n1 = node1;
         final PhylogenyNode n2 = node2;
         return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
@@ -101,6 +115,10 @@ public class PhylogenyMethods {
         return farthest_d;
     }
 
+    final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+        return calculateLCA( n1, n2 ).getNodeData().getEvent();
+    }
+
     @Override
     public Object clone() throws CloneNotSupportedException {
         throw new CloneNotSupportedException();
@@ -114,6 +132,24 @@ public class PhylogenyMethods {
         return _farthest_2;
     }
 
+    final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
+        if ( n.isInternal() ) {
+            throw new IllegalArgumentException( "node is not external" );
+        }
+        final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            final PhylogenyNode i = it.next();
+            if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
+                to_delete.add( i );
+            }
+        }
+        for( final PhylogenyNode d : to_delete ) {
+            phy.deleteSubtree( d, true );
+        }
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
+    }
+
     /**
      * Returns the LCA of PhylogenyNodes node1 and node2.
      * 
@@ -122,22 +158,68 @@ public class PhylogenyMethods {
      * @param node2
      * @return LCA of 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() );
+    public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == node2 ) {
+            return node1;
+        }
+        if ( ( node1.getParent() == node2.getParent() ) ) {
+            return node1.getParent();
+        }
+        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 {
+                if ( node1 == node2 ) {
+                    return node1;
+                }
+                node1 = node1.getParent();
+                node2 = node2.getParent();
+                depth1--;
+                depth2--;
+            }
         }
-        while ( !_temp_hash_set.contains( n2.getId() ) && !n2.isRoot() ) {
-            n2 = n2.getParent();
+        throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
+    }
+
+    public static final void preOrderReId( final Phylogeny phy ) {
+        if ( phy.isEmpty() ) {
+            return;
         }
-        if ( !_temp_hash_set.contains( n2.getId() ) ) {
-            throw new IllegalArgumentException( "attempt to get LCA of two nodes which do not share a common root" );
+        phy.setIdToNodeMap( null );
+        int i = PhylogenyNode.getNodeCount();
+        for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+            it.next().setId( i++ );
         }
-        return n2;
+        PhylogenyNode.setNodeCount( i );
+    }
+
+    /**
+     * 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 ) {
+        while ( node1 != node2 ) {
+            if ( node1.getId() > node2.getId() ) {
+                node1 = node1.getParent();
+            }
+            else {
+                node2 = node2.getParent();
+            }
+        }
+        return node1;
     }
 
     /**
@@ -154,20 +236,338 @@ public class PhylogenyMethods {
      *         of this Phylogeny, null if this Phylogeny is empty or if n is
      *         internal
      */
-    public List<PhylogenyNode> getOrthologousNodes( final Phylogeny phy, final PhylogenyNode node ) {
+    public final static List<PhylogenyNode> getOrthologousNodes( final Phylogeny phy, final PhylogenyNode node ) {
         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+        PhylogenyMethods.preOrderReId( phy );
         final PhylogenyNodeIterator it = phy.iteratorExternalForward();
         while ( it.hasNext() ) {
             final PhylogenyNode temp_node = it.next();
-            if ( ( temp_node != node ) && isAreOrthologous( node, temp_node ) ) {
+            if ( ( temp_node != node ) && !calculateLCAonTreeWithIdsInPreOrder( node, temp_node ).isDuplication() ) {
                 nodes.add( temp_node );
             }
         }
         return nodes;
     }
 
-    public boolean isAreOrthologous( final PhylogenyNode node1, final PhylogenyNode node2 ) {
-        return !obtainLCA( node1, node2 ).isDuplication();
+    public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
+        final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            nodes.put( n.getName(), n );
+        }
+        return nodes;
+    }
+
+    public 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() ] );
+    }
+
+    final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
+                if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+                    double d = -1.0;
+                    try {
+                        d = Double.parseDouble( n.getName() );
+                    }
+                    catch ( final Exception e ) {
+                        d = -1.0;
+                    }
+                    if ( d >= 0.0 ) {
+                        n.getBranchData().addConfidence( new Confidence( d, "" ) );
+                        n.setName( "" );
+                    }
+                }
+            }
+        }
+    }
+
+    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 void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
+        class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                return 0;
+            }
+        }
+        class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                return 0;
+            }
+        }
+        class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
+
+            @Override
+            public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+                if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+                    return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+                }
+                if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+                                .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                        return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+                                .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+                    }
+                }
+                if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+                        return n1.getNodeData().getSequence().getName().toLowerCase()
+                                .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+                    }
+                    if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+                            && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+                        return n1.getNodeData().getSequence().getSymbol()
+                                .compareTo( n2.getNodeData().getSequence().getSymbol() );
+                    }
+                    if ( ( n1.getNodeData().getSequence().getAccession() != null )
+                            && ( n2.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+                            && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+                        return n1.getNodeData().getSequence().getAccession().getValue()
+                                .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+                    }
+                }
+                return 0;
+            }
+        }
+        Comparator<PhylogenyNode> c;
+        switch ( pri ) {
+            case SEQUENCE:
+                c = new PhylogenyNodeSortSequencePriority();
+                break;
+            case NODE_NAME:
+                c = new PhylogenyNodeSortNodeNamePriority();
+                break;
+            default:
+                c = new PhylogenyNodeSortTaxonomyPriority();
+        }
+        final List<PhylogenyNode> descs = node.getDescendants();
+        Collections.sort( descs, c );
+        int i = 0;
+        for( final PhylogenyNode desc : descs ) {
+            node.setChildNode( i++, desc );
+        }
+    }
+
+    final static public void transferNodeNameToField( final Phylogeny phy,
+                                                      final PhylogenyMethods.PhylogenyNodeField field,
+                                                      final boolean external_only ) throws PhyloXmlDataFormatException {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( external_only && n.isInternal() ) {
+                continue;
+            }
+            final String name = n.getName().trim();
+            if ( !ForesterUtil.isEmpty( name ) ) {
+                switch ( field ) {
+                    case TAXONOMY_CODE:
+                        n.setName( "" );
+                        setTaxonomyCode( n, name );
+                        break;
+                    case TAXONOMY_SCIENTIFIC_NAME:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        n.getNodeData().getTaxonomy().setScientificName( name );
+                        break;
+                    case TAXONOMY_COMMON_NAME:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        n.getNodeData().getTaxonomy().setCommonName( name );
+                        break;
+                    case SEQUENCE_SYMBOL:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasSequence() ) {
+                            n.getNodeData().setSequence( new Sequence() );
+                        }
+                        n.getNodeData().getSequence().setSymbol( name );
+                        break;
+                    case SEQUENCE_NAME:
+                        n.setName( "" );
+                        if ( !n.getNodeData().isHasSequence() ) {
+                            n.getNodeData().setSequence( new Sequence() );
+                        }
+                        n.getNodeData().getSequence().setName( name );
+                        break;
+                    case TAXONOMY_ID_UNIPROT_1: {
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        String id = name;
+                        final int i = name.indexOf( '_' );
+                        if ( i > 0 ) {
+                            id = name.substring( 0, i );
+                        }
+                        else {
+                            n.setName( "" );
+                        }
+                        n.getNodeData().getTaxonomy()
+                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+                        break;
+                    }
+                    case TAXONOMY_ID_UNIPROT_2: {
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        String id = name;
+                        final int i = name.indexOf( '_' );
+                        if ( i > 0 ) {
+                            id = name.substring( i + 1, name.length() );
+                        }
+                        else {
+                            n.setName( "" );
+                        }
+                        n.getNodeData().getTaxonomy()
+                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+                        break;
+                    }
+                    case TAXONOMY_ID: {
+                        if ( !n.getNodeData().isHasTaxonomy() ) {
+                            n.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
+                        n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
+                        break;
+                    }
+                }
+            }
+        }
     }
 
     static double addPhylogenyDistances( final double a, final double b ) {
@@ -180,19 +580,17 @@ public class PhylogenyMethods {
         else if ( b >= 0.0 ) {
             return b;
         }
-        return PhylogenyNode.DISTANCE_DEFAULT;
+        return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
     }
 
-    // Helper for getUltraParalogousNodes( PhylogenyNode ).
-    public static boolean areAllChildrenDuplications( final PhylogenyNode n ) {
+    public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
         if ( n.isExternal() ) {
-            return false;
+            return true;
         }
         else {
             if ( n.isDuplication() ) {
-                //FIXME test me!
                 for( final PhylogenyNode desc : n.getDescendants() ) {
-                    if ( !areAllChildrenDuplications( desc ) ) {
+                    if ( !isAllDecendentsAreDuplications( desc ) ) {
                         return false;
                     }
                 }
@@ -204,28 +602,6 @@ public class PhylogenyMethods {
         }
     }
 
-    public static int calculateDepth( final PhylogenyNode node ) {
-        PhylogenyNode n = node;
-        int steps = 0;
-        while ( !n.isRoot() ) {
-            steps++;
-            n = n.getParent();
-        }
-        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();
-            }
-            n = n.getParent();
-        }
-        return d;
-    }
-
     public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
         if ( node.isExternal() ) {
             return 0;
@@ -253,7 +629,7 @@ 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;
             }
@@ -265,7 +641,7 @@ 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;
             }
@@ -273,6 +649,17 @@ public class PhylogenyMethods {
         return max;
     }
 
+    public static int countNumberOfPolytomies( final Phylogeny phy ) {
+        int count = 0;
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
+                count++;
+            }
+        }
+        return count;
+    }
+
     public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
@@ -284,13 +671,39 @@ public class PhylogenyMethods {
         return stats;
     }
 
-    public static DescriptiveStatistics calculatConfidenceStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
-            if ( !n.isExternal() ) {
+            if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
+                stats.addValue( n.getDistanceToParent() );
+            }
+        }
+        return stats;
+    }
+
+    public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+        final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && !n.isRoot() ) {
                 if ( n.getBranchData().isHasConfidences() ) {
-                    stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
+                    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 );
+                    }
                 }
             }
         }
@@ -389,31 +802,33 @@ public class PhylogenyMethods {
     }
 
     public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
-        phy.hashIDs();
+        phy.clearHashIdToNodeMap();
         for( final Integer id : to_delete ) {
             phy.deleteSubtree( phy.getNode( id ), true );
         }
-        phy.hashIDs();
+        phy.clearHashIdToNodeMap();
+        phy.externalNodesHaveChanged();
     }
 
     public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
             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 );
             }
         }
+        p.clearHashIdToNodeMap();
+        p.externalNodesHaveChanged();
     }
 
     public static void deleteExternalNodesPositiveSelection( final Set<Taxonomy> species_to_keep, final Phylogeny phy ) {
@@ -430,9 +845,8 @@ public class PhylogenyMethods {
                 throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
             }
         }
-        phy.hashIDs();
+        phy.clearHashIdToNodeMap();
         phy.externalNodesHaveChanged();
-        //  deleteExternalNodesNegativeSelection( to_delete, phy );
     }
 
     public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
@@ -626,12 +1040,12 @@ 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();
         }
@@ -649,13 +1063,14 @@ public class PhylogenyMethods {
      * @param n
      *            external PhylogenyNode whose strictly speciation related Nodes
      *            are to be returned
-     * @return Vector of references to all strictly speciation related Nodes of
+     * @return 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;
+        PhylogenyNode node = n;
+        PhylogenyNode deepest = null;
         final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
         if ( !node.isExternal() ) {
             return null;
@@ -732,9 +1147,9 @@ public class PhylogenyMethods {
         // FIXME test me
         PhylogenyNode node = n;
         if ( !node.isExternal() ) {
-            return null;
+            throw new IllegalArgumentException( "attempt to get ultra-paralogous nodes of internal node" );
         }
-        while ( !node.isRoot() && node.getParent().isDuplication() && areAllChildrenDuplications( node.getParent() ) ) {
+        while ( !node.isRoot() && node.getParent().isDuplication() && isAllDecendentsAreDuplications( node.getParent() ) ) {
             node = node.getParent();
         }
         final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
@@ -899,8 +1314,9 @@ 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;
@@ -923,6 +1339,8 @@ public class PhylogenyMethods {
         }
         if ( remove_me.isExternal() ) {
             phylogeny.deleteSubtree( remove_me, false );
+            phylogeny.clearHashIdToNodeMap();
+            phylogeny.externalNodesHaveChanged();
         }
         else {
             final PhylogenyNode parent = remove_me.getParent();
@@ -934,7 +1352,7 @@ public class PhylogenyMethods {
                                                                  desc.getDistanceToParent() ) );
             }
             remove_me.setParent( null );
-            phylogeny.setIdHash( null );
+            phylogeny.clearHashIdToNodeMap();
             phylogeny.externalNodesHaveChanged();
         }
     }
@@ -942,7 +1360,8 @@ public class PhylogenyMethods {
     public static List<PhylogenyNode> searchData( final String query,
                                                   final Phylogeny phy,
                                                   final boolean case_sensitive,
-                                                  final boolean partial ) {
+                                                  final boolean partial,
+                                                  final boolean search_domains ) {
         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         if ( phy.isEmpty() || ( query == null ) ) {
             return nodes;
@@ -1002,7 +1421,7 @@ public class PhylogenyMethods {
                               partial ) ) {
                 match = true;
             }
-            if ( !match && node.getNodeData().isHasSequence()
+            if ( search_domains && !match && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
                 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
@@ -1038,7 +1457,8 @@ public class PhylogenyMethods {
     public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
                                                             final Phylogeny phy,
                                                             final boolean case_sensitive,
-                                                            final boolean partial ) {
+                                                            final boolean partial,
+                                                            final boolean search_domains ) {
         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
             return nodes;
@@ -1101,7 +1521,7 @@ public class PhylogenyMethods {
                                   partial ) ) {
                     match = true;
                 }
-                if ( !match && node.getNodeData().isHasSequence()
+                if ( search_domains && !match && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                     final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
                     I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
@@ -1126,22 +1546,6 @@ public class PhylogenyMethods {
                             break I;
                         }
                     }
-                    //                    final String[] bcp_ary = node.getNodeData().getBinaryCharacters()
-                    //                            .getPresentCharactersAsStringArray();
-                    //                    I: for( final String bc : bcp_ary ) {
-                    //                        if ( match( bc, query, case_sensitive, partial ) ) {
-                    //                            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 ) ) {
-                    //                            match = true;
-                    //                            break I;
-                    //                        }
-                    //                    }
                 }
                 if ( !match ) {
                     all_matched = false;
@@ -1215,8 +1619,10 @@ public class PhylogenyMethods {
      * 
      * @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() );
         }
@@ -1235,19 +1641,98 @@ public class PhylogenyMethods {
      */
     public static int 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 );
+            }
+            //  ref_ext_taxo.add( getSpecies( 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() );
+            }
         }
+        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() ) ) ) {
                 nodes_to_delete.add( n );
             }
         }
         for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
             to_be_stripped.deleteSubtree( phylogenyNode, true );
         }
+        to_be_stripped.clearHashIdToNodeMap();
+        to_be_stripped.externalNodesHaveChanged();
         return nodes_to_delete.size();
     }
+
+    /**
+     * Arranges the order of childern for each node of this Phylogeny in such a
+     * way that either the branch with more children is on top (right) or on
+     * bottom (left), dependent on the value of boolean order.
+     * 
+     * @param order
+     *            decides in which direction to order
+     * @param pri 
+     */
+    public static void orderAppearance( final PhylogenyNode n,
+                                        final boolean order,
+                                        final boolean order_ext_alphabetically,
+                                        final DESCENDANT_SORT_PRIORITY pri ) {
+        if ( n.isExternal() ) {
+            return;
+        }
+        else {
+            PhylogenyNode temp = null;
+            if ( ( n.getNumberOfDescendants() == 2 )
+                    && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
+                    && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
+                temp = n.getChildNode1();
+                n.setChild1( n.getChildNode2() );
+                n.setChild2( temp );
+            }
+            else if ( order_ext_alphabetically ) {
+                boolean all_ext = true;
+                for( final PhylogenyNode i : n.getDescendants() ) {
+                    if ( !i.isExternal() ) {
+                        all_ext = false;
+                        break;
+                    }
+                }
+                if ( all_ext ) {
+                    PhylogenyMethods.sortNodeDescendents( n, pri );
+                }
+            }
+            for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+                orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
+            }
+        }
+    }
+
+    public static enum PhylogenyNodeField {
+        CLADE_NAME,
+        TAXONOMY_CODE,
+        TAXONOMY_SCIENTIFIC_NAME,
+        TAXONOMY_COMMON_NAME,
+        SEQUENCE_SYMBOL,
+        SEQUENCE_NAME,
+        TAXONOMY_ID_UNIPROT_1,
+        TAXONOMY_ID_UNIPROT_2,
+        TAXONOMY_ID;
+    }
+
+    public static enum TAXONOMY_EXTRACTION {
+        NO, YES, PFAM_STYLE_ONLY;
+    }
+
+    public static enum DESCENDANT_SORT_PRIORITY {
+        TAXONOMY, SEQUENCE, NODE_NAME;
+    }
 }