-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/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.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
-import org.forester.io.parsers.PhylogenyParser;
-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.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;
-import org.forester.util.FailedConditionCheckException;
-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 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 ) );
- }
-
- 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 );
- }
- }
- }
- _farthest_1 = node_1;
- _farthest_2 = node_2;
- return farthest_d;
- }
-
- @Override
- public Object clone() throws CloneNotSupportedException {
- throw new CloneNotSupportedException();
- }
-
- public PhylogenyNode getFarthestNode1() {
- return _farthest_1;
- }
-
- public PhylogenyNode getFarthestNode2() {
- return _farthest_2;
- }
-
- /**
- * Returns the LCA of PhylogenyNodes node1 and node2.
- *
- *
- * @param node1
- * @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() );
- }
- 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;
- }
-
- /**
- * 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
- */
- 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();
- }
-
- 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;
- }
-
- 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 PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- final String name = n.getName().trim();
- if ( !ForesterUtil.isEmpty( name ) ) {
- switch ( field ) {
- case TAXONOMY_CODE:
- //temp hack
- // if ( name.length() > 5 ) {
- // n.setName( "" );
- // if ( !n.getNodeData().isHasTaxonomy() ) {
- // n.getNodeData().setTaxonomy( new Taxonomy() );
- // }
- // n.getNodeData().getTaxonomy().setScientificName( name );
- // break;
- // }
- //
- 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;
- }
- }
- }
- }
- }
-
- static double addPhylogenyDistances( final double a, final double b ) {
- if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
- return a + b;
- }
- else if ( a >= 0.0 ) {
- return a;
- }
- else if ( b >= 0.0 ) {
- return b;
- }
- return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
- }
-
- // Helper for getUltraParalogousNodes( PhylogenyNode ).
- public static boolean areAllChildrenDuplications( final PhylogenyNode n ) {
- if ( n.isExternal() ) {
- return false;
- }
- else {
- if ( n.isDuplication() ) {
- //FIXME test me!
- for( final PhylogenyNode desc : n.getDescendants() ) {
- if ( !areAllChildrenDuplications( desc ) ) {
- return false;
- }
- }
- return true;
- }
- else {
- return false;
- }
- }
- }
-
- public static 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;
- }
- short max = 0;
- for( PhylogenyNode d : node.getAllExternalDescendants() ) {
- short steps = 0;
- while ( d != node ) {
- if ( d.isCollapse() ) {
- steps = 0;
- }
- else {
- steps++;
- }
- d = d.getParent();
- }
- if ( max < steps ) {
- max = steps;
- }
- }
- return max;
- }
-
- public static int calculateMaxDepth( final Phylogeny phy ) {
- int max = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final int steps = calculateDepth( node );
- if ( steps > max ) {
- max = steps;
- }
- }
- return max;
- }
-
- public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
- double max = 0.0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final double d = calculateDistanceToRoot( node );
- if ( d > max ) {
- max = d;
- }
- }
- 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() );
- }
- }
- return stats;
- }
-
- public static DescriptiveStatistics calculatConfidenceStatistics( 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() );
- }
- }
- }
- return stats;
- }
-
- /**
- * Returns the set of distinct taxonomies of
- * all external nodes of node.
- * If at least one the external nodes has no taxonomy,
- * null is returned.
- *
- */
- public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- tax_set.add( n.getNodeData().getTaxonomy() );
- }
- return tax_set;
- }
-
- /**
- * Returns a map of distinct taxonomies of
- * all external nodes of node.
- * If at least one of the external nodes has no taxonomy,
- * null is returned.
- *
- */
- public static SortedMap<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- final SortedMap<Taxonomy, Integer> tax_map = new TreeMap<Taxonomy, Integer>();
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- final Taxonomy t = n.getNodeData().getTaxonomy();
- if ( tax_map.containsKey( t ) ) {
- tax_map.put( t, tax_map.get( t ) + 1 );
- }
- else {
- tax_map.put( t, 1 );
- }
- }
- return tax_map;
- }
-
- public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- int x = 0;
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- x++;
- }
- }
- return x;
- }
-
- /**
- * Deep copies the phylogeny originating from this node.
- */
- static PhylogenyNode copySubTree( final PhylogenyNode source ) {
- if ( source == null ) {
- return null;
- }
- else {
- final PhylogenyNode newnode = source.copyNodeData();
- if ( !source.isExternal() ) {
- for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
- newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
- }
- }
- return newnode;
- }
- }
-
- /**
- * Shallow copies the phylogeny originating from this node.
- */
- static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
- if ( source == null ) {
- return null;
- }
- else {
- final PhylogenyNode newnode = source.copyNodeDataShallow();
- if ( !source.isExternal() ) {
- for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
- newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
- }
- }
- return newnode;
- }
- }
-
- public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
- phy.hashIDs();
- for( final Integer id : to_delete ) {
- phy.deleteSubtree( phy.getNode( id ), true );
- }
- phy.hashIDs();
- }
-
- 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 ] ) ) {
- continue;
- }
- List<PhylogenyNode> nodes = null;
- nodes = p.getNodes( node_names_to_delete[ i ] );
- 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 ] + "\"" );
- }
- 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 );
- }
-
- public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
- final Phylogeny p ) {
- final PhylogenyNodeIterator it = p.iteratorExternalForward();
- final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
- int i = 0;
- Arrays.sort( node_names_to_keep );
- while ( it.hasNext() ) {
- final String curent_name = it.next().getName();
- if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
- to_delete[ i++ ] = curent_name;
- }
- }
- PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
- final List<String> deleted = new ArrayList<String>();
- for( final String n : to_delete ) {
- if ( !ForesterUtil.isEmpty( n ) ) {
- deleted.add( n );
- }
- }
- 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() );
- }
- }
- }
- return descs;
- }
-
- /**
- *
- * Convenience method
- *
- * @param node
- * @return
- */
- public static Color getBranchColorValue( final PhylogenyNode node ) {
- if ( node.getBranchData().getBranchColor() == null ) {
- return null;
- }
- return node.getBranchData().getBranchColor().getValue();
- }
-
- /**
- * Convenience method
- */
- public static double getBranchWidthValue( final PhylogenyNode node ) {
- if ( !node.getBranchData().isHasBranchWidth() ) {
- return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;
- }
- return node.getBranchData().getBranchWidth().getValue();
- }
-
- /**
- * Convenience method
- */
- public static double getConfidenceValue( final PhylogenyNode node ) {
- if ( !node.getBranchData().isHasConfidences() ) {
- return Confidence.CONFIDENCE_DEFAULT_VALUE;
- }
- return node.getBranchData().getConfidence( 0 ).getValue();
- }
-
- /**
- * Convenience method
- */
- public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {
- if ( !node.getBranchData().isHasConfidences() ) {
- return new double[ 0 ];
- }
- final double[] values = new double[ node.getBranchData().getConfidences().size() ];
- int i = 0;
- for( final Confidence c : node.getBranchData().getConfidences() ) {
- values[ i++ ] = c.getValue();
- }
- 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;
- }
-
- /**
- * 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();
- Taxonomy tax = null;
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- else if ( tax == null ) {
- tax = n.getNodeData().getTaxonomy();
- }
- else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {
- return null;
- }
- }
- return tax;
- }
-
- public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {
- final List<PhylogenyNode> children = node.getAllExternalDescendants();
- PhylogenyNode farthest = null;
- double longest = -Double.MAX_VALUE;
- for( final PhylogenyNode child : children ) {
- if ( PhylogenyMethods.getDistance( child, node ) > longest ) {
- farthest = child;
- longest = PhylogenyMethods.getDistance( child, node );
- }
- }
- return farthest;
- }
-
- public static PhylogenyMethods getInstance() {
- if ( PhylogenyMethods._instance == null ) {
- PhylogenyMethods._instance = new PhylogenyMethods();
- }
- return PhylogenyMethods._instance;
- }
-
- /**
- * Returns the largest confidence value found on phy.
- */
- static public double getMaximumConfidenceValue( final Phylogeny phy ) {
- double max = -Double.MAX_VALUE;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final double s = PhylogenyMethods.getConfidenceValue( iter.next() );
- if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {
- max = s;
- }
- }
- return max;
- }
-
- static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {
- int min = Integer.MAX_VALUE;
- int d = 0;
- PhylogenyNode n;
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
- n = it.next();
- if ( n.isInternal() ) {
- d = n.getNumberOfDescendants();
- if ( d < min ) {
- min = d;
- }
- }
- }
- return min;
- }
-
- /**
- * Convenience method for display purposes.
- * Not intended for algorithms.
- */
- public static String getSpecies( final PhylogenyNode node ) {
- 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();
- }
- 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.
- */
- public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
- return "";
- }
- 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();
- }
- 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;
- }
- }
- }
- }
- return sn;
- }
-
- public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- if ( node.getChildNode( i ).isExternal() ) {
- return true;
- }
- }
- return false;
- }
-
- /*
- * This is case insensitive.
- *
- */
- public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
- final String[] providers ) {
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
- final String my_tax_prov = tax.getIdentifier().getProvider();
- for( final String provider : providers ) {
- if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
- return true;
- }
- }
- return false;
- }
- else {
- return false;
- }
- }
-
- 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 ) {
- 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();
- }
- 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,
- final double max_bootstrap_value,
- final double max_normalized_value ) {
- for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.isInternal() ) {
- final double confidence = getConfidenceValue( node );
- if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( confidence >= max_bootstrap_value ) {
- setBootstrapConfidence( node, max_normalized_value );
- }
- else {
- setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
- }
- }
- }
- }
- }
-
- public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- nodes.add( iter.next() );
- }
- return nodes;
- }
-
- public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
- for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- double red = 0.0;
- double green = 0.0;
- double blue = 0.0;
- int n = 0;
- if ( node.isInternal() ) {
- for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
- final PhylogenyNode child_node = iterator.next();
- final Color child_color = getBranchColorValue( child_node );
- if ( child_color != null ) {
- ++n;
- red += child_color.getRed();
- green += child_color.getGreen();
- blue += child_color.getBlue();
- }
- }
- setBranchColorValue( node,
- new Color( ForesterUtil.roundToInt( red / n ),
- ForesterUtil.roundToInt( green / n ),
- ForesterUtil.roundToInt( blue / n ) ) );
- }
- }
- }
-
- 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.isExternal() ) {
- phylogeny.deleteSubtree( remove_me, false );
- }
- else {
- final PhylogenyNode parent = remove_me.getParent();
- final List<PhylogenyNode> descs = remove_me.getDescendants();
- parent.removeChildNode( remove_me );
- for( final PhylogenyNode desc : descs ) {
- parent.addAsChild( desc );
- desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
- desc.getDistanceToParent() ) );
- }
- remove_me.setParent( null );
- phylogeny.setIdHash( null );
- 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>();
- if ( phy.isEmpty() || ( query == null ) ) {
- return nodes;
- }
- if ( ForesterUtil.isEmpty( query ) ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- boolean match = false;
- if ( match( node.getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- else if ( 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 ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match
- && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && match( node.getNodeData().getSequence().getAccession().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- if ( !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 ) {
- if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
- Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( match ) {
- nodes.add( node );
- }
- }
- 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>();
- 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 ) {
- boolean match = false;
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- if ( match( node.getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- else if ( 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 ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
- match = true;
- }
- if ( !match
- && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && match( node.getNodeData().getSequence().getAccession().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- if ( !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 ) {
- if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- }
- if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
- Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
- it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
- I: while ( it.hasNext() ) {
- if ( match( it.next(), query, case_sensitive, partial ) ) {
- match = true;
- 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;
- break;
- }
- }
- if ( all_matched ) {
- nodes.add( node );
- }
- }
- return nodes;
- }
-
- /**
- * Convenience method.
- * 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" );
- }
-
- public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
- if ( node.getBranchData().getBranchColor() == null ) {
- node.getBranchData().setBranchColor( new BranchColor() );
- }
- node.getBranchData().getBranchColor().setValue( color );
- }
-
- /**
- * Convenience method
- */
- public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {
- node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );
- }
-
- /**
- * Convenience method.
- * 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, "" );
- }
-
- /**
- * Convenience method.
- * 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;
- if ( node.getBranchData().getNumberOfConfidences() > 0 ) {
- c = node.getBranchData().getConfidence( 0 );
- }
- else {
- c = new Confidence();
- node.getBranchData().addConfidence( c );
- }
- c.setType( type );
- c.setValue( confidence_value );
- }
-
- public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node.getNodeData().getTaxonomy().setScientificName( scientific_name );
- }
-
- /**
- * Convenience method to set the taxonomy code of a phylogeny node.
- *
- *
- * @param node
- * @param taxonomy_code
- */
- public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
- }
-
- /**
- * 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
- */
- 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() ) );
- }
- for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !ref_ext_taxo.contains( getSpecies( n ) ) ) {
- nodes_to_delete.add( n );
- }
- }
- for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
- to_be_stripped.deleteSubtree( phylogenyNode, true );
- }
- return nodes_to_delete.size();
- }
-
- 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;
- }
-
- public static enum TAXONOMY_EXTRACTION {
- NO, YES, PFAM_STYLE_ONLY;
- }
-
- public static enum DESCENDANT_SORT_PRIORITY {
- TAXONOMY, SEQUENCE, NODE_NAME;
- }
-}
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2009 Christian M. Zmasek\r
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
+\r
+package org.forester.phylogeny;\r
+\r
+import java.awt.Color;\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.Arrays;\r
+import java.util.Collections;\r
+import java.util.Comparator;\r
+import java.util.HashMap;\r
+import java.util.HashSet;\r
+import java.util.Iterator;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
+import java.util.regex.Matcher;\r
+import java.util.regex.Pattern;\r
+import java.util.regex.PatternSyntaxException;\r
+\r
+import org.forester.io.parsers.FastaParser;\r
+import org.forester.io.parsers.PhylogenyParser;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;\r
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
+import org.forester.io.parsers.util.PhylogenyParserException;\r
+import org.forester.msa.Msa;\r
+import org.forester.phylogeny.data.Accession;\r
+import org.forester.phylogeny.data.Annotation;\r
+import org.forester.phylogeny.data.BranchColor;\r
+import org.forester.phylogeny.data.BranchWidth;\r
+import org.forester.phylogeny.data.Confidence;\r
+import org.forester.phylogeny.data.DomainArchitecture;\r
+import org.forester.phylogeny.data.Event;\r
+import org.forester.phylogeny.data.Identifier;\r
+import org.forester.phylogeny.data.PhylogenyDataUtil;\r
+import org.forester.phylogeny.data.Sequence;\r
+import org.forester.phylogeny.data.Taxonomy;\r
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;\r
+import org.forester.phylogeny.factories.PhylogenyFactory;\r
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
+import org.forester.util.BasicDescriptiveStatistics;\r
+import org.forester.util.DescriptiveStatistics;\r
+import org.forester.util.ForesterUtil;\r
+\r
+public class PhylogenyMethods {\r
+\r
+ private PhylogenyMethods() {\r
+ // Hidden constructor.\r
+ }\r
+\r
+ @Override\r
+ public Object clone() throws CloneNotSupportedException {\r
+ throw new CloneNotSupportedException();\r
+ }\r
+\r
+ public static boolean extractFastaInformation( final Phylogeny phy ) {\r
+ boolean could_extract = false;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ if ( !ForesterUtil.isEmpty( node.getName() ) ) {\r
+ final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );\r
+ if ( name_m.lookingAt() ) {\r
+ could_extract = true;\r
+ final String acc_source = name_m.group( 1 );\r
+ final String acc = name_m.group( 2 );\r
+ final String seq_name = name_m.group( 3 );\r
+ final String tax_sn = name_m.group( 4 );\r
+ if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {\r
+ ForesterUtil.ensurePresenceOfSequence( node );\r
+ node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
+ ForesterUtil.ensurePresenceOfSequence( node );\r
+ node.getNodeData().getSequence( 0 ).setName( seq_name );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( tax_sn ) ) {\r
+ ForesterUtil.ensurePresenceOfTaxonomy( node );\r
+ node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return could_extract;\r
+ }\r
+\r
+ public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {\r
+ stats.addValue( n.getDistanceToParent() );\r
+ }\r
+ }\r
+ return stats;\r
+ }\r
+\r
+ public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {\r
+ final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ if ( n.getBranchData().isHasConfidences() ) {\r
+ for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {\r
+ final Confidence c = n.getBranchData().getConfidences().get( i );\r
+ if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {\r
+ stats.add( i, new BasicDescriptiveStatistics() );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( c.getType() ) ) {\r
+ if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {\r
+ if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {\r
+ throw new IllegalArgumentException( "support values in node [" + n.toString()\r
+ + "] appear inconsistently ordered" );\r
+ }\r
+ }\r
+ stats.get( i ).setDescription( c.getType() );\r
+ }\r
+ stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return stats;\r
+ }\r
+\r
+ /**\r
+ * Calculates the distance between PhylogenyNodes node1 and node2.\r
+ *\r
+ *\r
+ * @param node1\r
+ * @param node2\r
+ * @return distance between node1 and node2\r
+ */\r
+ public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {\r
+ final PhylogenyNode lca = calculateLCA( node1, node2 );\r
+ final PhylogenyNode n1 = node1;\r
+ final PhylogenyNode n2 = node2;\r
+ return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );\r
+ }\r
+\r
+ /**\r
+ * Returns the LCA of PhylogenyNodes node1 and node2.\r
+ *\r
+ *\r
+ * @param node1\r
+ * @param node2\r
+ * @return LCA of node1 and node2\r
+ */\r
+ public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {\r
+ if ( node1 == null ) {\r
+ throw new IllegalArgumentException( "first argument (node) is null" );\r
+ }\r
+ if ( node2 == null ) {\r
+ throw new IllegalArgumentException( "second argument (node) is null" );\r
+ }\r
+ if ( node1 == node2 ) {\r
+ return node1;\r
+ }\r
+ if ( ( node1.getParent() == node2.getParent() ) ) {\r
+ return node1.getParent();\r
+ }\r
+ int depth1 = node1.calculateDepth();\r
+ int depth2 = node2.calculateDepth();\r
+ while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {\r
+ if ( depth1 > depth2 ) {\r
+ node1 = node1.getParent();\r
+ depth1--;\r
+ }\r
+ else if ( depth2 > depth1 ) {\r
+ node2 = node2.getParent();\r
+ depth2--;\r
+ }\r
+ else {\r
+ if ( node1 == node2 ) {\r
+ return node1;\r
+ }\r
+ node1 = node1.getParent();\r
+ node2 = node2.getParent();\r
+ depth1--;\r
+ depth2--;\r
+ }\r
+ }\r
+ throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );\r
+ }\r
+\r
+ /**\r
+ * Returns the LCA of PhylogenyNodes node1 and node2.\r
+ * Precondition: ids are in pre-order (or level-order).\r
+ *\r
+ *\r
+ * @param node1\r
+ * @param node2\r
+ * @return LCA of node1 and node2\r
+ */\r
+ public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {\r
+ if ( node1 == null ) {\r
+ throw new IllegalArgumentException( "first argument (node) is null" );\r
+ }\r
+ if ( node2 == null ) {\r
+ throw new IllegalArgumentException( "second argument (node) is null" );\r
+ }\r
+ while ( node1 != node2 ) {\r
+ if ( node1.getId() > node2.getId() ) {\r
+ node1 = node1.getParent();\r
+ }\r
+ else {\r
+ node2 = node2.getParent();\r
+ }\r
+ }\r
+ return node1;\r
+ }\r
+\r
+ public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {\r
+ if ( node.isExternal() ) {\r
+ return 0;\r
+ }\r
+ short max = 0;\r
+ for( PhylogenyNode d : node.getAllExternalDescendants() ) {\r
+ short steps = 0;\r
+ while ( d != node ) {\r
+ if ( d.isCollapse() ) {\r
+ steps = 0;\r
+ }\r
+ else {\r
+ steps++;\r
+ }\r
+ d = d.getParent();\r
+ }\r
+ if ( max < steps ) {\r
+ max = steps;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ public static int calculateMaxDepth( final Phylogeny phy ) {\r
+ int max = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final int steps = node.calculateDepth();\r
+ if ( steps > max ) {\r
+ max = steps;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {\r
+ double max = 0.0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final double d = node.calculateDistanceToRoot();\r
+ if ( d > max ) {\r
+ max = d;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ public static PhylogenyNode calculateNodeWithMaxDistanceToRoot( final Phylogeny phy ) {\r
+ double max = 0.0;\r
+ PhylogenyNode max_node = phy.getFirstExternalNode();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final double d = node.calculateDistanceToRoot();\r
+ if ( d > max ) {\r
+ max = d;\r
+ max_node = node;\r
+ }\r
+ }\r
+ return max_node;\r
+ }\r
+\r
+ public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();\r
+ int x = 0;\r
+ for( final PhylogenyNode n : descs ) {\r
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {\r
+ x++;\r
+ }\r
+ }\r
+ return x;\r
+ }\r
+\r
+ public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() ) {\r
+ stats.addValue( n.getNumberOfDescendants() );\r
+ }\r
+ }\r
+ return stats;\r
+ }\r
+\r
+ public final static void collapseSubtreeStructure( final PhylogenyNode n ) {\r
+ final List<PhylogenyNode> eds = n.getAllExternalDescendants();\r
+ final List<Double> d = new ArrayList<Double>();\r
+ for( final PhylogenyNode ed : eds ) {\r
+ d.add( calculateDistanceToAncestor( n, ed ) );\r
+ }\r
+ for( int i = 0; i < eds.size(); ++i ) {\r
+ n.setChildNode( i, eds.get( i ) );\r
+ eds.get( i ).setDistanceToParent( d.get( i ) );\r
+ }\r
+ }\r
+\r
+ public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {\r
+ int count = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {\r
+ count++;\r
+ }\r
+ }\r
+ return count;\r
+ }\r
+\r
+ public static int countNumberOfPolytomies( final Phylogeny phy ) {\r
+ int count = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {\r
+ count++;\r
+ }\r
+ }\r
+ return count;\r
+ }\r
+\r
+ public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {\r
+ final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();\r
+ final List<PhylogenyNode> ext = phy.getExternalNodes();\r
+ for( final PhylogenyNode n : ext ) {\r
+ nodes.put( n.getName(), n );\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {\r
+ for( final Long id : to_delete ) {\r
+ phy.deleteSubtree( phy.getNode( id ), true );\r
+ }\r
+ phy.clearHashIdToNodeMap();\r
+ phy.externalNodesHaveChanged();\r
+ }\r
+\r
+ public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )\r
+ throws IllegalArgumentException {\r
+ for( final String element : node_names_to_delete ) {\r
+ if ( ForesterUtil.isEmpty( element ) ) {\r
+ continue;\r
+ }\r
+ List<PhylogenyNode> nodes = null;\r
+ nodes = p.getNodes( element );\r
+ final Iterator<PhylogenyNode> it = nodes.iterator();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() ) {\r
+ throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );\r
+ }\r
+ p.deleteSubtree( n, true );\r
+ }\r
+ }\r
+ p.clearHashIdToNodeMap();\r
+ p.externalNodesHaveChanged();\r
+ }\r
+\r
+ public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,\r
+ final Phylogeny p ) {\r
+ final PhylogenyNodeIterator it = p.iteratorExternalForward();\r
+ final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];\r
+ int i = 0;\r
+ Arrays.sort( node_names_to_keep );\r
+ while ( it.hasNext() ) {\r
+ final String curent_name = it.next().getName();\r
+ if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {\r
+ to_delete[ i++ ] = curent_name;\r
+ }\r
+ }\r
+ PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );\r
+ final List<String> deleted = new ArrayList<String>();\r
+ for( final String n : to_delete ) {\r
+ if ( !ForesterUtil.isEmpty( n ) ) {\r
+ deleted.add( n );\r
+ }\r
+ }\r
+ return deleted;\r
+ }\r
+\r
+ public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {\r
+ final Set<Long> to_delete = new HashSet<Long>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.getNodeData().isHasTaxonomy() ) {\r
+ if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {\r
+ to_delete.add( n.getId() );\r
+ }\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );\r
+ }\r
+ }\r
+ deleteExternalNodesNegativeSelection( to_delete, phy );\r
+ }\r
+\r
+ final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {\r
+ final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode n = iter.next();\r
+ if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {\r
+ to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode d : to_delete ) {\r
+ PhylogenyMethods.removeNode( d, phy );\r
+ }\r
+ phy.clearHashIdToNodeMap();\r
+ phy.externalNodesHaveChanged();\r
+ }\r
+\r
+ final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {\r
+ if ( n.isInternal() ) {\r
+ throw new IllegalArgumentException( "node is not external" );\r
+ }\r
+ final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode i = it.next();\r
+ if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {\r
+ to_delete.add( i );\r
+ }\r
+ }\r
+ for( final PhylogenyNode d : to_delete ) {\r
+ phy.deleteSubtree( d, true );\r
+ }\r
+ phy.clearHashIdToNodeMap();\r
+ phy.externalNodesHaveChanged();\r
+ }\r
+\r
+ public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,\r
+ final double min_distance_to_root ) {\r
+ if ( min_distance_to_root <= 0 ) {\r
+ throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );\r
+ }\r
+ final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();\r
+ setAllIndicatorsToZero( phy );\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.getIndicator() != 0 ) {\r
+ continue;\r
+ }\r
+ l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );\r
+ if ( l.isEmpty() ) {\r
+ throw new RuntimeException( "this should not have happened" );\r
+ }\r
+ }\r
+ return l;\r
+ }\r
+\r
+ public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();\r
+ final Set<Long> encountered = new HashSet<Long>();\r
+ if ( !node.isExternal() ) {\r
+ final List<PhylogenyNode> exts = node.getAllExternalDescendants();\r
+ for( PhylogenyNode current : exts ) {\r
+ descs.add( current );\r
+ while ( current != node ) {\r
+ current = current.getParent();\r
+ if ( encountered.contains( current.getId() ) ) {\r
+ continue;\r
+ }\r
+ descs.add( current );\r
+ encountered.add( current.getId() );\r
+ }\r
+ }\r
+ }\r
+ return descs;\r
+ }\r
+\r
+ /**\r
+ *\r
+ * Convenience method\r
+ *\r
+ * @param node\r
+ * @return\r
+ */\r
+ public static Color getBranchColorValue( final PhylogenyNode node ) {\r
+ if ( node.getBranchData().getBranchColor() == null ) {\r
+ return null;\r
+ }\r
+ return node.getBranchData().getBranchColor().getValue();\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static double getBranchWidthValue( final PhylogenyNode node ) {\r
+ if ( !node.getBranchData().isHasBranchWidth() ) {\r
+ return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;\r
+ }\r
+ return node.getBranchData().getBranchWidth().getValue();\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static double getConfidenceValue( final PhylogenyNode node ) {\r
+ if ( !node.getBranchData().isHasConfidences() ) {\r
+ return Confidence.CONFIDENCE_DEFAULT_VALUE;\r
+ }\r
+ return node.getBranchData().getConfidence( 0 ).getValue();\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {\r
+ if ( !node.getBranchData().isHasConfidences() ) {\r
+ return new double[ 0 ];\r
+ }\r
+ final double[] values = new double[ node.getBranchData().getConfidences().size() ];\r
+ int i = 0;\r
+ for( final Confidence c : node.getBranchData().getConfidences() ) {\r
+ values[ i++ ] = c.getValue();\r
+ }\r
+ return values;\r
+ }\r
+\r
+ final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ return calculateLCA( n1, n2 ).getNodeData().getEvent();\r
+ }\r
+\r
+ /**\r
+ * Returns taxonomy t if all external descendants have\r
+ * the same taxonomy t, null otherwise.\r
+ *\r
+ */\r
+ public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();\r
+ Taxonomy tax = null;\r
+ for( final PhylogenyNode n : descs ) {\r
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {\r
+ return null;\r
+ }\r
+ else if ( tax == null ) {\r
+ tax = n.getNodeData().getTaxonomy();\r
+ }\r
+ else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {\r
+ return null;\r
+ }\r
+ }\r
+ return tax;\r
+ }\r
+\r
+ public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> children = node.getAllExternalDescendants();\r
+ PhylogenyNode farthest = null;\r
+ double longest = -Double.MAX_VALUE;\r
+ for( final PhylogenyNode child : children ) {\r
+ if ( PhylogenyMethods.getDistance( child, node ) > longest ) {\r
+ farthest = child;\r
+ longest = PhylogenyMethods.getDistance( child, node );\r
+ }\r
+ }\r
+ return farthest;\r
+ }\r
+\r
+ // public static PhylogenyMethods getInstance() {\r
+ // if ( PhylogenyMethods._instance == null ) {\r
+ // PhylogenyMethods._instance = new PhylogenyMethods();\r
+ // }\r
+ // return PhylogenyMethods._instance;\r
+ // }\r
+ /**\r
+ * Returns the largest confidence value found on phy.\r
+ */\r
+ static public double getMaximumConfidenceValue( final Phylogeny phy ) {\r
+ double max = -Double.MAX_VALUE;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final double s = PhylogenyMethods.getConfidenceValue( iter.next() );\r
+ if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {\r
+ max = s;\r
+ }\r
+ }\r
+ return max;\r
+ }\r
+\r
+ static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {\r
+ int min = Integer.MAX_VALUE;\r
+ int d = 0;\r
+ PhylogenyNode n;\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ n = it.next();\r
+ if ( n.isInternal() ) {\r
+ d = n.getNumberOfDescendants();\r
+ if ( d < min ) {\r
+ min = d;\r
+ }\r
+ }\r
+ }\r
+ return min;\r
+ }\r
+\r
+ /**\r
+ * Convenience method for display purposes.\r
+ * Not intended for algorithms.\r
+ */\r
+ public static String getSpecies( final PhylogenyNode node ) {\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ return "";\r
+ }\r
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {\r
+ return node.getNodeData().getTaxonomy().getScientificName();\r
+ }\r
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {\r
+ return node.getNodeData().getTaxonomy().getTaxonomyCode();\r
+ }\r
+ else {\r
+ return node.getNodeData().getTaxonomy().getCommonName();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Convenience method for display purposes.\r
+ * Not intended for algorithms.\r
+ */\r
+ public static String getTaxonomyIdentifier( final PhylogenyNode node ) {\r
+ if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {\r
+ return "";\r
+ }\r
+ return node.getNodeData().getTaxonomy().getIdentifier().getValue();\r
+ }\r
+\r
+ public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {\r
+ if ( n.isExternal() ) {\r
+ return true;\r
+ }\r
+ else {\r
+ if ( n.isDuplication() ) {\r
+ for( final PhylogenyNode desc : n.getDescendants() ) {\r
+ if ( !isAllDecendentsAreDuplications( desc ) ) {\r
+ return false;\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+\r
+ public static boolean isHasExternalDescendant( final PhylogenyNode node ) {\r
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {\r
+ if ( node.getChildNode( i ).isExternal() ) {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * This is case insensitive.\r
+ *\r
+ */\r
+ public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,\r
+ final String[] providers ) {\r
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {\r
+ final String my_tax_prov = tax.getIdentifier().getProvider();\r
+ for( final String provider : providers ) {\r
+ if ( provider.equalsIgnoreCase( my_tax_prov ) ) {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ public static void midpointRoot( final Phylogeny phylogeny ) {\r
+ if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {\r
+ return;\r
+ }\r
+ int counter = 0;\r
+ final int total_nodes = phylogeny.getNodeCount();\r
+ while ( true ) {\r
+ if ( ++counter > total_nodes ) {\r
+ throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );\r
+ }\r
+ PhylogenyNode a = null;\r
+ double da = 0;\r
+ double db = 0;\r
+ for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {\r
+ final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );\r
+ final double df = getDistance( f, phylogeny.getRoot() );\r
+ if ( df > 0 ) {\r
+ if ( df > da ) {\r
+ db = da;\r
+ da = df;\r
+ a = f;\r
+ }\r
+ else if ( df > db ) {\r
+ db = df;\r
+ }\r
+ }\r
+ }\r
+ final double diff = da - db;\r
+ if ( diff < 0.000001 ) {\r
+ break;\r
+ }\r
+ double x = da - ( diff / 2.0 );\r
+ while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {\r
+ x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );\r
+ a = a.getParent();\r
+ }\r
+ phylogeny.reRoot( a, x );\r
+ }\r
+ phylogeny.recalculateNumberOfExternalDescendants( true );\r
+ }\r
+\r
+ public static void normalizeBootstrapValues( final Phylogeny phylogeny,\r
+ final double max_bootstrap_value,\r
+ final double max_normalized_value ) {\r
+ for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ if ( node.isInternal() ) {\r
+ final double confidence = getConfidenceValue( node );\r
+ if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {\r
+ if ( confidence >= max_bootstrap_value ) {\r
+ setBootstrapConfidence( node, max_normalized_value );\r
+ }\r
+ else {\r
+ setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( phy.isEmpty() ) {\r
+ return nodes;\r
+ }\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ nodes.add( iter.next() );\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ /**\r
+ * Returns a map of distinct taxonomies of\r
+ * all external nodes of node.\r
+ * If at least one of the external nodes has no taxonomy,\r
+ * null is returned.\r
+ *\r
+ */\r
+ public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {\r
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();\r
+ final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();\r
+ for( final PhylogenyNode n : descs ) {\r
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {\r
+ return null;\r
+ }\r
+ final Taxonomy t = n.getNodeData().getTaxonomy();\r
+ if ( tax_map.containsKey( t ) ) {\r
+ tax_map.put( t, tax_map.get( t ) + 1 );\r
+ }\r
+ else {\r
+ tax_map.put( t, 1 );\r
+ }\r
+ }\r
+ return tax_map;\r
+ }\r
+\r
+ /**\r
+ * Arranges the order of childern for each node of this Phylogeny in such a\r
+ * way that either the branch with more children is on top (right) or on\r
+ * bottom (left), dependent on the value of boolean order.\r
+ *\r
+ * @param order\r
+ * decides in which direction to order\r
+ * @param pri\r
+ */\r
+ public static void orderAppearance( final PhylogenyNode n,\r
+ final boolean order,\r
+ final boolean order_ext_alphabetically,\r
+ final DESCENDANT_SORT_PRIORITY pri ) {\r
+ if ( n.isExternal() ) {\r
+ return;\r
+ }\r
+ else {\r
+ PhylogenyNode temp = null;\r
+ if ( ( n.getNumberOfDescendants() == 2 )\r
+ && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )\r
+ && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {\r
+ temp = n.getChildNode1();\r
+ n.setChild1( n.getChildNode2() );\r
+ n.setChild2( temp );\r
+ }\r
+ else if ( order_ext_alphabetically ) {\r
+ boolean all_ext = true;\r
+ for( final PhylogenyNode i : n.getDescendants() ) {\r
+ if ( !i.isExternal() ) {\r
+ all_ext = false;\r
+ break;\r
+ }\r
+ }\r
+ if ( all_ext ) {\r
+ PhylogenyMethods.sortNodeDescendents( n, pri );\r
+ }\r
+ }\r
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {\r
+ orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );\r
+ }\r
+ }\r
+ }\r
+\r
+ public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {\r
+ for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ double red = 0.0;\r
+ double green = 0.0;\r
+ double blue = 0.0;\r
+ int n = 0;\r
+ if ( node.isInternal() ) {\r
+ //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {\r
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {\r
+ final PhylogenyNode child_node = node.getChildNode( i );\r
+ final Color child_color = getBranchColorValue( child_node );\r
+ if ( child_color != null ) {\r
+ ++n;\r
+ red += child_color.getRed();\r
+ green += child_color.getGreen();\r
+ blue += child_color.getBlue();\r
+ }\r
+ }\r
+ setBranchColorValue( node,\r
+ new Color( ForesterUtil.roundToInt( red / n ),\r
+ ForesterUtil.roundToInt( green / n ),\r
+ ForesterUtil.roundToInt( blue / n ) ) );\r
+ }\r
+ }\r
+ }\r
+\r
+ public static final void preOrderReId( final Phylogeny phy ) {\r
+ if ( phy.isEmpty() ) {\r
+ return;\r
+ }\r
+ phy.setIdToNodeMap( null );\r
+ long i = PhylogenyNode.getNodeCount();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ it.next().setId( i++ );\r
+ }\r
+ PhylogenyNode.setNodeCount( i );\r
+ }\r
+\r
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ final Phylogeny[] trees = factory.create( file, parser );\r
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {\r
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );\r
+ }\r
+ return trees;\r
+ }\r
+\r
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )\r
+ throws IOException {\r
+ final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();\r
+ for( final File file : files ) {\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ final Phylogeny[] trees = factory.create( file, parser );\r
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {\r
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );\r
+ }\r
+ tree_list.addAll( Arrays.asList( trees ) );\r
+ }\r
+ return tree_list.toArray( new Phylogeny[ tree_list.size() ] );\r
+ }\r
+\r
+ public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {\r
+ if ( remove_me.isRoot() ) {\r
+ if ( remove_me.getNumberOfDescendants() == 1 ) {\r
+ final PhylogenyNode desc = remove_me.getDescendants().get( 0 );\r
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),\r
+ desc.getDistanceToParent() ) );\r
+ desc.setParent( null );\r
+ phylogeny.setRoot( desc );\r
+ phylogeny.clearHashIdToNodeMap();\r
+ }\r
+ else {\r
+ throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );\r
+ }\r
+ }\r
+ else if ( remove_me.isExternal() ) {\r
+ phylogeny.deleteSubtree( remove_me, false );\r
+ phylogeny.clearHashIdToNodeMap();\r
+ phylogeny.externalNodesHaveChanged();\r
+ }\r
+ else {\r
+ final PhylogenyNode parent = remove_me.getParent();\r
+ final List<PhylogenyNode> descs = remove_me.getDescendants();\r
+ parent.removeChildNode( remove_me );\r
+ for( final PhylogenyNode desc : descs ) {\r
+ parent.addAsChild( desc );\r
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),\r
+ desc.getDistanceToParent() ) );\r
+ }\r
+ remove_me.setParent( null );\r
+ phylogeny.clearHashIdToNodeMap();\r
+ phylogeny.externalNodesHaveChanged();\r
+ }\r
+ }\r
+\r
+ public static List<PhylogenyNode> searchData( final String query,\r
+ final Phylogeny phy,\r
+ final boolean case_sensitive,\r
+ final boolean partial,\r
+ final boolean regex,\r
+ final boolean search_domains ) {\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( phy.isEmpty() || ( query == null ) ) {\r
+ return nodes;\r
+ }\r
+ if ( ForesterUtil.isEmpty( query ) ) {\r
+ return nodes;\r
+ }\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ boolean match = false;\r
+ if ( match( node.getName(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getScientificName(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ regex ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && ( node.getNodeData().getTaxonomy().getIdentifier() != null )\r
+ && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ regex ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {\r
+ final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();\r
+ I: for( final String syn : syns ) {\r
+ if ( match( syn, query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match\r
+ && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAccession() != null )\r
+ && match( node.getNodeData().getSequence().getAccession().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ regex ) ) {\r
+ match = true;\r
+ }\r
+ if ( search_domains && !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {\r
+ final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();\r
+ I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {\r
+ if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {\r
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {\r
+ if ( match( ann.getDesc(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( ann.getRef(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {\r
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {\r
+ if ( match( x.getComment(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getSource(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getValue(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {\r
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial, regex ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( match ) {\r
+ nodes.add( node );\r
+ }\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,\r
+ final Phylogeny phy,\r
+ final boolean case_sensitive,\r
+ final boolean partial,\r
+ final boolean search_domains ) {\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {\r
+ return nodes;\r
+ }\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ boolean all_matched = true;\r
+ for( final String query : queries ) {\r
+ boolean match = false;\r
+ if ( ForesterUtil.isEmpty( query ) ) {\r
+ continue;\r
+ }\r
+ if ( match( node.getName(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ false ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getCommonName(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ false ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && match( node.getNodeData().getTaxonomy().getScientificName(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ false ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && ( node.getNodeData().getTaxonomy().getIdentifier() != null )\r
+ && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ false ) ) {\r
+ match = true;\r
+ }\r
+ else if ( node.getNodeData().isHasTaxonomy()\r
+ && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {\r
+ final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();\r
+ I: for( final String syn : syns ) {\r
+ if ( match( syn, query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match\r
+ && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ }\r
+ if ( !match\r
+ && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAccession() != null )\r
+ && match( node.getNodeData().getSequence().getAccession().getValue(),\r
+ query,\r
+ case_sensitive,\r
+ partial,\r
+ false ) ) {\r
+ match = true;\r
+ }\r
+ if ( search_domains && !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {\r
+ final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();\r
+ I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {\r
+ if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {\r
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {\r
+ if ( match( ann.getDesc(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( ann.getRef(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if ( !match && node.getNodeData().isHasSequence()\r
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {\r
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {\r
+ if ( match( x.getComment(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getSource(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ if ( match( x.getValue(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ //\r
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {\r
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();\r
+ I: while ( it.hasNext() ) {\r
+ if ( match( it.next(), query, case_sensitive, partial, false ) ) {\r
+ match = true;\r
+ break I;\r
+ }\r
+ }\r
+ }\r
+ if ( !match ) {\r
+ all_matched = false;\r
+ break;\r
+ }\r
+ }\r
+ if ( all_matched ) {\r
+ nodes.add( node );\r
+ }\r
+ }\r
+ return nodes;\r
+ }\r
+\r
+ public static void setAllIndicatorsToZero( final Phylogeny phy ) {\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {\r
+ it.next().setIndicator( ( byte ) 0 );\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Convenience method.\r
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise).\r
+ */\r
+ public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {\r
+ setConfidence( node, bootstrap_confidence_value, "bootstrap" );\r
+ }\r
+\r
+ public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {\r
+ if ( node.getBranchData().getBranchColor() == null ) {\r
+ node.getBranchData().setBranchColor( new BranchColor() );\r
+ }\r
+ node.getBranchData().getBranchColor().setValue( color );\r
+ }\r
+\r
+ /**\r
+ * Convenience method\r
+ */\r
+ public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {\r
+ node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );\r
+ }\r
+\r
+ /**\r
+ * Convenience method.\r
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise).\r
+ */\r
+ public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {\r
+ setConfidence( node, confidence_value, "" );\r
+ }\r
+\r
+ /**\r
+ * Convenience method.\r
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise).\r
+ */\r
+ public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {\r
+ Confidence c = null;\r
+ if ( node.getBranchData().getNumberOfConfidences() > 0 ) {\r
+ c = node.getBranchData().getConfidence( 0 );\r
+ }\r
+ else {\r
+ c = new Confidence();\r
+ node.getBranchData().addConfidence( c );\r
+ }\r
+ c.setType( type );\r
+ c.setValue( confidence_value );\r
+ }\r
+\r
+ public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ node.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ node.getNodeData().getTaxonomy().setScientificName( scientific_name );\r
+ }\r
+\r
+ /**\r
+ * Convenience method to set the taxonomy code of a phylogeny node.\r
+ *\r
+ *\r
+ * @param node\r
+ * @param taxonomy_code\r
+ * @throws PhyloXmlDataFormatException\r
+ */\r
+ public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )\r
+ throws PhyloXmlDataFormatException {\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ node.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );\r
+ }\r
+\r
+ final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {\r
+ Comparator<PhylogenyNode> c;\r
+ switch ( pri ) {\r
+ case SEQUENCE:\r
+ c = new PhylogenyNodeSortSequencePriority();\r
+ break;\r
+ case NODE_NAME:\r
+ c = new PhylogenyNodeSortNodeNamePriority();\r
+ break;\r
+ default:\r
+ c = new PhylogenyNodeSortTaxonomyPriority();\r
+ }\r
+ final List<PhylogenyNode> descs = node.getDescendants();\r
+ Collections.sort( descs, c );\r
+ int i = 0;\r
+ for( final PhylogenyNode desc : descs ) {\r
+ node.setChildNode( i++, desc );\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Removes from Phylogeny to_be_stripped all external Nodes which are\r
+ * associated with a species NOT found in Phylogeny reference.\r
+ *\r
+ * @param reference\r
+ * a reference Phylogeny\r
+ * @param to_be_stripped\r
+ * Phylogeny to be stripped\r
+ * @return nodes removed from to_be_stripped\r
+ */\r
+ public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,\r
+ final Phylogeny to_be_stripped ) {\r
+ final Set<String> ref_ext_taxo = new HashSet<String>();\r
+ for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ throw new IllegalArgumentException( "no taxonomic data in node: " + n );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {\r
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {\r
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {\r
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );\r
+ }\r
+ }\r
+ final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ nodes_to_delete.add( n );\r
+ }\r
+ else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n\r
+ .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {\r
+ nodes_to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode n : nodes_to_delete ) {\r
+ to_be_stripped.deleteSubtree( n, true );\r
+ }\r
+ to_be_stripped.clearHashIdToNodeMap();\r
+ to_be_stripped.externalNodesHaveChanged();\r
+ return nodes_to_delete;\r
+ }\r
+\r
+ final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ double value = -1;\r
+ try {\r
+ value = Double.parseDouble( n.getName() );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "\r
+ + e.getLocalizedMessage() );\r
+ }\r
+ if ( value >= 0.0 ) {\r
+ n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );\r
+ n.setName( "" );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ double value = -1;\r
+ try {\r
+ value = Double.parseDouble( n.getName() );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ return false;\r
+ }\r
+ if ( ( value < 0.0 ) || ( value > 100 ) ) {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+\r
+ final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy, final String confidence_type ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ transferInternalNodeNameToConfidence( confidence_type, it.next() );\r
+ }\r
+ }\r
+\r
+ private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {\r
+ if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {\r
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ double d = -1.0;\r
+ try {\r
+ d = Double.parseDouble( n.getName() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ d = -1.0;\r
+ }\r
+ if ( d >= 0.0 ) {\r
+ n.getBranchData().addConfidence( new Confidence( d, confidence_type ) );\r
+ n.setName( "" );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ final static public void transferNodeNameToField( final Phylogeny phy,\r
+ final PhylogenyNodeField field,\r
+ final boolean external_only ) throws PhyloXmlDataFormatException {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( external_only && n.isInternal() ) {\r
+ continue;\r
+ }\r
+ final String name = n.getName().trim();\r
+ if ( !ForesterUtil.isEmpty( name ) ) {\r
+ switch ( field ) {\r
+ case TAXONOMY_CODE:\r
+ n.setName( "" );\r
+ setTaxonomyCode( n, name );\r
+ break;\r
+ case TAXONOMY_SCIENTIFIC_NAME:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ n.getNodeData().getTaxonomy().setScientificName( name );\r
+ break;\r
+ case TAXONOMY_COMMON_NAME:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ n.getNodeData().getTaxonomy().setCommonName( name );\r
+ break;\r
+ case SEQUENCE_SYMBOL:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().setSequence( new Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setSymbol( name );\r
+ break;\r
+ case SEQUENCE_NAME:\r
+ n.setName( "" );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().setSequence( new Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setName( name );\r
+ break;\r
+ case TAXONOMY_ID_UNIPROT_1: {\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ String id = name;\r
+ final int i = name.indexOf( '_' );\r
+ if ( i > 0 ) {\r
+ id = name.substring( 0, i );\r
+ }\r
+ else {\r
+ n.setName( "" );\r
+ }\r
+ n.getNodeData().getTaxonomy()\r
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );\r
+ break;\r
+ }\r
+ case TAXONOMY_ID_UNIPROT_2: {\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ String id = name;\r
+ final int i = name.indexOf( '_' );\r
+ if ( i > 0 ) {\r
+ id = name.substring( i + 1, name.length() );\r
+ }\r
+ else {\r
+ n.setName( "" );\r
+ }\r
+ n.getNodeData().getTaxonomy()\r
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );\r
+ break;\r
+ }\r
+ case TAXONOMY_ID: {\r
+ if ( !n.getNodeData().isHasTaxonomy() ) {\r
+ n.getNodeData().setTaxonomy( new Taxonomy() );\r
+ }\r
+ n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ static double addPhylogenyDistances( final double a, final double b ) {\r
+ if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {\r
+ return a + b;\r
+ }\r
+ else if ( a >= 0.0 ) {\r
+ return a;\r
+ }\r
+ else if ( b >= 0.0 ) {\r
+ return b;\r
+ }\r
+ return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;\r
+ }\r
+\r
+ static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {\r
+ double d = 0;\r
+ boolean all_default = true;\r
+ while ( anc != desc ) {\r
+ if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
+ d += desc.getDistanceToParent();\r
+ if ( all_default ) {\r
+ all_default = false;\r
+ }\r
+ }\r
+ desc = desc.getParent();\r
+ }\r
+ if ( all_default ) {\r
+ return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;\r
+ }\r
+ return d;\r
+ }\r
+\r
+ /**\r
+ * Deep copies the phylogeny originating from this node.\r
+ */\r
+ static PhylogenyNode copySubTree( final PhylogenyNode source ) {\r
+ if ( source == null ) {\r
+ return null;\r
+ }\r
+ else {\r
+ final PhylogenyNode newnode = source.copyNodeData();\r
+ if ( !source.isExternal() ) {\r
+ for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {\r
+ newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );\r
+ }\r
+ }\r
+ return newnode;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Shallow copies the phylogeny originating from this node.\r
+ */\r
+ static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {\r
+ if ( source == null ) {\r
+ return null;\r
+ }\r
+ else {\r
+ final PhylogenyNode newnode = source.copyNodeDataShallow();\r
+ if ( !source.isExternal() ) {\r
+ for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {\r
+ newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );\r
+ }\r
+ }\r
+ return newnode;\r
+ }\r
+ }\r
+\r
+ private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,\r
+ final double min_distance_to_root ) {\r
+ final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();\r
+ final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );\r
+ for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {\r
+ if ( ext.getIndicator() != 0 ) {\r
+ throw new RuntimeException( "this should not have happened" );\r
+ }\r
+ ext.setIndicator( ( byte ) 1 );\r
+ l.add( ext );\r
+ }\r
+ return l;\r
+ }\r
+\r
+ /**\r
+ * Calculates the distance between PhylogenyNodes n1 and n2.\r
+ * PRECONDITION: n1 is a descendant of n2.\r
+ *\r
+ * @param n1\r
+ * a descendant of n2\r
+ * @param n2\r
+ * @return distance between n1 and n2\r
+ */\r
+ private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ double d = 0.0;\r
+ while ( n1 != n2 ) {\r
+ if ( n1.getDistanceToParent() > 0.0 ) {\r
+ d += n1.getDistanceToParent();\r
+ }\r
+ n1 = n1.getParent();\r
+ }\r
+ return d;\r
+ }\r
+\r
+ private static boolean match( final String s,\r
+ final String query,\r
+ final boolean case_sensitive,\r
+ final boolean partial,\r
+ final boolean regex ) {\r
+ if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {\r
+ return false;\r
+ }\r
+ String my_s = s.trim();\r
+ String my_query = query.trim();\r
+ if ( !case_sensitive && !regex ) {\r
+ my_s = my_s.toLowerCase();\r
+ my_query = my_query.toLowerCase();\r
+ }\r
+ if ( regex ) {\r
+ Pattern p = null;\r
+ try {\r
+ if ( case_sensitive ) {\r
+ p = Pattern.compile( my_query );\r
+ }\r
+ else {\r
+ p = Pattern.compile( my_query, Pattern.CASE_INSENSITIVE );\r
+ }\r
+ }\r
+ catch ( final PatternSyntaxException e ) {\r
+ return false;\r
+ }\r
+ if ( p != null ) {\r
+ return p.matcher( my_s ).find();\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+ else if ( partial ) {\r
+ return my_s.indexOf( my_query ) >= 0;\r
+ }\r
+ else {\r
+ Pattern p = null;\r
+ try {\r
+ p = Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" );\r
+ }\r
+ catch ( final PatternSyntaxException e ) {\r
+ return false;\r
+ }\r
+ if ( p != null ) {\r
+ return p.matcher( my_s ).find();\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+\r
+ private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {\r
+ PhylogenyNode n = node;\r
+ PhylogenyNode prev = node;\r
+ while ( min_distance_to_root < n.calculateDistanceToRoot() ) {\r
+ prev = n;\r
+ n = n.getParent();\r
+ }\r
+ return prev;\r
+ }\r
+\r
+ public static enum DESCENDANT_SORT_PRIORITY {\r
+ NODE_NAME, SEQUENCE, TAXONOMY;\r
+ }\r
+\r
+ public static enum PhylogenyNodeField {\r
+ CLADE_NAME,\r
+ SEQUENCE_NAME,\r
+ SEQUENCE_SYMBOL,\r
+ TAXONOMY_CODE,\r
+ TAXONOMY_COMMON_NAME,\r
+ TAXONOMY_ID,\r
+ TAXONOMY_ID_UNIPROT_1,\r
+ TAXONOMY_ID_UNIPROT_2,\r
+ TAXONOMY_SCIENTIFIC_NAME;\r
+ }\r
+\r
+ public static void addMolecularSeqsToTree( final Phylogeny phy, final Msa msa ) {\r
+ for( int s = 0; s < msa.getNumberOfSequences(); ++s ) {\r
+ final org.forester.sequence.MolecularSequence seq = msa.getSequence( s );\r
+ final PhylogenyNode node = phy.getNode( seq.getIdentifier() );\r
+ final org.forester.phylogeny.data.Sequence new_seq = new Sequence();\r
+ new_seq.setMolecularSequenceAligned( true );\r
+ new_seq.setMolecularSequence( seq.getMolecularSequenceAsString() );\r
+ new_seq.setName( seq.getIdentifier() );\r
+ try {\r
+ new_seq.setType( PhyloXmlUtil.SEQ_TYPE_PROTEIN );\r
+ }\r
+ catch ( final PhyloXmlDataFormatException ignore ) {\r
+ // do nothing\r
+ }\r
+ node.getNodeData().addSequence( new_seq );\r
+ }\r
+ }\r
+\r
+ final private static class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {\r
+\r
+ @Override\r
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ }\r
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getGeneName()\r
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {\r
+ return n1.getNodeData().getSequence().getSymbol()\r
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );\r
+ }\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {\r
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );\r
+ }\r
+ return 0;\r
+ }\r
+ }\r
+\r
+ final private static class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {\r
+\r
+ @Override\r
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getGeneName()\r
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {\r
+ return n1.getNodeData().getSequence().getSymbol()\r
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );\r
+ }\r
+ }\r
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {\r
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );\r
+ }\r
+ return 0;\r
+ }\r
+ }\r
+\r
+ final private static class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {\r
+\r
+ @Override\r
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {\r
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );\r
+ }\r
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {\r
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()\r
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );\r
+ }\r
+ }\r
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getName().toLowerCase()\r
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {\r
+ return n1.getNodeData().getSequence().getGeneName()\r
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );\r
+ }\r
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )\r
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {\r
+ return n1.getNodeData().getSequence().getSymbol()\r
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );\r
+ }\r
+ }\r
+ return 0;\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff