2 // FORESTER -- software libraries and applications
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3 // for evolutionary biology research and applications.
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5 // Copyright (C) 2008-2009 Christian M. Zmasek
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6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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7 // All rights reserved
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9 // This library is free software; you can redistribute it and/or
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10 // modify it under the terms of the GNU Lesser General Public
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11 // License as published by the Free Software Foundation; either
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12 // version 2.1 of the License, or (at your option) any later version.
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14 // This library is distributed in the hope that it will be useful,
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15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 // Lesser General Public License for more details.
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19 // You should have received a copy of the GNU Lesser General Public
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20 // License along with this library; if not, write to the Free Software
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21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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23 // Contact: phylosoft @ gmail . com
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24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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26 package org.forester.phylogeny;
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28 import java.awt.Color;
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29 import java.io.File;
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30 import java.io.IOException;
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31 import java.util.ArrayList;
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32 import java.util.Arrays;
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33 import java.util.Collections;
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34 import java.util.Comparator;
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35 import java.util.HashMap;
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36 import java.util.HashSet;
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37 import java.util.Iterator;
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38 import java.util.List;
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39 import java.util.Map;
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40 import java.util.Set;
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41 import java.util.regex.Matcher;
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42 import java.util.regex.Pattern;
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44 import org.forester.io.parsers.FastaParser;
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45 import org.forester.io.parsers.PhylogenyParser;
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46 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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47 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
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48 import org.forester.io.parsers.util.PhylogenyParserException;
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49 import org.forester.msa.Msa;
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50 import org.forester.phylogeny.data.Accession;
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51 import org.forester.phylogeny.data.Annotation;
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52 import org.forester.phylogeny.data.BranchColor;
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53 import org.forester.phylogeny.data.BranchWidth;
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54 import org.forester.phylogeny.data.Confidence;
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55 import org.forester.phylogeny.data.DomainArchitecture;
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56 import org.forester.phylogeny.data.Event;
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57 import org.forester.phylogeny.data.Identifier;
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58 import org.forester.phylogeny.data.PhylogenyDataUtil;
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59 import org.forester.phylogeny.data.Sequence;
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60 import org.forester.phylogeny.data.Taxonomy;
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61 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
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62 import org.forester.phylogeny.factories.PhylogenyFactory;
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63 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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64 import org.forester.util.BasicDescriptiveStatistics;
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65 import org.forester.util.DescriptiveStatistics;
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66 import org.forester.util.ForesterUtil;
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68 public class PhylogenyMethods {
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70 private PhylogenyMethods() {
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71 // Hidden constructor.
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75 public Object clone() throws CloneNotSupportedException {
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76 throw new CloneNotSupportedException();
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79 public static boolean extractFastaInformation( final Phylogeny phy ) {
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80 boolean could_extract = false;
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81 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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82 final PhylogenyNode node = iter.next();
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83 if ( !ForesterUtil.isEmpty( node.getName() ) ) {
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84 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
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85 if ( name_m.lookingAt() ) {
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86 could_extract = true;
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87 final String acc_source = name_m.group( 1 );
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88 final String acc = name_m.group( 2 );
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89 final String seq_name = name_m.group( 3 );
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90 final String tax_sn = name_m.group( 4 );
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91 if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
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92 ForesterUtil.ensurePresenceOfSequence( node );
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93 node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
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95 if ( !ForesterUtil.isEmpty( seq_name ) ) {
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96 ForesterUtil.ensurePresenceOfSequence( node );
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97 node.getNodeData().getSequence( 0 ).setName( seq_name );
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99 if ( !ForesterUtil.isEmpty( tax_sn ) ) {
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100 ForesterUtil.ensurePresenceOfTaxonomy( node );
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101 node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
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106 return could_extract;
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109 public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
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110 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
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111 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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112 final PhylogenyNode n = iter.next();
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113 if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
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114 stats.addValue( n.getDistanceToParent() );
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120 public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
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121 final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
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122 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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123 final PhylogenyNode n = iter.next();
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124 if ( !n.isExternal() && !n.isRoot() ) {
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125 if ( n.getBranchData().isHasConfidences() ) {
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126 for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
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127 final Confidence c = n.getBranchData().getConfidences().get( i );
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128 if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
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129 stats.add( i, new BasicDescriptiveStatistics() );
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131 if ( !ForesterUtil.isEmpty( c.getType() ) ) {
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132 if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
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133 if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
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134 throw new IllegalArgumentException( "support values in node [" + n.toString()
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135 + "] appear inconsistently ordered" );
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138 stats.get( i ).setDescription( c.getType() );
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140 stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
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149 * Calculates the distance between PhylogenyNodes node1 and node2.
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154 * @return distance between node1 and node2
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156 public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
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157 final PhylogenyNode lca = calculateLCA( node1, node2 );
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158 final PhylogenyNode n1 = node1;
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159 final PhylogenyNode n2 = node2;
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160 return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
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164 * Returns the LCA of PhylogenyNodes node1 and node2.
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169 * @return LCA of node1 and node2
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171 public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
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172 if ( node1 == null ) {
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173 throw new IllegalArgumentException( "first argument (node) is null" );
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175 if ( node2 == null ) {
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176 throw new IllegalArgumentException( "second argument (node) is null" );
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178 if ( node1 == node2 ) {
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181 if ( ( node1.getParent() == node2.getParent() ) ) {
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182 return node1.getParent();
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184 int depth1 = node1.calculateDepth();
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185 int depth2 = node2.calculateDepth();
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186 while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {
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187 if ( depth1 > depth2 ) {
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188 node1 = node1.getParent();
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191 else if ( depth2 > depth1 ) {
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192 node2 = node2.getParent();
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196 if ( node1 == node2 ) {
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199 node1 = node1.getParent();
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200 node2 = node2.getParent();
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205 throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
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209 * Returns the LCA of PhylogenyNodes node1 and node2.
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210 * Precondition: ids are in pre-order (or level-order).
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215 * @return LCA of node1 and node2
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217 public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
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218 if ( node1 == null ) {
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219 throw new IllegalArgumentException( "first argument (node) is null" );
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221 if ( node2 == null ) {
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222 throw new IllegalArgumentException( "second argument (node) is null" );
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224 while ( node1 != node2 ) {
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225 if ( node1.getId() > node2.getId() ) {
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226 node1 = node1.getParent();
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229 node2 = node2.getParent();
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235 public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
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236 if ( node.isExternal() ) {
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240 for( PhylogenyNode d : node.getAllExternalDescendants() ) {
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242 while ( d != node ) {
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243 if ( d.isCollapse() ) {
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251 if ( max < steps ) {
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258 public static int calculateMaxDepth( final Phylogeny phy ) {
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260 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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261 final PhylogenyNode node = iter.next();
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262 final int steps = node.calculateDepth();
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263 if ( steps > max ) {
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270 public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
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272 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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273 final PhylogenyNode node = iter.next();
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274 final double d = node.calculateDistanceToRoot();
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282 public static PhylogenyNode calculateNodeWithMaxDistanceToRoot( final Phylogeny phy ) {
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284 PhylogenyNode max_node = phy.getFirstExternalNode();
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285 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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286 final PhylogenyNode node = iter.next();
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287 final double d = node.calculateDistanceToRoot();
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296 public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
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297 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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299 for( final PhylogenyNode n : descs ) {
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300 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
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307 public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
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308 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
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309 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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310 final PhylogenyNode n = iter.next();
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311 if ( !n.isExternal() ) {
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312 stats.addValue( n.getNumberOfDescendants() );
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318 public final static void collapseSubtreeStructure( final PhylogenyNode n ) {
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319 final List<PhylogenyNode> eds = n.getAllExternalDescendants();
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320 final List<Double> d = new ArrayList<Double>();
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321 for( final PhylogenyNode ed : eds ) {
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322 d.add( calculateDistanceToAncestor( n, ed ) );
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324 for( int i = 0; i < eds.size(); ++i ) {
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325 n.setChildNode( i, eds.get( i ) );
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326 eds.get( i ).setDistanceToParent( d.get( i ) );
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330 public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
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332 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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333 final PhylogenyNode n = iter.next();
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334 if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {
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341 public static int countNumberOfPolytomies( final Phylogeny phy ) {
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343 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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344 final PhylogenyNode n = iter.next();
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345 if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
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352 public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
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353 final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
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354 final List<PhylogenyNode> ext = phy.getExternalNodes();
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355 for( final PhylogenyNode n : ext ) {
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356 nodes.put( n.getName(), n );
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361 public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
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362 for( final Long id : to_delete ) {
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363 phy.deleteSubtree( phy.getNode( id ), true );
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365 phy.clearHashIdToNodeMap();
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366 phy.externalNodesHaveChanged();
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369 public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
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370 throws IllegalArgumentException {
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371 for( final String element : node_names_to_delete ) {
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372 if ( ForesterUtil.isEmpty( element ) ) {
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375 List<PhylogenyNode> nodes = null;
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376 nodes = p.getNodes( element );
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377 final Iterator<PhylogenyNode> it = nodes.iterator();
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378 while ( it.hasNext() ) {
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379 final PhylogenyNode n = it.next();
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380 if ( !n.isExternal() ) {
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381 throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
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383 p.deleteSubtree( n, true );
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386 p.clearHashIdToNodeMap();
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387 p.externalNodesHaveChanged();
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390 public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
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391 final Phylogeny p ) {
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392 final PhylogenyNodeIterator it = p.iteratorExternalForward();
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393 final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
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395 Arrays.sort( node_names_to_keep );
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396 while ( it.hasNext() ) {
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397 final String curent_name = it.next().getName();
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398 if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
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399 to_delete[ i++ ] = curent_name;
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402 PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
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403 final List<String> deleted = new ArrayList<String>();
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404 for( final String n : to_delete ) {
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405 if ( !ForesterUtil.isEmpty( n ) ) {
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412 public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {
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413 final Set<Long> to_delete = new HashSet<Long>();
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414 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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415 final PhylogenyNode n = it.next();
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416 if ( n.getNodeData().isHasTaxonomy() ) {
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417 if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
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418 to_delete.add( n.getId() );
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422 throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
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425 deleteExternalNodesNegativeSelection( to_delete, phy );
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428 final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
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429 final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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430 for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
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431 final PhylogenyNode n = iter.next();
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432 if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {
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433 to_delete.add( n );
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436 for( final PhylogenyNode d : to_delete ) {
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437 PhylogenyMethods.removeNode( d, phy );
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439 phy.clearHashIdToNodeMap();
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440 phy.externalNodesHaveChanged();
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443 final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
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444 if ( n.isInternal() ) {
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445 throw new IllegalArgumentException( "node is not external" );
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447 final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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448 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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449 final PhylogenyNode i = it.next();
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450 if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
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451 to_delete.add( i );
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454 for( final PhylogenyNode d : to_delete ) {
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455 phy.deleteSubtree( d, true );
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457 phy.clearHashIdToNodeMap();
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458 phy.externalNodesHaveChanged();
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461 public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,
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462 final double min_distance_to_root ) {
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463 if ( min_distance_to_root <= 0 ) {
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464 throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );
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466 final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();
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467 setAllIndicatorsToZero( phy );
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468 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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469 final PhylogenyNode n = it.next();
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470 if ( n.getIndicator() != 0 ) {
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473 l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
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474 if ( l.isEmpty() ) {
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475 throw new RuntimeException( "this should not have happened" );
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481 public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
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482 final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
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483 final Set<Long> encountered = new HashSet<Long>();
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484 if ( !node.isExternal() ) {
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485 final List<PhylogenyNode> exts = node.getAllExternalDescendants();
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486 for( PhylogenyNode current : exts ) {
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487 descs.add( current );
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488 while ( current != node ) {
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489 current = current.getParent();
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490 if ( encountered.contains( current.getId() ) ) {
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493 descs.add( current );
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494 encountered.add( current.getId() );
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503 * Convenience method
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508 public static Color getBranchColorValue( final PhylogenyNode node ) {
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509 if ( node.getBranchData().getBranchColor() == null ) {
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512 return node.getBranchData().getBranchColor().getValue();
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516 * Convenience method
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518 public static double getBranchWidthValue( final PhylogenyNode node ) {
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519 if ( !node.getBranchData().isHasBranchWidth() ) {
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520 return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;
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522 return node.getBranchData().getBranchWidth().getValue();
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526 * Convenience method
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528 public static double getConfidenceValue( final PhylogenyNode node ) {
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529 if ( !node.getBranchData().isHasConfidences() ) {
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530 return Confidence.CONFIDENCE_DEFAULT_VALUE;
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532 return node.getBranchData().getConfidence( 0 ).getValue();
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536 * Convenience method
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538 public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {
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539 if ( !node.getBranchData().isHasConfidences() ) {
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540 return new double[ 0 ];
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542 final double[] values = new double[ node.getBranchData().getConfidences().size() ];
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544 for( final Confidence c : node.getBranchData().getConfidences() ) {
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545 values[ i++ ] = c.getValue();
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550 final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
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551 return calculateLCA( n1, n2 ).getNodeData().getEvent();
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555 * Returns taxonomy t if all external descendants have
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556 * the same taxonomy t, null otherwise.
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559 public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {
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560 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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561 Taxonomy tax = null;
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562 for( final PhylogenyNode n : descs ) {
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563 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
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566 else if ( tax == null ) {
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567 tax = n.getNodeData().getTaxonomy();
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569 else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {
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576 public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {
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577 final List<PhylogenyNode> children = node.getAllExternalDescendants();
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578 PhylogenyNode farthest = null;
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579 double longest = -Double.MAX_VALUE;
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580 for( final PhylogenyNode child : children ) {
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581 if ( PhylogenyMethods.getDistance( child, node ) > longest ) {
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583 longest = PhylogenyMethods.getDistance( child, node );
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589 // public static PhylogenyMethods getInstance() {
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590 // if ( PhylogenyMethods._instance == null ) {
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591 // PhylogenyMethods._instance = new PhylogenyMethods();
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593 // return PhylogenyMethods._instance;
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596 * Returns the largest confidence value found on phy.
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598 static public double getMaximumConfidenceValue( final Phylogeny phy ) {
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599 double max = -Double.MAX_VALUE;
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600 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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601 final double s = PhylogenyMethods.getConfidenceValue( iter.next() );
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602 if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {
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609 static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {
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610 int min = Integer.MAX_VALUE;
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613 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
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615 if ( n.isInternal() ) {
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616 d = n.getNumberOfDescendants();
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626 * Convenience method for display purposes.
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627 * Not intended for algorithms.
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629 public static String getSpecies( final PhylogenyNode node ) {
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630 if ( !node.getNodeData().isHasTaxonomy() ) {
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633 else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
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634 return node.getNodeData().getTaxonomy().getScientificName();
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636 if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
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637 return node.getNodeData().getTaxonomy().getTaxonomyCode();
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640 return node.getNodeData().getTaxonomy().getCommonName();
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645 * Convenience method for display purposes.
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646 * Not intended for algorithms.
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648 public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
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649 if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
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652 return node.getNodeData().getTaxonomy().getIdentifier().getValue();
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655 public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
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656 if ( n.isExternal() ) {
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660 if ( n.isDuplication() ) {
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661 for( final PhylogenyNode desc : n.getDescendants() ) {
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662 if ( !isAllDecendentsAreDuplications( desc ) ) {
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674 public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
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675 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
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676 if ( node.getChildNode( i ).isExternal() ) {
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684 * This is case insensitive.
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687 public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
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688 final String[] providers ) {
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689 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
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690 final String my_tax_prov = tax.getIdentifier().getProvider();
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691 for( final String provider : providers ) {
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692 if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
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703 public static void midpointRoot( final Phylogeny phylogeny ) {
\r
704 if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {
\r
708 final int total_nodes = phylogeny.getNodeCount();
\r
710 if ( ++counter > total_nodes ) {
\r
711 throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );
\r
713 PhylogenyNode a = null;
\r
716 for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {
\r
717 final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );
\r
718 final double df = getDistance( f, phylogeny.getRoot() );
\r
725 else if ( df > db ) {
\r
730 final double diff = da - db;
\r
731 if ( diff < 0.000001 ) {
\r
734 double x = da - ( diff / 2.0 );
\r
735 while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {
\r
736 x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );
\r
739 phylogeny.reRoot( a, x );
\r
741 phylogeny.recalculateNumberOfExternalDescendants( true );
\r
744 public static void normalizeBootstrapValues( final Phylogeny phylogeny,
\r
745 final double max_bootstrap_value,
\r
746 final double max_normalized_value ) {
\r
747 for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
\r
748 final PhylogenyNode node = iter.next();
\r
749 if ( node.isInternal() ) {
\r
750 final double confidence = getConfidenceValue( node );
\r
751 if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
\r
752 if ( confidence >= max_bootstrap_value ) {
\r
753 setBootstrapConfidence( node, max_normalized_value );
\r
756 setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
\r
763 public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
\r
764 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
765 if ( phy.isEmpty() ) {
\r
768 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
769 nodes.add( iter.next() );
\r
775 * Returns a map of distinct taxonomies of
\r
776 * all external nodes of node.
\r
777 * If at least one of the external nodes has no taxonomy,
\r
778 * null is returned.
\r
781 public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
\r
782 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
\r
783 final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();
\r
784 for( final PhylogenyNode n : descs ) {
\r
785 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
\r
788 final Taxonomy t = n.getNodeData().getTaxonomy();
\r
789 if ( tax_map.containsKey( t ) ) {
\r
790 tax_map.put( t, tax_map.get( t ) + 1 );
\r
793 tax_map.put( t, 1 );
\r
800 * Arranges the order of childern for each node of this Phylogeny in such a
\r
801 * way that either the branch with more children is on top (right) or on
\r
802 * bottom (left), dependent on the value of boolean order.
\r
805 * decides in which direction to order
\r
808 public static void orderAppearance( final PhylogenyNode n,
\r
809 final boolean order,
\r
810 final boolean order_ext_alphabetically,
\r
811 final DESCENDANT_SORT_PRIORITY pri ) {
\r
812 if ( n.isExternal() ) {
\r
816 PhylogenyNode temp = null;
\r
817 if ( ( n.getNumberOfDescendants() == 2 )
\r
818 && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
\r
819 && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
\r
820 temp = n.getChildNode1();
\r
821 n.setChild1( n.getChildNode2() );
\r
822 n.setChild2( temp );
\r
824 else if ( order_ext_alphabetically ) {
\r
825 boolean all_ext = true;
\r
826 for( final PhylogenyNode i : n.getDescendants() ) {
\r
827 if ( !i.isExternal() ) {
\r
833 PhylogenyMethods.sortNodeDescendents( n, pri );
\r
836 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
\r
837 orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
\r
842 public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
\r
843 for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
\r
844 final PhylogenyNode node = iter.next();
\r
846 double green = 0.0;
\r
849 if ( node.isInternal() ) {
\r
850 //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
\r
851 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
\r
852 final PhylogenyNode child_node = node.getChildNode( i );
\r
853 final Color child_color = getBranchColorValue( child_node );
\r
854 if ( child_color != null ) {
\r
856 red += child_color.getRed();
\r
857 green += child_color.getGreen();
\r
858 blue += child_color.getBlue();
\r
861 setBranchColorValue( node,
\r
862 new Color( ForesterUtil.roundToInt( red / n ),
\r
863 ForesterUtil.roundToInt( green / n ),
\r
864 ForesterUtil.roundToInt( blue / n ) ) );
\r
869 public static final void preOrderReId( final Phylogeny phy ) {
\r
870 if ( phy.isEmpty() ) {
\r
873 phy.setIdToNodeMap( null );
\r
874 long i = PhylogenyNode.getNodeCount();
\r
875 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
\r
876 it.next().setId( i++ );
\r
878 PhylogenyNode.setNodeCount( i );
\r
881 public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
\r
882 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
883 final Phylogeny[] trees = factory.create( file, parser );
\r
884 if ( ( trees == null ) || ( trees.length == 0 ) ) {
\r
885 throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
\r
890 public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
\r
891 throws IOException {
\r
892 final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
\r
893 for( final File file : files ) {
\r
894 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
895 final Phylogeny[] trees = factory.create( file, parser );
\r
896 if ( ( trees == null ) || ( trees.length == 0 ) ) {
\r
897 throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
\r
899 tree_list.addAll( Arrays.asList( trees ) );
\r
901 return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
\r
904 public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
\r
905 if ( remove_me.isRoot() ) {
\r
906 if ( remove_me.getNumberOfDescendants() == 1 ) {
\r
907 final PhylogenyNode desc = remove_me.getDescendants().get( 0 );
\r
908 desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
\r
909 desc.getDistanceToParent() ) );
\r
910 desc.setParent( null );
\r
911 phylogeny.setRoot( desc );
\r
912 phylogeny.clearHashIdToNodeMap();
\r
915 throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );
\r
918 else if ( remove_me.isExternal() ) {
\r
919 phylogeny.deleteSubtree( remove_me, false );
\r
920 phylogeny.clearHashIdToNodeMap();
\r
921 phylogeny.externalNodesHaveChanged();
\r
924 final PhylogenyNode parent = remove_me.getParent();
\r
925 final List<PhylogenyNode> descs = remove_me.getDescendants();
\r
926 parent.removeChildNode( remove_me );
\r
927 for( final PhylogenyNode desc : descs ) {
\r
928 parent.addAsChild( desc );
\r
929 desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
\r
930 desc.getDistanceToParent() ) );
\r
932 remove_me.setParent( null );
\r
933 phylogeny.clearHashIdToNodeMap();
\r
934 phylogeny.externalNodesHaveChanged();
\r
938 public static List<PhylogenyNode> searchData( final String query,
\r
939 final Phylogeny phy,
\r
940 final boolean case_sensitive,
\r
941 final boolean partial,
\r
942 final boolean search_domains ) {
\r
943 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
944 if ( phy.isEmpty() || ( query == null ) ) {
\r
947 if ( ForesterUtil.isEmpty( query ) ) {
\r
950 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
951 final PhylogenyNode node = iter.next();
\r
952 boolean match = false;
\r
953 if ( match( node.getName(), query, case_sensitive, partial ) ) {
\r
956 else if ( node.getNodeData().isHasTaxonomy()
\r
957 && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
\r
960 else if ( node.getNodeData().isHasTaxonomy()
\r
961 && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
\r
964 else if ( node.getNodeData().isHasTaxonomy()
\r
965 && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
\r
968 else if ( node.getNodeData().isHasTaxonomy()
\r
969 && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
\r
970 && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
\r
976 else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
\r
977 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
\r
978 I: for( final String syn : syns ) {
\r
979 if ( match( syn, query, case_sensitive, partial ) ) {
\r
985 if ( !match && node.getNodeData().isHasSequence()
\r
986 && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
\r
989 if ( !match && node.getNodeData().isHasSequence()
\r
990 && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
\r
993 if ( !match && node.getNodeData().isHasSequence()
\r
994 && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
\r
998 && node.getNodeData().isHasSequence()
\r
999 && ( node.getNodeData().getSequence().getAccession() != null )
\r
1000 && match( node.getNodeData().getSequence().getAccession().getValue(),
\r
1006 if ( search_domains && !match && node.getNodeData().isHasSequence()
\r
1007 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
\r
1008 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
\r
1009 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
\r
1010 if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
\r
1017 if ( !match && node.getNodeData().isHasSequence()
\r
1018 && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
\r
1019 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
\r
1020 if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
\r
1024 if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
\r
1030 if ( !match && node.getNodeData().isHasSequence()
\r
1031 && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
\r
1032 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
\r
1033 if ( match( x.getComment(), query, case_sensitive, partial ) ) {
\r
1037 if ( match( x.getSource(), query, case_sensitive, partial ) ) {
\r
1041 if ( match( x.getValue(), query, case_sensitive, partial ) ) {
\r
1048 if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
\r
1049 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
\r
1050 I: while ( it.hasNext() ) {
\r
1051 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1056 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
\r
1057 I: while ( it.hasNext() ) {
\r
1058 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1065 nodes.add( node );
\r
1071 public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
\r
1072 final Phylogeny phy,
\r
1073 final boolean case_sensitive,
\r
1074 final boolean partial,
\r
1075 final boolean search_domains ) {
\r
1076 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
1077 if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
\r
1080 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
1081 final PhylogenyNode node = iter.next();
\r
1082 boolean all_matched = true;
\r
1083 for( final String query : queries ) {
\r
1084 boolean match = false;
\r
1085 if ( ForesterUtil.isEmpty( query ) ) {
\r
1088 if ( match( node.getName(), query, case_sensitive, partial ) ) {
\r
1091 else if ( node.getNodeData().isHasTaxonomy()
\r
1092 && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
\r
1095 else if ( node.getNodeData().isHasTaxonomy()
\r
1096 && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
\r
1099 else if ( node.getNodeData().isHasTaxonomy()
\r
1100 && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
\r
1103 else if ( node.getNodeData().isHasTaxonomy()
\r
1104 && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1105 && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
\r
1111 else if ( node.getNodeData().isHasTaxonomy()
\r
1112 && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
\r
1113 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
\r
1114 I: for( final String syn : syns ) {
\r
1115 if ( match( syn, query, case_sensitive, partial ) ) {
\r
1121 if ( !match && node.getNodeData().isHasSequence()
\r
1122 && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
\r
1125 if ( !match && node.getNodeData().isHasSequence()
\r
1126 && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
\r
1129 if ( !match && node.getNodeData().isHasSequence()
\r
1130 && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
\r
1134 && node.getNodeData().isHasSequence()
\r
1135 && ( node.getNodeData().getSequence().getAccession() != null )
\r
1136 && match( node.getNodeData().getSequence().getAccession().getValue(),
\r
1142 if ( search_domains && !match && node.getNodeData().isHasSequence()
\r
1143 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
\r
1144 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
\r
1145 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
\r
1146 if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
\r
1153 if ( !match && node.getNodeData().isHasSequence()
\r
1154 && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
\r
1155 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
\r
1156 if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
\r
1160 if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
\r
1166 if ( !match && node.getNodeData().isHasSequence()
\r
1167 && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
\r
1168 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
\r
1169 if ( match( x.getComment(), query, case_sensitive, partial ) ) {
\r
1173 if ( match( x.getSource(), query, case_sensitive, partial ) ) {
\r
1177 if ( match( x.getValue(), query, case_sensitive, partial ) ) {
\r
1184 if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
\r
1185 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
\r
1186 I: while ( it.hasNext() ) {
\r
1187 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1192 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
\r
1193 I: while ( it.hasNext() ) {
\r
1194 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1201 all_matched = false;
\r
1205 if ( all_matched ) {
\r
1206 nodes.add( node );
\r
1212 public static void setAllIndicatorsToZero( final Phylogeny phy ) {
\r
1213 for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
\r
1214 it.next().setIndicator( ( byte ) 0 );
\r
1219 * Convenience method.
\r
1220 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1222 public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {
\r
1223 setConfidence( node, bootstrap_confidence_value, "bootstrap" );
\r
1226 public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
\r
1227 if ( node.getBranchData().getBranchColor() == null ) {
\r
1228 node.getBranchData().setBranchColor( new BranchColor() );
\r
1230 node.getBranchData().getBranchColor().setValue( color );
\r
1234 * Convenience method
\r
1236 public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {
\r
1237 node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );
\r
1241 * Convenience method.
\r
1242 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1244 public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {
\r
1245 setConfidence( node, confidence_value, "" );
\r
1249 * Convenience method.
\r
1250 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1252 public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {
\r
1253 Confidence c = null;
\r
1254 if ( node.getBranchData().getNumberOfConfidences() > 0 ) {
\r
1255 c = node.getBranchData().getConfidence( 0 );
\r
1258 c = new Confidence();
\r
1259 node.getBranchData().addConfidence( c );
\r
1261 c.setType( type );
\r
1262 c.setValue( confidence_value );
\r
1265 public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {
\r
1266 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1267 node.getNodeData().setTaxonomy( new Taxonomy() );
\r
1269 node.getNodeData().getTaxonomy().setScientificName( scientific_name );
\r
1273 * Convenience method to set the taxonomy code of a phylogeny node.
\r
1277 * @param taxonomy_code
\r
1278 * @throws PhyloXmlDataFormatException
\r
1280 public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )
\r
1281 throws PhyloXmlDataFormatException {
\r
1282 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1283 node.getNodeData().setTaxonomy( new Taxonomy() );
\r
1285 node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
\r
1288 final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
\r
1289 class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
\r
1292 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1293 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1294 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1295 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1296 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1297 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1299 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1300 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1301 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1302 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1304 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
\r
1305 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
\r
1306 return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
\r
1307 .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
\r
1310 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1311 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1312 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1313 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1314 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1316 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1317 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1318 return n1.getNodeData().getSequence().getSymbol()
\r
1319 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1321 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1322 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1323 return n1.getNodeData().getSequence().getGeneName()
\r
1324 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1326 if ( ( n1.getNodeData().getSequence().getAccession() != null )
\r
1327 && ( n2.getNodeData().getSequence().getAccession() != null )
\r
1328 && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
\r
1329 && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
1330 return n1.getNodeData().getSequence().getAccession().getValue()
\r
1331 .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
\r
1334 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1335 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1340 class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
\r
1343 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1344 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1345 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1346 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1347 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1348 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1350 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1351 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1352 return n1.getNodeData().getSequence().getSymbol()
\r
1353 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1355 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1356 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1357 return n1.getNodeData().getSequence().getGeneName()
\r
1358 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1360 if ( ( n1.getNodeData().getSequence().getAccession() != null )
\r
1361 && ( n2.getNodeData().getSequence().getAccession() != null )
\r
1362 && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
\r
1363 && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
1364 return n1.getNodeData().getSequence().getAccession().getValue()
\r
1365 .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
\r
1368 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1369 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1370 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1371 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1372 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1374 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1375 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1376 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1377 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1379 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
\r
1380 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
\r
1381 return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
\r
1382 .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
\r
1385 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1386 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1391 class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
\r
1394 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1395 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1396 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1398 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1399 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1400 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1401 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1402 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1404 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1405 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1406 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1407 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1409 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
\r
1410 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
\r
1411 return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
\r
1412 .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
\r
1415 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1416 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1417 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1418 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1419 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1421 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1422 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1423 return n1.getNodeData().getSequence().getSymbol()
\r
1424 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1426 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1427 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1428 return n1.getNodeData().getSequence().getGeneName()
\r
1429 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1431 if ( ( n1.getNodeData().getSequence().getAccession() != null )
\r
1432 && ( n2.getNodeData().getSequence().getAccession() != null )
\r
1433 && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
\r
1434 && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
1435 return n1.getNodeData().getSequence().getAccession().getValue()
\r
1436 .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
\r
1442 Comparator<PhylogenyNode> c;
\r
1445 c = new PhylogenyNodeSortSequencePriority();
\r
1448 c = new PhylogenyNodeSortNodeNamePriority();
\r
1451 c = new PhylogenyNodeSortTaxonomyPriority();
\r
1453 final List<PhylogenyNode> descs = node.getDescendants();
\r
1454 Collections.sort( descs, c );
\r
1456 for( final PhylogenyNode desc : descs ) {
\r
1457 node.setChildNode( i++, desc );
\r
1462 * Removes from Phylogeny to_be_stripped all external Nodes which are
\r
1463 * associated with a species NOT found in Phylogeny reference.
\r
1465 * @param reference
\r
1466 * a reference Phylogeny
\r
1467 * @param to_be_stripped
\r
1468 * Phylogeny to be stripped
\r
1469 * @return nodes removed from to_be_stripped
\r
1471 public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
\r
1472 final Phylogeny to_be_stripped ) {
\r
1473 final Set<String> ref_ext_taxo = new HashSet<String>();
\r
1474 for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
\r
1475 final PhylogenyNode n = it.next();
\r
1476 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1477 throw new IllegalArgumentException( "no taxonomic data in node: " + n );
\r
1479 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
\r
1480 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );
\r
1482 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
\r
1483 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1485 if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1486 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
\r
1487 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );
\r
1490 final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
\r
1491 for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
\r
1492 final PhylogenyNode n = it.next();
\r
1493 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1494 nodes_to_delete.add( n );
\r
1496 else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
\r
1497 && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1498 && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n
\r
1499 .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
\r
1500 nodes_to_delete.add( n );
\r
1503 for( final PhylogenyNode n : nodes_to_delete ) {
\r
1504 to_be_stripped.deleteSubtree( n, true );
\r
1506 to_be_stripped.clearHashIdToNodeMap();
\r
1507 to_be_stripped.externalNodesHaveChanged();
\r
1508 return nodes_to_delete;
\r
1511 final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
\r
1512 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1513 while ( it.hasNext() ) {
\r
1514 final PhylogenyNode n = it.next();
\r
1515 if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1516 double value = -1;
\r
1518 value = Double.parseDouble( n.getName() );
\r
1520 catch ( final NumberFormatException e ) {
\r
1521 throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
\r
1522 + e.getLocalizedMessage() );
\r
1524 if ( value >= 0.0 ) {
\r
1525 n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
\r
1532 final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {
\r
1533 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1534 while ( it.hasNext() ) {
\r
1535 final PhylogenyNode n = it.next();
\r
1536 if ( !n.isExternal() && !n.isRoot() ) {
\r
1537 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1538 double value = -1;
\r
1540 value = Double.parseDouble( n.getName() );
\r
1542 catch ( final NumberFormatException e ) {
\r
1545 if ( ( value < 0.0 ) || ( value > 100 ) ) {
\r
1554 final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy, final String confidence_type ) {
\r
1555 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1556 while ( it.hasNext() ) {
\r
1557 transferInternalNodeNameToConfidence( confidence_type, it.next() );
\r
1561 private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {
\r
1562 if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
\r
1563 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1566 d = Double.parseDouble( n.getName() );
\r
1568 catch ( final Exception e ) {
\r
1572 n.getBranchData().addConfidence( new Confidence( d, confidence_type ) );
\r
1579 final static public void transferNodeNameToField( final Phylogeny phy,
\r
1580 final PhylogenyNodeField field,
\r
1581 final boolean external_only ) throws PhyloXmlDataFormatException {
\r
1582 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1583 while ( it.hasNext() ) {
\r
1584 final PhylogenyNode n = it.next();
\r
1585 if ( external_only && n.isInternal() ) {
\r
1588 final String name = n.getName().trim();
\r
1589 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1590 switch ( field ) {
\r
1591 case TAXONOMY_CODE:
\r
1593 setTaxonomyCode( n, name );
\r
1595 case TAXONOMY_SCIENTIFIC_NAME:
\r
1597 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1598 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1600 n.getNodeData().getTaxonomy().setScientificName( name );
\r
1602 case TAXONOMY_COMMON_NAME:
\r
1604 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1605 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1607 n.getNodeData().getTaxonomy().setCommonName( name );
\r
1609 case SEQUENCE_SYMBOL:
\r
1611 if ( !n.getNodeData().isHasSequence() ) {
\r
1612 n.getNodeData().setSequence( new Sequence() );
\r
1614 n.getNodeData().getSequence().setSymbol( name );
\r
1616 case SEQUENCE_NAME:
\r
1618 if ( !n.getNodeData().isHasSequence() ) {
\r
1619 n.getNodeData().setSequence( new Sequence() );
\r
1621 n.getNodeData().getSequence().setName( name );
\r
1623 case TAXONOMY_ID_UNIPROT_1: {
\r
1624 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1625 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1628 final int i = name.indexOf( '_' );
\r
1630 id = name.substring( 0, i );
\r
1635 n.getNodeData().getTaxonomy()
\r
1636 .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
\r
1639 case TAXONOMY_ID_UNIPROT_2: {
\r
1640 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1641 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1644 final int i = name.indexOf( '_' );
\r
1646 id = name.substring( i + 1, name.length() );
\r
1651 n.getNodeData().getTaxonomy()
\r
1652 .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
\r
1655 case TAXONOMY_ID: {
\r
1656 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1657 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1659 n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
\r
1667 static double addPhylogenyDistances( final double a, final double b ) {
\r
1668 if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
\r
1671 else if ( a >= 0.0 ) {
\r
1674 else if ( b >= 0.0 ) {
\r
1677 return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
\r
1680 static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {
\r
1682 boolean all_default = true;
\r
1683 while ( anc != desc ) {
\r
1684 if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
\r
1685 d += desc.getDistanceToParent();
\r
1686 if ( all_default ) {
\r
1687 all_default = false;
\r
1690 desc = desc.getParent();
\r
1692 if ( all_default ) {
\r
1693 return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
\r
1699 * Deep copies the phylogeny originating from this node.
\r
1701 static PhylogenyNode copySubTree( final PhylogenyNode source ) {
\r
1702 if ( source == null ) {
\r
1706 final PhylogenyNode newnode = source.copyNodeData();
\r
1707 if ( !source.isExternal() ) {
\r
1708 for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
\r
1709 newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
\r
1717 * Shallow copies the phylogeny originating from this node.
\r
1719 static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
\r
1720 if ( source == null ) {
\r
1724 final PhylogenyNode newnode = source.copyNodeDataShallow();
\r
1725 if ( !source.isExternal() ) {
\r
1726 for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
\r
1727 newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
\r
1734 private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,
\r
1735 final double min_distance_to_root ) {
\r
1736 final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();
\r
1737 final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );
\r
1738 for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {
\r
1739 if ( ext.getIndicator() != 0 ) {
\r
1740 throw new RuntimeException( "this should not have happened" );
\r
1742 ext.setIndicator( ( byte ) 1 );
\r
1749 * Calculates the distance between PhylogenyNodes n1 and n2.
\r
1750 * PRECONDITION: n1 is a descendant of n2.
\r
1753 * a descendant of n2
\r
1755 * @return distance between n1 and n2
\r
1757 private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1759 while ( n1 != n2 ) {
\r
1760 if ( n1.getDistanceToParent() > 0.0 ) {
\r
1761 d += n1.getDistanceToParent();
\r
1763 n1 = n1.getParent();
\r
1768 private static boolean match( final String s,
\r
1769 final String query,
\r
1770 final boolean case_sensitive,
\r
1771 final boolean partial ) {
\r
1772 if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
\r
1775 String my_s = s.trim();
\r
1776 String my_query = query.trim();
\r
1777 if ( !case_sensitive ) {
\r
1778 my_s = my_s.toLowerCase();
\r
1779 my_query = my_query.toLowerCase();
\r
1782 return my_s.indexOf( my_query ) >= 0;
\r
1785 return Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" ).matcher( my_s ).find();
\r
1789 private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {
\r
1790 PhylogenyNode n = node;
\r
1791 PhylogenyNode prev = node;
\r
1792 while ( min_distance_to_root < n.calculateDistanceToRoot() ) {
\r
1794 n = n.getParent();
\r
1799 public static enum DESCENDANT_SORT_PRIORITY {
\r
1800 NODE_NAME, SEQUENCE, TAXONOMY;
\r
1803 public static enum PhylogenyNodeField {
\r
1808 TAXONOMY_COMMON_NAME,
\r
1810 TAXONOMY_ID_UNIPROT_1,
\r
1811 TAXONOMY_ID_UNIPROT_2,
\r
1812 TAXONOMY_SCIENTIFIC_NAME;
\r
1815 public static void addMolecularSeqsToTree( final Phylogeny phy, final Msa msa ) {
\r
1816 for( int s = 0; s < msa.getNumberOfSequences(); ++s ) {
\r
1817 final org.forester.sequence.MolecularSequence seq = msa.getSequence( s );
\r
1818 final PhylogenyNode node = phy.getNode( seq.getIdentifier() );
\r
1819 final org.forester.phylogeny.data.Sequence new_seq = new Sequence();
\r
1820 new_seq.setMolecularSequenceAligned( true );
\r
1821 new_seq.setMolecularSequence( seq.getMolecularSequenceAsString() );
\r
1822 new_seq.setName( seq.getIdentifier() );
\r
1824 new_seq.setType( PhyloXmlUtil.SEQ_TYPE_PROTEIN );
\r
1826 catch ( final PhyloXmlDataFormatException ignore ) {
\r
1829 node.getNodeData().addSequence( new_seq );
\r