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.phylogeny.data.Accession;
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50 import org.forester.phylogeny.data.Annotation;
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51 import org.forester.phylogeny.data.BranchColor;
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52 import org.forester.phylogeny.data.BranchWidth;
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53 import org.forester.phylogeny.data.Confidence;
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54 import org.forester.phylogeny.data.DomainArchitecture;
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55 import org.forester.phylogeny.data.Event;
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56 import org.forester.phylogeny.data.Identifier;
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57 import org.forester.phylogeny.data.PhylogenyDataUtil;
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58 import org.forester.phylogeny.data.Sequence;
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59 import org.forester.phylogeny.data.Taxonomy;
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60 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
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61 import org.forester.phylogeny.factories.PhylogenyFactory;
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62 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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63 import org.forester.util.BasicDescriptiveStatistics;
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64 import org.forester.util.DescriptiveStatistics;
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65 import org.forester.util.ForesterUtil;
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67 public class PhylogenyMethods {
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69 private PhylogenyMethods() {
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70 // Hidden constructor.
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74 public Object clone() throws CloneNotSupportedException {
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75 throw new CloneNotSupportedException();
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78 public static boolean extractFastaInformation( final Phylogeny phy ) {
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79 boolean could_extract = false;
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80 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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81 final PhylogenyNode node = iter.next();
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82 if ( !ForesterUtil.isEmpty( node.getName() ) ) {
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83 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
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84 if ( name_m.lookingAt() ) {
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85 could_extract = true;
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86 final String acc_source = name_m.group( 1 );
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87 final String acc = name_m.group( 2 );
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88 final String seq_name = name_m.group( 3 );
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89 final String tax_sn = name_m.group( 4 );
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90 if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
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91 ForesterUtil.ensurePresenceOfSequence( node );
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92 node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
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94 if ( !ForesterUtil.isEmpty( seq_name ) ) {
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95 ForesterUtil.ensurePresenceOfSequence( node );
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96 node.getNodeData().getSequence( 0 ).setName( seq_name );
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98 if ( !ForesterUtil.isEmpty( tax_sn ) ) {
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99 ForesterUtil.ensurePresenceOfTaxonomy( node );
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100 node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
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105 return could_extract;
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108 public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
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109 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
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110 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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111 final PhylogenyNode n = iter.next();
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112 if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
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113 stats.addValue( n.getDistanceToParent() );
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119 public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
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120 final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
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121 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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122 final PhylogenyNode n = iter.next();
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123 if ( !n.isExternal() && !n.isRoot() ) {
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124 if ( n.getBranchData().isHasConfidences() ) {
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125 for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
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126 final Confidence c = n.getBranchData().getConfidences().get( i );
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127 if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
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128 stats.add( i, new BasicDescriptiveStatistics() );
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130 if ( !ForesterUtil.isEmpty( c.getType() ) ) {
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131 if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
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132 if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
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133 throw new IllegalArgumentException( "support values in node [" + n.toString()
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134 + "] appear inconsistently ordered" );
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137 stats.get( i ).setDescription( c.getType() );
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139 stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
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148 * Calculates the distance between PhylogenyNodes node1 and node2.
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153 * @return distance between node1 and node2
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155 public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
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156 final PhylogenyNode lca = calculateLCA( node1, node2 );
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157 final PhylogenyNode n1 = node1;
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158 final PhylogenyNode n2 = node2;
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159 return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
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163 * Returns the LCA of PhylogenyNodes node1 and node2.
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168 * @return LCA of node1 and node2
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170 public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
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171 if ( node1 == null ) {
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172 throw new IllegalArgumentException( "first argument (node) is null" );
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174 if ( node2 == null ) {
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175 throw new IllegalArgumentException( "second argument (node) is null" );
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177 if ( node1 == node2 ) {
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180 if ( ( node1.getParent() == node2.getParent() ) ) {
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181 return node1.getParent();
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183 int depth1 = node1.calculateDepth();
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184 int depth2 = node2.calculateDepth();
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185 while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {
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186 if ( depth1 > depth2 ) {
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187 node1 = node1.getParent();
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190 else if ( depth2 > depth1 ) {
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191 node2 = node2.getParent();
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195 if ( node1 == node2 ) {
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198 node1 = node1.getParent();
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199 node2 = node2.getParent();
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204 throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
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208 * Returns the LCA of PhylogenyNodes node1 and node2.
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209 * Precondition: ids are in pre-order (or level-order).
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214 * @return LCA of node1 and node2
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216 public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
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217 if ( node1 == null ) {
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218 throw new IllegalArgumentException( "first argument (node) is null" );
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220 if ( node2 == null ) {
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221 throw new IllegalArgumentException( "second argument (node) is null" );
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223 while ( node1 != node2 ) {
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224 if ( node1.getId() > node2.getId() ) {
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225 node1 = node1.getParent();
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228 node2 = node2.getParent();
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234 public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
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235 if ( node.isExternal() ) {
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239 for( PhylogenyNode d : node.getAllExternalDescendants() ) {
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241 while ( d != node ) {
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242 if ( d.isCollapse() ) {
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250 if ( max < steps ) {
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257 public static int calculateMaxDepth( final Phylogeny phy ) {
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259 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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260 final PhylogenyNode node = iter.next();
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261 final int steps = node.calculateDepth();
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262 if ( steps > max ) {
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269 public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
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271 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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272 final PhylogenyNode node = iter.next();
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273 final double d = node.calculateDistanceToRoot();
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281 public static PhylogenyNode calculateNodeWithMaxDistanceToRoot( final Phylogeny phy ) {
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283 PhylogenyNode max_node = phy.getFirstExternalNode();
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284 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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285 final PhylogenyNode node = iter.next();
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286 final double d = node.calculateDistanceToRoot();
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295 public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
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296 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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298 for( final PhylogenyNode n : descs ) {
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299 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
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306 public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
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307 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
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308 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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309 final PhylogenyNode n = iter.next();
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310 if ( !n.isExternal() ) {
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311 stats.addValue( n.getNumberOfDescendants() );
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317 public final static void collapseSubtreeStructure( final PhylogenyNode n ) {
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318 final List<PhylogenyNode> eds = n.getAllExternalDescendants();
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319 final List<Double> d = new ArrayList<Double>();
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320 for( final PhylogenyNode ed : eds ) {
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321 d.add( calculateDistanceToAncestor( n, ed ) );
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323 for( int i = 0; i < eds.size(); ++i ) {
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324 n.setChildNode( i, eds.get( i ) );
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325 eds.get( i ).setDistanceToParent( d.get( i ) );
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329 public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
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331 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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332 final PhylogenyNode n = iter.next();
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333 if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {
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340 public static int countNumberOfPolytomies( final Phylogeny phy ) {
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342 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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343 final PhylogenyNode n = iter.next();
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344 if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
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351 public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
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352 final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
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353 final List<PhylogenyNode> ext = phy.getExternalNodes();
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354 for( final PhylogenyNode n : ext ) {
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355 nodes.put( n.getName(), n );
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360 public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
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361 for( final Long id : to_delete ) {
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362 phy.deleteSubtree( phy.getNode( id ), true );
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364 phy.clearHashIdToNodeMap();
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365 phy.externalNodesHaveChanged();
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368 public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
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369 throws IllegalArgumentException {
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370 for( final String element : node_names_to_delete ) {
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371 if ( ForesterUtil.isEmpty( element ) ) {
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374 List<PhylogenyNode> nodes = null;
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375 nodes = p.getNodes( element );
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376 final Iterator<PhylogenyNode> it = nodes.iterator();
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377 while ( it.hasNext() ) {
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378 final PhylogenyNode n = it.next();
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379 if ( !n.isExternal() ) {
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380 throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
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382 p.deleteSubtree( n, true );
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385 p.clearHashIdToNodeMap();
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386 p.externalNodesHaveChanged();
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389 public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
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390 final Phylogeny p ) {
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391 final PhylogenyNodeIterator it = p.iteratorExternalForward();
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392 final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
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394 Arrays.sort( node_names_to_keep );
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395 while ( it.hasNext() ) {
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396 final String curent_name = it.next().getName();
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397 if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
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398 to_delete[ i++ ] = curent_name;
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401 PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
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402 final List<String> deleted = new ArrayList<String>();
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403 for( final String n : to_delete ) {
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404 if ( !ForesterUtil.isEmpty( n ) ) {
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411 public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {
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412 final Set<Long> to_delete = new HashSet<Long>();
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413 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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414 final PhylogenyNode n = it.next();
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415 if ( n.getNodeData().isHasTaxonomy() ) {
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416 if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
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417 to_delete.add( n.getId() );
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421 throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
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424 deleteExternalNodesNegativeSelection( to_delete, phy );
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427 final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
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428 final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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429 for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
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430 final PhylogenyNode n = iter.next();
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431 if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {
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432 to_delete.add( n );
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435 for( final PhylogenyNode d : to_delete ) {
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436 PhylogenyMethods.removeNode( d, phy );
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438 phy.clearHashIdToNodeMap();
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439 phy.externalNodesHaveChanged();
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442 final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
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443 if ( n.isInternal() ) {
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444 throw new IllegalArgumentException( "node is not external" );
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446 final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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447 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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448 final PhylogenyNode i = it.next();
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449 if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
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450 to_delete.add( i );
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453 for( final PhylogenyNode d : to_delete ) {
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454 phy.deleteSubtree( d, true );
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456 phy.clearHashIdToNodeMap();
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457 phy.externalNodesHaveChanged();
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460 public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,
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461 final double min_distance_to_root ) {
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462 if ( min_distance_to_root <= 0 ) {
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463 throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );
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465 final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();
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466 setAllIndicatorsToZero( phy );
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467 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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468 final PhylogenyNode n = it.next();
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469 if ( n.getIndicator() != 0 ) {
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472 l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
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473 if ( l.isEmpty() ) {
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474 throw new RuntimeException( "this should not have happened" );
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480 public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
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481 final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
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482 final Set<Long> encountered = new HashSet<Long>();
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483 if ( !node.isExternal() ) {
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484 final List<PhylogenyNode> exts = node.getAllExternalDescendants();
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485 for( PhylogenyNode current : exts ) {
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486 descs.add( current );
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487 while ( current != node ) {
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488 current = current.getParent();
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489 if ( encountered.contains( current.getId() ) ) {
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492 descs.add( current );
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493 encountered.add( current.getId() );
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502 * Convenience method
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507 public static Color getBranchColorValue( final PhylogenyNode node ) {
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508 if ( node.getBranchData().getBranchColor() == null ) {
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511 return node.getBranchData().getBranchColor().getValue();
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515 * Convenience method
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517 public static double getBranchWidthValue( final PhylogenyNode node ) {
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518 if ( !node.getBranchData().isHasBranchWidth() ) {
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519 return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;
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521 return node.getBranchData().getBranchWidth().getValue();
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525 * Convenience method
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527 public static double getConfidenceValue( final PhylogenyNode node ) {
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528 if ( !node.getBranchData().isHasConfidences() ) {
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529 return Confidence.CONFIDENCE_DEFAULT_VALUE;
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531 return node.getBranchData().getConfidence( 0 ).getValue();
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535 * Convenience method
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537 public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {
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538 if ( !node.getBranchData().isHasConfidences() ) {
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539 return new double[ 0 ];
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541 final double[] values = new double[ node.getBranchData().getConfidences().size() ];
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543 for( final Confidence c : node.getBranchData().getConfidences() ) {
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544 values[ i++ ] = c.getValue();
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549 final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
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550 return calculateLCA( n1, n2 ).getNodeData().getEvent();
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554 * Returns taxonomy t if all external descendants have
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555 * the same taxonomy t, null otherwise.
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558 public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {
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559 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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560 Taxonomy tax = null;
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561 for( final PhylogenyNode n : descs ) {
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562 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
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565 else if ( tax == null ) {
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566 tax = n.getNodeData().getTaxonomy();
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568 else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {
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575 public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {
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576 final List<PhylogenyNode> children = node.getAllExternalDescendants();
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577 PhylogenyNode farthest = null;
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578 double longest = -Double.MAX_VALUE;
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579 for( final PhylogenyNode child : children ) {
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580 if ( PhylogenyMethods.getDistance( child, node ) > longest ) {
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582 longest = PhylogenyMethods.getDistance( child, node );
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588 // public static PhylogenyMethods getInstance() {
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589 // if ( PhylogenyMethods._instance == null ) {
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590 // PhylogenyMethods._instance = new PhylogenyMethods();
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592 // return PhylogenyMethods._instance;
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595 * Returns the largest confidence value found on phy.
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597 static public double getMaximumConfidenceValue( final Phylogeny phy ) {
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598 double max = -Double.MAX_VALUE;
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599 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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600 final double s = PhylogenyMethods.getConfidenceValue( iter.next() );
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601 if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {
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608 static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {
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609 int min = Integer.MAX_VALUE;
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612 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
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614 if ( n.isInternal() ) {
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615 d = n.getNumberOfDescendants();
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625 * Convenience method for display purposes.
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626 * Not intended for algorithms.
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628 public static String getSpecies( final PhylogenyNode node ) {
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629 if ( !node.getNodeData().isHasTaxonomy() ) {
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632 else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
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633 return node.getNodeData().getTaxonomy().getScientificName();
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635 if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
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636 return node.getNodeData().getTaxonomy().getTaxonomyCode();
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639 return node.getNodeData().getTaxonomy().getCommonName();
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644 * Convenience method for display purposes.
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645 * Not intended for algorithms.
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647 public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
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648 if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
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651 return node.getNodeData().getTaxonomy().getIdentifier().getValue();
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654 public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
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655 if ( n.isExternal() ) {
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659 if ( n.isDuplication() ) {
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660 for( final PhylogenyNode desc : n.getDescendants() ) {
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661 if ( !isAllDecendentsAreDuplications( desc ) ) {
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673 public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
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674 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
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675 if ( node.getChildNode( i ).isExternal() ) {
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683 * This is case insensitive.
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686 public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
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687 final String[] providers ) {
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688 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
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689 final String my_tax_prov = tax.getIdentifier().getProvider();
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690 for( final String provider : providers ) {
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691 if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
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702 public static void midpointRoot( final Phylogeny phylogeny ) {
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703 if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {
\r
707 final int total_nodes = phylogeny.getNodeCount();
\r
709 if ( ++counter > total_nodes ) {
\r
710 throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );
\r
712 PhylogenyNode a = null;
\r
715 for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {
\r
716 final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );
\r
717 final double df = getDistance( f, phylogeny.getRoot() );
\r
724 else if ( df > db ) {
\r
729 final double diff = da - db;
\r
730 if ( diff < 0.000001 ) {
\r
733 double x = da - ( diff / 2.0 );
\r
734 while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {
\r
735 x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );
\r
738 phylogeny.reRoot( a, x );
\r
740 phylogeny.recalculateNumberOfExternalDescendants( true );
\r
743 public static void normalizeBootstrapValues( final Phylogeny phylogeny,
\r
744 final double max_bootstrap_value,
\r
745 final double max_normalized_value ) {
\r
746 for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
\r
747 final PhylogenyNode node = iter.next();
\r
748 if ( node.isInternal() ) {
\r
749 final double confidence = getConfidenceValue( node );
\r
750 if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
\r
751 if ( confidence >= max_bootstrap_value ) {
\r
752 setBootstrapConfidence( node, max_normalized_value );
\r
755 setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
\r
762 public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
\r
763 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
764 if ( phy.isEmpty() ) {
\r
767 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
768 nodes.add( iter.next() );
\r
774 * Returns a map of distinct taxonomies of
\r
775 * all external nodes of node.
\r
776 * If at least one of the external nodes has no taxonomy,
\r
777 * null is returned.
\r
780 public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
\r
781 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
\r
782 final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();
\r
783 for( final PhylogenyNode n : descs ) {
\r
784 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
\r
787 final Taxonomy t = n.getNodeData().getTaxonomy();
\r
788 if ( tax_map.containsKey( t ) ) {
\r
789 tax_map.put( t, tax_map.get( t ) + 1 );
\r
792 tax_map.put( t, 1 );
\r
799 * Arranges the order of childern for each node of this Phylogeny in such a
\r
800 * way that either the branch with more children is on top (right) or on
\r
801 * bottom (left), dependent on the value of boolean order.
\r
804 * decides in which direction to order
\r
807 public static void orderAppearance( final PhylogenyNode n,
\r
808 final boolean order,
\r
809 final boolean order_ext_alphabetically,
\r
810 final DESCENDANT_SORT_PRIORITY pri ) {
\r
811 if ( n.isExternal() ) {
\r
815 PhylogenyNode temp = null;
\r
816 if ( ( n.getNumberOfDescendants() == 2 )
\r
817 && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
\r
818 && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
\r
819 temp = n.getChildNode1();
\r
820 n.setChild1( n.getChildNode2() );
\r
821 n.setChild2( temp );
\r
823 else if ( order_ext_alphabetically ) {
\r
824 boolean all_ext = true;
\r
825 for( final PhylogenyNode i : n.getDescendants() ) {
\r
826 if ( !i.isExternal() ) {
\r
832 PhylogenyMethods.sortNodeDescendents( n, pri );
\r
835 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
\r
836 orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
\r
841 public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
\r
842 for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
\r
843 final PhylogenyNode node = iter.next();
\r
845 double green = 0.0;
\r
848 if ( node.isInternal() ) {
\r
849 //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
\r
850 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
\r
851 final PhylogenyNode child_node = node.getChildNode( i );
\r
852 final Color child_color = getBranchColorValue( child_node );
\r
853 if ( child_color != null ) {
\r
855 red += child_color.getRed();
\r
856 green += child_color.getGreen();
\r
857 blue += child_color.getBlue();
\r
860 setBranchColorValue( node,
\r
861 new Color( ForesterUtil.roundToInt( red / n ),
\r
862 ForesterUtil.roundToInt( green / n ),
\r
863 ForesterUtil.roundToInt( blue / n ) ) );
\r
868 public static final void preOrderReId( final Phylogeny phy ) {
\r
869 if ( phy.isEmpty() ) {
\r
872 phy.setIdToNodeMap( null );
\r
873 long i = PhylogenyNode.getNodeCount();
\r
874 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
\r
875 it.next().setId( i++ );
\r
877 PhylogenyNode.setNodeCount( i );
\r
880 public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
\r
881 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
882 final Phylogeny[] trees = factory.create( file, parser );
\r
883 if ( ( trees == null ) || ( trees.length == 0 ) ) {
\r
884 throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
\r
889 public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
\r
890 throws IOException {
\r
891 final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
\r
892 for( final File file : files ) {
\r
893 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
894 final Phylogeny[] trees = factory.create( file, parser );
\r
895 if ( ( trees == null ) || ( trees.length == 0 ) ) {
\r
896 throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
\r
898 tree_list.addAll( Arrays.asList( trees ) );
\r
900 return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
\r
903 public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
\r
904 if ( remove_me.isRoot() ) {
\r
905 if ( remove_me.getNumberOfDescendants() == 1 ) {
\r
906 final PhylogenyNode desc = remove_me.getDescendants().get( 0 );
\r
907 desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
\r
908 desc.getDistanceToParent() ) );
\r
909 desc.setParent( null );
\r
910 phylogeny.setRoot( desc );
\r
911 phylogeny.clearHashIdToNodeMap();
\r
914 throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );
\r
917 else if ( remove_me.isExternal() ) {
\r
918 phylogeny.deleteSubtree( remove_me, false );
\r
919 phylogeny.clearHashIdToNodeMap();
\r
920 phylogeny.externalNodesHaveChanged();
\r
923 final PhylogenyNode parent = remove_me.getParent();
\r
924 final List<PhylogenyNode> descs = remove_me.getDescendants();
\r
925 parent.removeChildNode( remove_me );
\r
926 for( final PhylogenyNode desc : descs ) {
\r
927 parent.addAsChild( desc );
\r
928 desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
\r
929 desc.getDistanceToParent() ) );
\r
931 remove_me.setParent( null );
\r
932 phylogeny.clearHashIdToNodeMap();
\r
933 phylogeny.externalNodesHaveChanged();
\r
937 public static List<PhylogenyNode> searchData( final String query,
\r
938 final Phylogeny phy,
\r
939 final boolean case_sensitive,
\r
940 final boolean partial,
\r
941 final boolean search_domains ) {
\r
942 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
943 if ( phy.isEmpty() || ( query == null ) ) {
\r
946 if ( ForesterUtil.isEmpty( query ) ) {
\r
949 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
950 final PhylogenyNode node = iter.next();
\r
951 boolean match = false;
\r
952 if ( match( node.getName(), query, case_sensitive, partial ) ) {
\r
955 else if ( node.getNodeData().isHasTaxonomy()
\r
956 && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
\r
959 else if ( node.getNodeData().isHasTaxonomy()
\r
960 && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
\r
963 else if ( node.getNodeData().isHasTaxonomy()
\r
964 && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
\r
967 else if ( node.getNodeData().isHasTaxonomy()
\r
968 && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
\r
969 && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
\r
975 else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
\r
976 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
\r
977 I: for( final String syn : syns ) {
\r
978 if ( match( syn, query, case_sensitive, partial ) ) {
\r
984 if ( !match && node.getNodeData().isHasSequence()
\r
985 && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
\r
988 if ( !match && node.getNodeData().isHasSequence()
\r
989 && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
\r
992 if ( !match && node.getNodeData().isHasSequence()
\r
993 && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
\r
997 && node.getNodeData().isHasSequence()
\r
998 && ( node.getNodeData().getSequence().getAccession() != null )
\r
999 && match( node.getNodeData().getSequence().getAccession().getValue(),
\r
1005 if ( search_domains && !match && node.getNodeData().isHasSequence()
\r
1006 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
\r
1007 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
\r
1008 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
\r
1009 if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
\r
1016 if ( !match && node.getNodeData().isHasSequence()
\r
1017 && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
\r
1018 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
\r
1019 if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
\r
1023 if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
\r
1029 if ( !match && node.getNodeData().isHasSequence()
\r
1030 && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
\r
1031 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
\r
1032 if ( match( x.getComment(), query, case_sensitive, partial ) ) {
\r
1036 if ( match( x.getSource(), query, case_sensitive, partial ) ) {
\r
1040 if ( match( x.getValue(), query, case_sensitive, partial ) ) {
\r
1047 if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
\r
1048 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
\r
1049 I: while ( it.hasNext() ) {
\r
1050 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1055 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
\r
1056 I: while ( it.hasNext() ) {
\r
1057 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1064 nodes.add( node );
\r
1070 public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
\r
1071 final Phylogeny phy,
\r
1072 final boolean case_sensitive,
\r
1073 final boolean partial,
\r
1074 final boolean search_domains ) {
\r
1075 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
1076 if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
\r
1079 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
1080 final PhylogenyNode node = iter.next();
\r
1081 boolean all_matched = true;
\r
1082 for( final String query : queries ) {
\r
1083 boolean match = false;
\r
1084 if ( ForesterUtil.isEmpty( query ) ) {
\r
1087 if ( match( node.getName(), query, case_sensitive, partial ) ) {
\r
1090 else if ( node.getNodeData().isHasTaxonomy()
\r
1091 && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
\r
1094 else if ( node.getNodeData().isHasTaxonomy()
\r
1095 && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
\r
1098 else if ( node.getNodeData().isHasTaxonomy()
\r
1099 && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
\r
1102 else if ( node.getNodeData().isHasTaxonomy()
\r
1103 && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1104 && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
\r
1110 else if ( node.getNodeData().isHasTaxonomy()
\r
1111 && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
\r
1112 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
\r
1113 I: for( final String syn : syns ) {
\r
1114 if ( match( syn, query, case_sensitive, partial ) ) {
\r
1120 if ( !match && node.getNodeData().isHasSequence()
\r
1121 && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
\r
1124 if ( !match && node.getNodeData().isHasSequence()
\r
1125 && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
\r
1128 if ( !match && node.getNodeData().isHasSequence()
\r
1129 && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
\r
1133 && node.getNodeData().isHasSequence()
\r
1134 && ( node.getNodeData().getSequence().getAccession() != null )
\r
1135 && match( node.getNodeData().getSequence().getAccession().getValue(),
\r
1141 if ( search_domains && !match && node.getNodeData().isHasSequence()
\r
1142 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
\r
1143 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
\r
1144 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
\r
1145 if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
\r
1152 if ( !match && node.getNodeData().isHasSequence()
\r
1153 && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
\r
1154 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
\r
1155 if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
\r
1159 if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
\r
1165 if ( !match && node.getNodeData().isHasSequence()
\r
1166 && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
\r
1167 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
\r
1168 if ( match( x.getComment(), query, case_sensitive, partial ) ) {
\r
1172 if ( match( x.getSource(), query, case_sensitive, partial ) ) {
\r
1176 if ( match( x.getValue(), query, case_sensitive, partial ) ) {
\r
1183 if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
\r
1184 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
\r
1185 I: while ( it.hasNext() ) {
\r
1186 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1191 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
\r
1192 I: while ( it.hasNext() ) {
\r
1193 if ( match( it.next(), query, case_sensitive, partial ) ) {
\r
1200 all_matched = false;
\r
1204 if ( all_matched ) {
\r
1205 nodes.add( node );
\r
1211 public static void setAllIndicatorsToZero( final Phylogeny phy ) {
\r
1212 for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
\r
1213 it.next().setIndicator( ( byte ) 0 );
\r
1218 * Convenience method.
\r
1219 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1221 public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {
\r
1222 setConfidence( node, bootstrap_confidence_value, "bootstrap" );
\r
1225 public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
\r
1226 if ( node.getBranchData().getBranchColor() == null ) {
\r
1227 node.getBranchData().setBranchColor( new BranchColor() );
\r
1229 node.getBranchData().getBranchColor().setValue( color );
\r
1233 * Convenience method
\r
1235 public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {
\r
1236 node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );
\r
1240 * Convenience method.
\r
1241 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1243 public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {
\r
1244 setConfidence( node, confidence_value, "" );
\r
1248 * Convenience method.
\r
1249 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1251 public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {
\r
1252 Confidence c = null;
\r
1253 if ( node.getBranchData().getNumberOfConfidences() > 0 ) {
\r
1254 c = node.getBranchData().getConfidence( 0 );
\r
1257 c = new Confidence();
\r
1258 node.getBranchData().addConfidence( c );
\r
1260 c.setType( type );
\r
1261 c.setValue( confidence_value );
\r
1264 public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {
\r
1265 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1266 node.getNodeData().setTaxonomy( new Taxonomy() );
\r
1268 node.getNodeData().getTaxonomy().setScientificName( scientific_name );
\r
1272 * Convenience method to set the taxonomy code of a phylogeny node.
\r
1276 * @param taxonomy_code
\r
1277 * @throws PhyloXmlDataFormatException
\r
1279 public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )
\r
1280 throws PhyloXmlDataFormatException {
\r
1281 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1282 node.getNodeData().setTaxonomy( new Taxonomy() );
\r
1284 node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
\r
1287 final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
\r
1288 class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
\r
1291 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1292 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1293 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1294 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1295 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1296 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1298 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1299 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1300 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1301 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1303 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
\r
1304 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
\r
1305 return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
\r
1306 .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
\r
1309 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1310 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1311 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1312 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1313 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1315 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1316 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1317 return n1.getNodeData().getSequence().getSymbol()
\r
1318 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1320 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1321 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1322 return n1.getNodeData().getSequence().getGeneName()
\r
1323 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1325 if ( ( n1.getNodeData().getSequence().getAccession() != null )
\r
1326 && ( n2.getNodeData().getSequence().getAccession() != null )
\r
1327 && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
\r
1328 && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
1329 return n1.getNodeData().getSequence().getAccession().getValue()
\r
1330 .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
\r
1333 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1334 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1339 class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
\r
1342 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1343 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1344 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1345 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1346 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1347 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1349 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1350 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1351 return n1.getNodeData().getSequence().getSymbol()
\r
1352 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1354 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1355 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1356 return n1.getNodeData().getSequence().getGeneName()
\r
1357 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1359 if ( ( n1.getNodeData().getSequence().getAccession() != null )
\r
1360 && ( n2.getNodeData().getSequence().getAccession() != null )
\r
1361 && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
\r
1362 && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
1363 return n1.getNodeData().getSequence().getAccession().getValue()
\r
1364 .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
\r
1367 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1368 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1369 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1370 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1371 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1373 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1374 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1375 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1376 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1378 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
\r
1379 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
\r
1380 return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
\r
1381 .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
\r
1384 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1385 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1390 class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
\r
1393 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1394 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1395 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1397 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1398 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1399 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1400 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1401 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1403 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1404 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1405 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1406 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1408 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
\r
1409 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
\r
1410 return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
\r
1411 .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
\r
1414 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1415 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1416 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1417 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1418 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1420 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1421 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1422 return n1.getNodeData().getSequence().getSymbol()
\r
1423 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1425 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1426 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1427 return n1.getNodeData().getSequence().getGeneName()
\r
1428 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1430 if ( ( n1.getNodeData().getSequence().getAccession() != null )
\r
1431 && ( n2.getNodeData().getSequence().getAccession() != null )
\r
1432 && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
\r
1433 && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
\r
1434 return n1.getNodeData().getSequence().getAccession().getValue()
\r
1435 .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
\r
1441 Comparator<PhylogenyNode> c;
\r
1444 c = new PhylogenyNodeSortSequencePriority();
\r
1447 c = new PhylogenyNodeSortNodeNamePriority();
\r
1450 c = new PhylogenyNodeSortTaxonomyPriority();
\r
1452 final List<PhylogenyNode> descs = node.getDescendants();
\r
1453 Collections.sort( descs, c );
\r
1455 for( final PhylogenyNode desc : descs ) {
\r
1456 node.setChildNode( i++, desc );
\r
1461 * Removes from Phylogeny to_be_stripped all external Nodes which are
\r
1462 * associated with a species NOT found in Phylogeny reference.
\r
1464 * @param reference
\r
1465 * a reference Phylogeny
\r
1466 * @param to_be_stripped
\r
1467 * Phylogeny to be stripped
\r
1468 * @return nodes removed from to_be_stripped
\r
1470 public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
\r
1471 final Phylogeny to_be_stripped ) {
\r
1472 final Set<String> ref_ext_taxo = new HashSet<String>();
\r
1473 for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
\r
1474 final PhylogenyNode n = it.next();
\r
1475 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1476 throw new IllegalArgumentException( "no taxonomic data in node: " + n );
\r
1478 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
\r
1479 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );
\r
1481 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
\r
1482 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1484 if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1485 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
\r
1486 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );
\r
1489 final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
\r
1490 for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
\r
1491 final PhylogenyNode n = it.next();
\r
1492 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1493 nodes_to_delete.add( n );
\r
1495 else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
\r
1496 && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1497 && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n
\r
1498 .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
\r
1499 nodes_to_delete.add( n );
\r
1502 for( final PhylogenyNode n : nodes_to_delete ) {
\r
1503 to_be_stripped.deleteSubtree( n, true );
\r
1505 to_be_stripped.clearHashIdToNodeMap();
\r
1506 to_be_stripped.externalNodesHaveChanged();
\r
1507 return nodes_to_delete;
\r
1510 final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
\r
1511 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1512 while ( it.hasNext() ) {
\r
1513 final PhylogenyNode n = it.next();
\r
1514 if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1515 double value = -1;
\r
1517 value = Double.parseDouble( n.getName() );
\r
1519 catch ( final NumberFormatException e ) {
\r
1520 throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
\r
1521 + e.getLocalizedMessage() );
\r
1523 if ( value >= 0.0 ) {
\r
1524 n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
\r
1531 final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {
\r
1532 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1533 while ( it.hasNext() ) {
\r
1534 final PhylogenyNode n = it.next();
\r
1535 if ( !n.isExternal() && !n.isRoot() ) {
\r
1536 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1537 double value = -1;
\r
1539 value = Double.parseDouble( n.getName() );
\r
1541 catch ( final NumberFormatException e ) {
\r
1544 if ( ( value < 0.0 ) || ( value > 100 ) ) {
\r
1553 final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy, final String confidence_type ) {
\r
1554 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1555 while ( it.hasNext() ) {
\r
1556 transferInternalNodeNameToConfidence( confidence_type, it.next() );
\r
1560 private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {
\r
1561 if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
\r
1562 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1565 d = Double.parseDouble( n.getName() );
\r
1567 catch ( final Exception e ) {
\r
1571 n.getBranchData().addConfidence( new Confidence( d, confidence_type ) );
\r
1578 final static public void transferNodeNameToField( final Phylogeny phy,
\r
1579 final PhylogenyNodeField field,
\r
1580 final boolean external_only ) throws PhyloXmlDataFormatException {
\r
1581 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1582 while ( it.hasNext() ) {
\r
1583 final PhylogenyNode n = it.next();
\r
1584 if ( external_only && n.isInternal() ) {
\r
1587 final String name = n.getName().trim();
\r
1588 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1589 switch ( field ) {
\r
1590 case TAXONOMY_CODE:
\r
1592 setTaxonomyCode( n, name );
\r
1594 case TAXONOMY_SCIENTIFIC_NAME:
\r
1596 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1597 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1599 n.getNodeData().getTaxonomy().setScientificName( name );
\r
1601 case TAXONOMY_COMMON_NAME:
\r
1603 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1604 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1606 n.getNodeData().getTaxonomy().setCommonName( name );
\r
1608 case SEQUENCE_SYMBOL:
\r
1610 if ( !n.getNodeData().isHasSequence() ) {
\r
1611 n.getNodeData().setSequence( new Sequence() );
\r
1613 n.getNodeData().getSequence().setSymbol( name );
\r
1615 case SEQUENCE_NAME:
\r
1617 if ( !n.getNodeData().isHasSequence() ) {
\r
1618 n.getNodeData().setSequence( new Sequence() );
\r
1620 n.getNodeData().getSequence().setName( name );
\r
1622 case TAXONOMY_ID_UNIPROT_1: {
\r
1623 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1624 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1627 final int i = name.indexOf( '_' );
\r
1629 id = name.substring( 0, i );
\r
1634 n.getNodeData().getTaxonomy()
\r
1635 .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
\r
1638 case TAXONOMY_ID_UNIPROT_2: {
\r
1639 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1640 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1643 final int i = name.indexOf( '_' );
\r
1645 id = name.substring( i + 1, name.length() );
\r
1650 n.getNodeData().getTaxonomy()
\r
1651 .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
\r
1654 case TAXONOMY_ID: {
\r
1655 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1656 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1658 n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
\r
1666 static double addPhylogenyDistances( final double a, final double b ) {
\r
1667 if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
\r
1670 else if ( a >= 0.0 ) {
\r
1673 else if ( b >= 0.0 ) {
\r
1676 return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
\r
1679 static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {
\r
1681 boolean all_default = true;
\r
1682 while ( anc != desc ) {
\r
1683 if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
\r
1684 d += desc.getDistanceToParent();
\r
1685 if ( all_default ) {
\r
1686 all_default = false;
\r
1689 desc = desc.getParent();
\r
1691 if ( all_default ) {
\r
1692 return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
\r
1698 * Deep copies the phylogeny originating from this node.
\r
1700 static PhylogenyNode copySubTree( final PhylogenyNode source ) {
\r
1701 if ( source == null ) {
\r
1705 final PhylogenyNode newnode = source.copyNodeData();
\r
1706 if ( !source.isExternal() ) {
\r
1707 for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
\r
1708 newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
\r
1716 * Shallow copies the phylogeny originating from this node.
\r
1718 static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
\r
1719 if ( source == null ) {
\r
1723 final PhylogenyNode newnode = source.copyNodeDataShallow();
\r
1724 if ( !source.isExternal() ) {
\r
1725 for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
\r
1726 newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
\r
1733 private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,
\r
1734 final double min_distance_to_root ) {
\r
1735 final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();
\r
1736 final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );
\r
1737 for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {
\r
1738 if ( ext.getIndicator() != 0 ) {
\r
1739 throw new RuntimeException( "this should not have happened" );
\r
1741 ext.setIndicator( ( byte ) 1 );
\r
1748 * Calculates the distance between PhylogenyNodes n1 and n2.
\r
1749 * PRECONDITION: n1 is a descendant of n2.
\r
1752 * a descendant of n2
\r
1754 * @return distance between n1 and n2
\r
1756 private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1758 while ( n1 != n2 ) {
\r
1759 if ( n1.getDistanceToParent() > 0.0 ) {
\r
1760 d += n1.getDistanceToParent();
\r
1762 n1 = n1.getParent();
\r
1767 private static boolean match( final String s,
\r
1768 final String query,
\r
1769 final boolean case_sensitive,
\r
1770 final boolean partial ) {
\r
1771 if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
\r
1774 String my_s = s.trim();
\r
1775 String my_query = query.trim();
\r
1776 if ( !case_sensitive ) {
\r
1777 my_s = my_s.toLowerCase();
\r
1778 my_query = my_query.toLowerCase();
\r
1781 return my_s.indexOf( my_query ) >= 0;
\r
1784 return Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" ).matcher( my_s ).find();
\r
1788 private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {
\r
1789 PhylogenyNode n = node;
\r
1790 PhylogenyNode prev = node;
\r
1791 while ( min_distance_to_root < n.calculateDistanceToRoot() ) {
\r
1793 n = n.getParent();
\r
1798 public static enum DESCENDANT_SORT_PRIORITY {
\r
1799 NODE_NAME, SEQUENCE, TAXONOMY;
\r
1802 public static enum PhylogenyNodeField {
\r
1807 TAXONOMY_COMMON_NAME,
\r
1809 TAXONOMY_ID_UNIPROT_1,
\r
1810 TAXONOMY_ID_UNIPROT_2,
\r
1811 TAXONOMY_SCIENTIFIC_NAME;
\r