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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43 import java.util.regex.PatternSyntaxException;
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45 import org.forester.io.parsers.FastaParser;
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46 import org.forester.io.parsers.PhylogenyParser;
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47 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
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48 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
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49 import org.forester.io.parsers.util.PhylogenyParserException;
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50 import org.forester.msa.Msa;
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51 import org.forester.phylogeny.data.Accession;
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52 import org.forester.phylogeny.data.Annotation;
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53 import org.forester.phylogeny.data.BranchColor;
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54 import org.forester.phylogeny.data.BranchWidth;
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55 import org.forester.phylogeny.data.Confidence;
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56 import org.forester.phylogeny.data.DomainArchitecture;
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57 import org.forester.phylogeny.data.Event;
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58 import org.forester.phylogeny.data.Identifier;
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59 import org.forester.phylogeny.data.PhylogenyDataUtil;
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60 import org.forester.phylogeny.data.Sequence;
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61 import org.forester.phylogeny.data.Taxonomy;
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62 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
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63 import org.forester.phylogeny.factories.PhylogenyFactory;
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64 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
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65 import org.forester.util.BasicDescriptiveStatistics;
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66 import org.forester.util.DescriptiveStatistics;
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67 import org.forester.util.ForesterUtil;
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69 public class PhylogenyMethods {
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71 private PhylogenyMethods() {
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72 // Hidden constructor.
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76 public Object clone() throws CloneNotSupportedException {
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77 throw new CloneNotSupportedException();
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80 public static boolean extractFastaInformation( final Phylogeny phy ) {
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81 boolean could_extract = false;
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82 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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83 final PhylogenyNode node = iter.next();
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84 if ( !ForesterUtil.isEmpty( node.getName() ) ) {
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85 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
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86 if ( name_m.lookingAt() ) {
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87 could_extract = true;
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88 final String acc_source = name_m.group( 1 );
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89 final String acc = name_m.group( 2 );
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90 final String seq_name = name_m.group( 3 );
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91 final String tax_sn = name_m.group( 4 );
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92 if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
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93 ForesterUtil.ensurePresenceOfSequence( node );
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94 node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
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96 if ( !ForesterUtil.isEmpty( seq_name ) ) {
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97 ForesterUtil.ensurePresenceOfSequence( node );
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98 node.getNodeData().getSequence( 0 ).setName( seq_name );
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100 if ( !ForesterUtil.isEmpty( tax_sn ) ) {
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101 ForesterUtil.ensurePresenceOfTaxonomy( node );
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102 node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
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107 return could_extract;
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110 public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
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111 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
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112 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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113 final PhylogenyNode n = iter.next();
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114 if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
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115 stats.addValue( n.getDistanceToParent() );
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121 public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
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122 final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
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123 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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124 final PhylogenyNode n = iter.next();
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125 if ( !n.isExternal() && !n.isRoot() ) {
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126 if ( n.getBranchData().isHasConfidences() ) {
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127 for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
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128 final Confidence c = n.getBranchData().getConfidences().get( i );
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129 if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
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130 stats.add( i, new BasicDescriptiveStatistics() );
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132 if ( !ForesterUtil.isEmpty( c.getType() ) ) {
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133 if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
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134 if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
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135 throw new IllegalArgumentException( "support values in node [" + n.toString()
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136 + "] appear inconsistently ordered" );
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139 stats.get( i ).setDescription( c.getType() );
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141 stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
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150 * Calculates the distance between PhylogenyNodes node1 and node2.
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155 * @return distance between node1 and node2
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157 public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
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158 final PhylogenyNode lca = calculateLCA( node1, node2 );
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159 final PhylogenyNode n1 = node1;
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160 final PhylogenyNode n2 = node2;
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161 return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
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165 * Returns the LCA of PhylogenyNodes node1 and node2.
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170 * @return LCA of node1 and node2
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172 public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
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173 if ( node1 == null ) {
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174 throw new IllegalArgumentException( "first argument (node) is null" );
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176 if ( node2 == null ) {
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177 throw new IllegalArgumentException( "second argument (node) is null" );
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179 if ( node1 == node2 ) {
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182 if ( ( node1.getParent() == node2.getParent() ) ) {
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183 return node1.getParent();
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185 int depth1 = node1.calculateDepth();
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186 int depth2 = node2.calculateDepth();
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187 while ( ( depth1 > -1 ) && ( depth2 > -1 ) ) {
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188 if ( depth1 > depth2 ) {
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189 node1 = node1.getParent();
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192 else if ( depth2 > depth1 ) {
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193 node2 = node2.getParent();
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197 if ( node1 == node2 ) {
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200 node1 = node1.getParent();
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201 node2 = node2.getParent();
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206 throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
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210 * Returns the LCA of PhylogenyNodes node1 and node2.
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211 * Precondition: ids are in pre-order (or level-order).
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216 * @return LCA of node1 and node2
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218 public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
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219 if ( node1 == null ) {
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220 throw new IllegalArgumentException( "first argument (node) is null" );
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222 if ( node2 == null ) {
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223 throw new IllegalArgumentException( "second argument (node) is null" );
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225 while ( node1 != node2 ) {
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226 if ( node1.getId() > node2.getId() ) {
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227 node1 = node1.getParent();
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230 node2 = node2.getParent();
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236 public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
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237 if ( node.isExternal() ) {
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241 for( PhylogenyNode d : node.getAllExternalDescendants() ) {
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243 while ( d != node ) {
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244 if ( d.isCollapse() ) {
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252 if ( max < steps ) {
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259 public static int calculateMaxDepth( final Phylogeny phy ) {
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261 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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262 final PhylogenyNode node = iter.next();
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263 final int steps = node.calculateDepth();
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264 if ( steps > max ) {
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271 public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
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273 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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274 final PhylogenyNode node = iter.next();
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275 final double d = node.calculateDistanceToRoot();
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283 public static PhylogenyNode calculateNodeWithMaxDistanceToRoot( final Phylogeny phy ) {
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285 PhylogenyNode max_node = phy.getFirstExternalNode();
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286 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
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287 final PhylogenyNode node = iter.next();
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288 final double d = node.calculateDistanceToRoot();
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297 public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
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298 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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300 for( final PhylogenyNode n : descs ) {
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301 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
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308 public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
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309 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
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310 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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311 final PhylogenyNode n = iter.next();
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312 if ( !n.isExternal() ) {
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313 stats.addValue( n.getNumberOfDescendants() );
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319 public final static void collapseSubtreeStructure( final PhylogenyNode n ) {
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320 final List<PhylogenyNode> eds = n.getAllExternalDescendants();
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321 final List<Double> d = new ArrayList<Double>();
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322 for( final PhylogenyNode ed : eds ) {
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323 d.add( calculateDistanceToAncestor( n, ed ) );
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325 for( int i = 0; i < eds.size(); ++i ) {
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326 n.setChildNode( i, eds.get( i ) );
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327 eds.get( i ).setDistanceToParent( d.get( i ) );
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331 public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
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333 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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334 final PhylogenyNode n = iter.next();
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335 if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {
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342 public static int countNumberOfPolytomies( final Phylogeny phy ) {
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344 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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345 final PhylogenyNode n = iter.next();
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346 if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
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353 public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
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354 final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
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355 final List<PhylogenyNode> ext = phy.getExternalNodes();
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356 for( final PhylogenyNode n : ext ) {
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357 nodes.put( n.getName(), n );
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362 public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
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363 for( final Long id : to_delete ) {
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364 phy.deleteSubtree( phy.getNode( id ), true );
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366 phy.clearHashIdToNodeMap();
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367 phy.externalNodesHaveChanged();
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370 public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
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371 throws IllegalArgumentException {
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372 for( final String element : node_names_to_delete ) {
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373 if ( ForesterUtil.isEmpty( element ) ) {
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376 List<PhylogenyNode> nodes = null;
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377 nodes = p.getNodes( element );
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378 final Iterator<PhylogenyNode> it = nodes.iterator();
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379 while ( it.hasNext() ) {
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380 final PhylogenyNode n = it.next();
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381 if ( !n.isExternal() ) {
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382 throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
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384 p.deleteSubtree( n, true );
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387 p.clearHashIdToNodeMap();
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388 p.externalNodesHaveChanged();
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391 public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
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392 final Phylogeny p ) {
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393 final PhylogenyNodeIterator it = p.iteratorExternalForward();
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394 final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
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396 Arrays.sort( node_names_to_keep );
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397 while ( it.hasNext() ) {
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398 final String curent_name = it.next().getName();
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399 if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
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400 to_delete[ i++ ] = curent_name;
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403 PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
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404 final List<String> deleted = new ArrayList<String>();
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405 for( final String n : to_delete ) {
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406 if ( !ForesterUtil.isEmpty( n ) ) {
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413 public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {
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414 final Set<Long> to_delete = new HashSet<Long>();
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415 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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416 final PhylogenyNode n = it.next();
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417 if ( n.getNodeData().isHasTaxonomy() ) {
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418 if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
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419 to_delete.add( n.getId() );
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423 throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
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426 deleteExternalNodesNegativeSelection( to_delete, phy );
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429 final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
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430 final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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431 for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
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432 final PhylogenyNode n = iter.next();
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433 if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {
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434 to_delete.add( n );
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437 for( final PhylogenyNode d : to_delete ) {
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438 PhylogenyMethods.removeNode( d, phy );
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440 phy.clearHashIdToNodeMap();
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441 phy.externalNodesHaveChanged();
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444 final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
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445 if ( n.isInternal() ) {
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446 throw new IllegalArgumentException( "node is not external" );
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448 final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
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449 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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450 final PhylogenyNode i = it.next();
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451 if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
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452 to_delete.add( i );
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455 for( final PhylogenyNode d : to_delete ) {
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456 phy.deleteSubtree( d, true );
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458 phy.clearHashIdToNodeMap();
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459 phy.externalNodesHaveChanged();
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462 public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,
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463 final double min_distance_to_root ) {
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464 if ( min_distance_to_root <= 0 ) {
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465 throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );
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467 final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();
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468 setAllIndicatorsToZero( phy );
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469 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
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470 final PhylogenyNode n = it.next();
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471 if ( n.getIndicator() != 0 ) {
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474 l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
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475 if ( l.isEmpty() ) {
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476 throw new RuntimeException( "this should not have happened" );
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482 public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
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483 final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
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484 final Set<Long> encountered = new HashSet<Long>();
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485 if ( !node.isExternal() ) {
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486 final List<PhylogenyNode> exts = node.getAllExternalDescendants();
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487 for( PhylogenyNode current : exts ) {
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488 descs.add( current );
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489 while ( current != node ) {
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490 current = current.getParent();
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491 if ( encountered.contains( current.getId() ) ) {
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494 descs.add( current );
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495 encountered.add( current.getId() );
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504 * Convenience method
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509 public static Color getBranchColorValue( final PhylogenyNode node ) {
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510 if ( node.getBranchData().getBranchColor() == null ) {
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513 return node.getBranchData().getBranchColor().getValue();
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517 * Convenience method
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519 public static double getBranchWidthValue( final PhylogenyNode node ) {
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520 if ( !node.getBranchData().isHasBranchWidth() ) {
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521 return BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE;
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523 return node.getBranchData().getBranchWidth().getValue();
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527 * Convenience method
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529 public static double getConfidenceValue( final PhylogenyNode node ) {
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530 if ( !node.getBranchData().isHasConfidences() ) {
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531 return Confidence.CONFIDENCE_DEFAULT_VALUE;
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533 return node.getBranchData().getConfidence( 0 ).getValue();
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537 * Convenience method
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539 public static double[] getConfidenceValuesAsArray( final PhylogenyNode node ) {
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540 if ( !node.getBranchData().isHasConfidences() ) {
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541 return new double[ 0 ];
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543 final double[] values = new double[ node.getBranchData().getConfidences().size() ];
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545 for( final Confidence c : node.getBranchData().getConfidences() ) {
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546 values[ i++ ] = c.getValue();
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551 final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
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552 return calculateLCA( n1, n2 ).getNodeData().getEvent();
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556 * Returns taxonomy t if all external descendants have
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557 * the same taxonomy t, null otherwise.
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560 public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {
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561 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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562 Taxonomy tax = null;
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563 for( final PhylogenyNode n : descs ) {
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564 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
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567 else if ( tax == null ) {
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568 tax = n.getNodeData().getTaxonomy();
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570 else if ( n.getNodeData().getTaxonomy().isEmpty() || !tax.isEqual( n.getNodeData().getTaxonomy() ) ) {
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577 public static PhylogenyNode getFurthestDescendant( final PhylogenyNode node ) {
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578 final List<PhylogenyNode> children = node.getAllExternalDescendants();
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579 PhylogenyNode farthest = null;
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580 double longest = -Double.MAX_VALUE;
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581 for( final PhylogenyNode child : children ) {
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582 if ( PhylogenyMethods.getDistance( child, node ) > longest ) {
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584 longest = PhylogenyMethods.getDistance( child, node );
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590 // public static PhylogenyMethods getInstance() {
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591 // if ( PhylogenyMethods._instance == null ) {
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592 // PhylogenyMethods._instance = new PhylogenyMethods();
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594 // return PhylogenyMethods._instance;
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597 * Returns the largest confidence value found on phy.
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599 static public double getMaximumConfidenceValue( final Phylogeny phy ) {
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600 double max = -Double.MAX_VALUE;
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601 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
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602 final double s = PhylogenyMethods.getConfidenceValue( iter.next() );
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603 if ( ( s != Confidence.CONFIDENCE_DEFAULT_VALUE ) && ( s > max ) ) {
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610 static public int getMinimumDescendentsPerInternalNodes( final Phylogeny phy ) {
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611 int min = Integer.MAX_VALUE;
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614 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
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616 if ( n.isInternal() ) {
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617 d = n.getNumberOfDescendants();
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627 * Convenience method for display purposes.
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628 * Not intended for algorithms.
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630 public static String getSpecies( final PhylogenyNode node ) {
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631 if ( !node.getNodeData().isHasTaxonomy() ) {
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634 else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
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635 return node.getNodeData().getTaxonomy().getScientificName();
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637 if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
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638 return node.getNodeData().getTaxonomy().getTaxonomyCode();
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641 return node.getNodeData().getTaxonomy().getCommonName();
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646 * Convenience method for display purposes.
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647 * Not intended for algorithms.
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649 public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
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650 if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
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653 return node.getNodeData().getTaxonomy().getIdentifier().getValue();
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656 public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
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657 if ( n.isExternal() ) {
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661 if ( n.isDuplication() ) {
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662 for( final PhylogenyNode desc : n.getDescendants() ) {
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663 if ( !isAllDecendentsAreDuplications( desc ) ) {
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675 public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
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676 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
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677 if ( node.getChildNode( i ).isExternal() ) {
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685 * This is case insensitive.
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688 public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
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689 final String[] providers ) {
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690 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
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691 final String my_tax_prov = tax.getIdentifier().getProvider();
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692 for( final String provider : providers ) {
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693 if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
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704 public static void midpointRoot( final Phylogeny phylogeny ) {
\r
705 if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {
\r
709 final int total_nodes = phylogeny.getNodeCount();
\r
711 if ( ++counter > total_nodes ) {
\r
712 throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );
\r
714 PhylogenyNode a = null;
\r
717 for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {
\r
718 final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );
\r
719 final double df = getDistance( f, phylogeny.getRoot() );
\r
726 else if ( df > db ) {
\r
731 final double diff = da - db;
\r
732 if ( diff < 0.000001 ) {
\r
735 double x = da - ( diff / 2.0 );
\r
736 while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {
\r
737 x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );
\r
740 phylogeny.reRoot( a, x );
\r
742 phylogeny.recalculateNumberOfExternalDescendants( true );
\r
745 public static void normalizeBootstrapValues( final Phylogeny phylogeny,
\r
746 final double max_bootstrap_value,
\r
747 final double max_normalized_value ) {
\r
748 for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
\r
749 final PhylogenyNode node = iter.next();
\r
750 if ( node.isInternal() ) {
\r
751 final double confidence = getConfidenceValue( node );
\r
752 if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
\r
753 if ( confidence >= max_bootstrap_value ) {
\r
754 setBootstrapConfidence( node, max_normalized_value );
\r
757 setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
\r
764 public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
\r
765 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
766 if ( phy.isEmpty() ) {
\r
769 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
770 nodes.add( iter.next() );
\r
776 * Returns a map of distinct taxonomies of
\r
777 * all external nodes of node.
\r
778 * If at least one of the external nodes has no taxonomy,
\r
779 * null is returned.
\r
782 public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
\r
783 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
\r
784 final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();
\r
785 for( final PhylogenyNode n : descs ) {
\r
786 if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
\r
789 final Taxonomy t = n.getNodeData().getTaxonomy();
\r
790 if ( tax_map.containsKey( t ) ) {
\r
791 tax_map.put( t, tax_map.get( t ) + 1 );
\r
794 tax_map.put( t, 1 );
\r
801 * Arranges the order of childern for each node of this Phylogeny in such a
\r
802 * way that either the branch with more children is on top (right) or on
\r
803 * bottom (left), dependent on the value of boolean order.
\r
806 * decides in which direction to order
\r
809 public static void orderAppearance( final PhylogenyNode n,
\r
810 final boolean order,
\r
811 final boolean order_ext_alphabetically,
\r
812 final DESCENDANT_SORT_PRIORITY pri ) {
\r
813 if ( n.isExternal() ) {
\r
817 PhylogenyNode temp = null;
\r
818 if ( ( n.getNumberOfDescendants() == 2 )
\r
819 && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
\r
820 && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
\r
821 temp = n.getChildNode1();
\r
822 n.setChild1( n.getChildNode2() );
\r
823 n.setChild2( temp );
\r
825 else if ( order_ext_alphabetically ) {
\r
826 boolean all_ext = true;
\r
827 for( final PhylogenyNode i : n.getDescendants() ) {
\r
828 if ( !i.isExternal() ) {
\r
834 PhylogenyMethods.sortNodeDescendents( n, pri );
\r
837 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
\r
838 orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
\r
843 public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
\r
844 for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
\r
845 final PhylogenyNode node = iter.next();
\r
847 double green = 0.0;
\r
850 if ( node.isInternal() ) {
\r
851 //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
\r
852 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
\r
853 final PhylogenyNode child_node = node.getChildNode( i );
\r
854 final Color child_color = getBranchColorValue( child_node );
\r
855 if ( child_color != null ) {
\r
857 red += child_color.getRed();
\r
858 green += child_color.getGreen();
\r
859 blue += child_color.getBlue();
\r
862 setBranchColorValue( node,
\r
863 new Color( ForesterUtil.roundToInt( red / n ),
\r
864 ForesterUtil.roundToInt( green / n ),
\r
865 ForesterUtil.roundToInt( blue / n ) ) );
\r
870 public static final void preOrderReId( final Phylogeny phy ) {
\r
871 if ( phy.isEmpty() ) {
\r
874 phy.setIdToNodeMap( null );
\r
875 long i = PhylogenyNode.getNodeCount();
\r
876 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
\r
877 it.next().setId( i++ );
\r
879 PhylogenyNode.setNodeCount( i );
\r
882 public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
\r
883 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
884 final Phylogeny[] trees = factory.create( file, parser );
\r
885 if ( ( trees == null ) || ( trees.length == 0 ) ) {
\r
886 throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
\r
891 public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
\r
892 throws IOException {
\r
893 final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
\r
894 for( final File file : files ) {
\r
895 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
\r
896 final Phylogeny[] trees = factory.create( file, parser );
\r
897 if ( ( trees == null ) || ( trees.length == 0 ) ) {
\r
898 throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
\r
900 tree_list.addAll( Arrays.asList( trees ) );
\r
902 return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
\r
905 public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
\r
906 if ( remove_me.isRoot() ) {
\r
907 if ( remove_me.getNumberOfDescendants() == 1 ) {
\r
908 final PhylogenyNode desc = remove_me.getDescendants().get( 0 );
\r
909 desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
\r
910 desc.getDistanceToParent() ) );
\r
911 desc.setParent( null );
\r
912 phylogeny.setRoot( desc );
\r
913 phylogeny.clearHashIdToNodeMap();
\r
916 throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );
\r
919 else if ( remove_me.isExternal() ) {
\r
920 phylogeny.deleteSubtree( remove_me, false );
\r
921 phylogeny.clearHashIdToNodeMap();
\r
922 phylogeny.externalNodesHaveChanged();
\r
925 final PhylogenyNode parent = remove_me.getParent();
\r
926 final List<PhylogenyNode> descs = remove_me.getDescendants();
\r
927 parent.removeChildNode( remove_me );
\r
928 for( final PhylogenyNode desc : descs ) {
\r
929 parent.addAsChild( desc );
\r
930 desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
\r
931 desc.getDistanceToParent() ) );
\r
933 remove_me.setParent( null );
\r
934 phylogeny.clearHashIdToNodeMap();
\r
935 phylogeny.externalNodesHaveChanged();
\r
940 private static enum NDF {
\r
957 private final String _text;
\r
959 NDF( final String text ) {
\r
963 public static NDF fromString( final String text ) {
\r
964 for( NDF n : NDF.values() ) {
\r
965 if ( text.startsWith( n._text ) ) {
\r
974 public static List<PhylogenyNode> searchData( final String query,
\r
975 final Phylogeny phy,
\r
976 final boolean case_sensitive,
\r
977 final boolean partial,
\r
978 final boolean regex,
\r
979 final boolean search_domains,
\r
980 final double domains_confidence_threshold ) {
\r
981 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
982 if ( phy.isEmpty() || ( query == null ) ) {
\r
985 if ( ForesterUtil.isEmpty( query ) ) {
\r
989 String my_query = query;
\r
992 if ( my_query.length() > 2 && my_query.indexOf( ":" ) == 2 ) {
\r
993 ndf = NDF.fromString( my_query );
\r
994 if ( ndf != null ) {
\r
995 my_query = my_query.substring( 3 );
\r
1000 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
1001 final PhylogenyNode node = iter.next();
\r
1002 boolean match = false;
\r
1005 if ( ( ndf == null || ndf == NDF.NN ) && match( node.getName(), my_query, case_sensitive, partial, regex ) ) {
\r
1008 else if ( ( ndf == null || ndf == NDF.TC ) && node.getNodeData().isHasTaxonomy()
\r
1009 && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), my_query, case_sensitive, partial, regex ) ) {
\r
1012 else if ( ( ndf == null || ndf == NDF.CN ) && node.getNodeData().isHasTaxonomy()
\r
1013 && match( node.getNodeData().getTaxonomy().getCommonName(), my_query, case_sensitive, partial, regex ) ) {
\r
1016 else if ( ( ndf == null || ndf == NDF.TS ) && node.getNodeData().isHasTaxonomy()
\r
1017 && match( node.getNodeData().getTaxonomy().getScientificName(),
\r
1024 else if ( ( ndf == null || ndf == NDF.TI ) &&
\r
1025 node.getNodeData().isHasTaxonomy()
\r
1026 && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1027 && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
\r
1035 ( ndf == null || ndf == NDF.SY ) &&
\r
1036 node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
\r
1037 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
\r
1038 I: for( final String syn : syns ) {
\r
1039 if ( match( syn, my_query, case_sensitive, partial, regex ) ) {
\r
1045 if ( !match && ( ndf == null || ndf == NDF.SN ) &&
\r
1046 node.getNodeData().isHasSequence()
\r
1047 && match( node.getNodeData().getSequence().getName(), my_query, case_sensitive, partial, regex ) ) {
\r
1050 if ( !match && ( ndf == null || ndf == NDF.GN ) &&
\r
1051 node.getNodeData().isHasSequence()
\r
1052 && match( node.getNodeData().getSequence().getGeneName(), my_query, case_sensitive, partial, regex ) ) {
\r
1055 if ( !match && ( ndf == null || ndf == NDF.SS ) &&
\r
1057 node.getNodeData().isHasSequence()
\r
1058 && match( node.getNodeData().getSequence().getSymbol(), my_query, case_sensitive, partial, regex ) ) {
\r
1061 if ( !match && ( ndf == null || ndf == NDF.SA ) &&
\r
1064 node.getNodeData().isHasSequence()
\r
1065 && ( node.getNodeData().getSequence().getAccession() != null )
\r
1066 && match( node.getNodeData().getSequence().getAccession().getValue(),
\r
1073 if ( !match && ( (ndf == null && search_domains ) || ndf == NDF.DO ) && node.getNodeData().isHasSequence()
\r
1074 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
\r
1075 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
\r
1076 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
\r
1077 if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold ) && ( match( da.getDomain( i ).getName(), my_query, case_sensitive, partial, regex ) ) ) {
\r
1084 !match && ( ndf == null || ndf == NDF.AN ) &&
\r
1085 node.getNodeData().isHasSequence()
\r
1086 && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
\r
1087 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
\r
1088 if ( match( ann.getDesc(), my_query, case_sensitive, partial, regex ) ) {
\r
1092 if ( match( ann.getRef(), my_query, case_sensitive, partial, regex ) ) {
\r
1098 if ( !match && ( ndf == null || ndf == NDF.XR ) &&
\r
1099 node.getNodeData().isHasSequence()
\r
1100 && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
\r
1101 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
\r
1102 if ( match( x.getComment(), my_query, case_sensitive, partial, regex ) ) {
\r
1106 if ( match( x.getSource(), my_query, case_sensitive, partial, regex ) ) {
\r
1110 if ( match( x.getValue(), my_query, case_sensitive, partial, regex ) ) {
\r
1117 if ( !match && ( ndf == null || ndf == NDF.BC ) &&
\r
1118 ( node.getNodeData().getBinaryCharacters() != null ) ) {
\r
1119 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
\r
1120 I: while ( it.hasNext() ) {
\r
1121 if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
\r
1126 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
\r
1127 I: while ( it.hasNext() ) {
\r
1128 if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
\r
1135 nodes.add( node );
\r
1141 public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
\r
1142 final Phylogeny phy,
\r
1143 final boolean case_sensitive,
\r
1144 final boolean partial,
\r
1145 final boolean search_domains ) {
\r
1146 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
\r
1147 if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
\r
1150 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
\r
1151 final PhylogenyNode node = iter.next();
\r
1152 boolean all_matched = true;
\r
1153 for( final String query : queries ) {
\r
1154 boolean match = false;
\r
1155 if ( ForesterUtil.isEmpty( query ) ) {
\r
1158 if ( match( node.getName(), query, case_sensitive, partial, false ) ) {
\r
1161 else if ( node.getNodeData().isHasTaxonomy()
\r
1162 && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
\r
1169 else if ( node.getNodeData().isHasTaxonomy()
\r
1170 && match( node.getNodeData().getTaxonomy().getCommonName(),
\r
1177 else if ( node.getNodeData().isHasTaxonomy()
\r
1178 && match( node.getNodeData().getTaxonomy().getScientificName(),
\r
1185 else if ( node.getNodeData().isHasTaxonomy()
\r
1186 && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1187 && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
\r
1194 else if ( node.getNodeData().isHasTaxonomy()
\r
1195 && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
\r
1196 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
\r
1197 I: for( final String syn : syns ) {
\r
1198 if ( match( syn, query, case_sensitive, partial, false ) ) {
\r
1204 if ( !match && node.getNodeData().isHasSequence()
\r
1205 && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial, false ) ) {
\r
1209 && node.getNodeData().isHasSequence()
\r
1210 && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial, false ) ) {
\r
1213 if ( !match && node.getNodeData().isHasSequence()
\r
1214 && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial, false ) ) {
\r
1218 && node.getNodeData().isHasSequence()
\r
1219 && ( node.getNodeData().getSequence().getAccession() != null )
\r
1220 && match( node.getNodeData().getSequence().getAccession().getValue(),
\r
1227 if ( search_domains && !match && node.getNodeData().isHasSequence()
\r
1228 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
\r
1229 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
\r
1230 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
\r
1231 if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) {
\r
1238 if ( !match && node.getNodeData().isHasSequence()
\r
1239 && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
\r
1240 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
\r
1241 if ( match( ann.getDesc(), query, case_sensitive, partial, false ) ) {
\r
1245 if ( match( ann.getRef(), query, case_sensitive, partial, false ) ) {
\r
1251 if ( !match && node.getNodeData().isHasSequence()
\r
1252 && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
\r
1253 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
\r
1254 if ( match( x.getComment(), query, case_sensitive, partial, false ) ) {
\r
1258 if ( match( x.getSource(), query, case_sensitive, partial, false ) ) {
\r
1262 if ( match( x.getValue(), query, case_sensitive, partial, false ) ) {
\r
1269 if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
\r
1270 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
\r
1271 I: while ( it.hasNext() ) {
\r
1272 if ( match( it.next(), query, case_sensitive, partial, false ) ) {
\r
1277 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
\r
1278 I: while ( it.hasNext() ) {
\r
1279 if ( match( it.next(), query, case_sensitive, partial, false ) ) {
\r
1286 all_matched = false;
\r
1290 if ( all_matched ) {
\r
1291 nodes.add( node );
\r
1297 public static void setAllIndicatorsToZero( final Phylogeny phy ) {
\r
1298 for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
\r
1299 it.next().setIndicator( ( byte ) 0 );
\r
1304 * Convenience method.
\r
1305 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1307 public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {
\r
1308 setConfidence( node, bootstrap_confidence_value, "bootstrap" );
\r
1311 public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
\r
1312 if ( node.getBranchData().getBranchColor() == null ) {
\r
1313 node.getBranchData().setBranchColor( new BranchColor() );
\r
1315 node.getBranchData().getBranchColor().setValue( color );
\r
1319 * Convenience method
\r
1321 public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {
\r
1322 node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );
\r
1326 * Convenience method.
\r
1327 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1329 public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {
\r
1330 setConfidence( node, confidence_value, "" );
\r
1334 * Convenience method.
\r
1335 * Sets value for the first confidence value (created if not present, values overwritten otherwise).
\r
1337 public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {
\r
1338 Confidence c = null;
\r
1339 if ( node.getBranchData().getNumberOfConfidences() > 0 ) {
\r
1340 c = node.getBranchData().getConfidence( 0 );
\r
1343 c = new Confidence();
\r
1344 node.getBranchData().addConfidence( c );
\r
1346 c.setType( type );
\r
1347 c.setValue( confidence_value );
\r
1350 public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {
\r
1351 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1352 node.getNodeData().setTaxonomy( new Taxonomy() );
\r
1354 node.getNodeData().getTaxonomy().setScientificName( scientific_name );
\r
1358 * Convenience method to set the taxonomy code of a phylogeny node.
\r
1362 * @param taxonomy_code
\r
1363 * @throws PhyloXmlDataFormatException
\r
1365 public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )
\r
1366 throws PhyloXmlDataFormatException {
\r
1367 if ( !node.getNodeData().isHasTaxonomy() ) {
\r
1368 node.getNodeData().setTaxonomy( new Taxonomy() );
\r
1370 node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
\r
1373 final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
\r
1374 Comparator<PhylogenyNode> c;
\r
1377 c = new PhylogenyNodeSortSequencePriority();
\r
1380 c = new PhylogenyNodeSortNodeNamePriority();
\r
1383 c = new PhylogenyNodeSortTaxonomyPriority();
\r
1385 final List<PhylogenyNode> descs = node.getDescendants();
\r
1386 Collections.sort( descs, c );
\r
1388 for( final PhylogenyNode desc : descs ) {
\r
1389 node.setChildNode( i++, desc );
\r
1394 * Removes from Phylogeny to_be_stripped all external Nodes which are
\r
1395 * associated with a species NOT found in Phylogeny reference.
\r
1397 * @param reference
\r
1398 * a reference Phylogeny
\r
1399 * @param to_be_stripped
\r
1400 * Phylogeny to be stripped
\r
1401 * @return nodes removed from to_be_stripped
\r
1403 public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
\r
1404 final Phylogeny to_be_stripped ) {
\r
1405 final Set<String> ref_ext_taxo = new HashSet<String>();
\r
1406 for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
\r
1407 final PhylogenyNode n = it.next();
\r
1408 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1409 throw new IllegalArgumentException( "no taxonomic data in node: " + n );
\r
1411 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
\r
1412 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );
\r
1414 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
\r
1415 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1417 if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )
\r
1418 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
\r
1419 ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );
\r
1422 final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
\r
1423 for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
\r
1424 final PhylogenyNode n = it.next();
\r
1425 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1426 nodes_to_delete.add( n );
\r
1428 else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
\r
1429 && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1430 && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n
\r
1431 .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
\r
1432 nodes_to_delete.add( n );
\r
1435 for( final PhylogenyNode n : nodes_to_delete ) {
\r
1436 to_be_stripped.deleteSubtree( n, true );
\r
1438 to_be_stripped.clearHashIdToNodeMap();
\r
1439 to_be_stripped.externalNodesHaveChanged();
\r
1440 return nodes_to_delete;
\r
1443 final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
\r
1444 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1445 while ( it.hasNext() ) {
\r
1446 final PhylogenyNode n = it.next();
\r
1447 if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1448 double value = -1;
\r
1450 value = Double.parseDouble( n.getName() );
\r
1452 catch ( final NumberFormatException e ) {
\r
1453 throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
\r
1454 + e.getLocalizedMessage() );
\r
1456 if ( value >= 0.0 ) {
\r
1457 n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
\r
1464 final static public boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {
\r
1465 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1466 while ( it.hasNext() ) {
\r
1467 final PhylogenyNode n = it.next();
\r
1468 if ( !n.isExternal() && !n.isRoot() ) {
\r
1469 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1470 double value = -1;
\r
1472 value = Double.parseDouble( n.getName() );
\r
1474 catch ( final NumberFormatException e ) {
\r
1477 if ( ( value < 0.0 ) || ( value > 100 ) ) {
\r
1486 final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy, final String confidence_type ) {
\r
1487 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1488 while ( it.hasNext() ) {
\r
1489 transferInternalNodeNameToConfidence( confidence_type, it.next() );
\r
1493 private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {
\r
1494 if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
\r
1495 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
\r
1498 d = Double.parseDouble( n.getName() );
\r
1500 catch ( final Exception e ) {
\r
1504 n.getBranchData().addConfidence( new Confidence( d, confidence_type ) );
\r
1511 final static public void transferNodeNameToField( final Phylogeny phy,
\r
1512 final PhylogenyNodeField field,
\r
1513 final boolean external_only ) throws PhyloXmlDataFormatException {
\r
1514 final PhylogenyNodeIterator it = phy.iteratorPostorder();
\r
1515 while ( it.hasNext() ) {
\r
1516 final PhylogenyNode n = it.next();
\r
1517 if ( external_only && n.isInternal() ) {
\r
1520 final String name = n.getName().trim();
\r
1521 if ( !ForesterUtil.isEmpty( name ) ) {
\r
1522 switch ( field ) {
\r
1523 case TAXONOMY_CODE:
\r
1525 setTaxonomyCode( n, name );
\r
1527 case TAXONOMY_SCIENTIFIC_NAME:
\r
1529 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1530 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1532 n.getNodeData().getTaxonomy().setScientificName( name );
\r
1534 case TAXONOMY_COMMON_NAME:
\r
1536 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1537 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1539 n.getNodeData().getTaxonomy().setCommonName( name );
\r
1541 case SEQUENCE_SYMBOL:
\r
1543 if ( !n.getNodeData().isHasSequence() ) {
\r
1544 n.getNodeData().setSequence( new Sequence() );
\r
1546 n.getNodeData().getSequence().setSymbol( name );
\r
1548 case SEQUENCE_NAME:
\r
1550 if ( !n.getNodeData().isHasSequence() ) {
\r
1551 n.getNodeData().setSequence( new Sequence() );
\r
1553 n.getNodeData().getSequence().setName( name );
\r
1555 case TAXONOMY_ID_UNIPROT_1: {
\r
1556 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1557 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1560 final int i = name.indexOf( '_' );
\r
1562 id = name.substring( 0, i );
\r
1567 n.getNodeData().getTaxonomy()
\r
1568 .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
\r
1571 case TAXONOMY_ID_UNIPROT_2: {
\r
1572 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1573 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1576 final int i = name.indexOf( '_' );
\r
1578 id = name.substring( i + 1, name.length() );
\r
1583 n.getNodeData().getTaxonomy()
\r
1584 .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
\r
1587 case TAXONOMY_ID: {
\r
1588 if ( !n.getNodeData().isHasTaxonomy() ) {
\r
1589 n.getNodeData().setTaxonomy( new Taxonomy() );
\r
1591 n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
\r
1599 static double addPhylogenyDistances( final double a, final double b ) {
\r
1600 if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
\r
1603 else if ( a >= 0.0 ) {
\r
1606 else if ( b >= 0.0 ) {
\r
1609 return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
\r
1612 static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {
\r
1614 boolean all_default = true;
\r
1615 while ( anc != desc ) {
\r
1616 if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
\r
1617 d += desc.getDistanceToParent();
\r
1618 if ( all_default ) {
\r
1619 all_default = false;
\r
1622 desc = desc.getParent();
\r
1624 if ( all_default ) {
\r
1625 return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
\r
1631 * Deep copies the phylogeny originating from this node.
\r
1633 static PhylogenyNode copySubTree( final PhylogenyNode source ) {
\r
1634 if ( source == null ) {
\r
1638 final PhylogenyNode newnode = source.copyNodeData();
\r
1639 if ( !source.isExternal() ) {
\r
1640 for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
\r
1641 newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
\r
1649 * Shallow copies the phylogeny originating from this node.
\r
1651 static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
\r
1652 if ( source == null ) {
\r
1656 final PhylogenyNode newnode = source.copyNodeDataShallow();
\r
1657 if ( !source.isExternal() ) {
\r
1658 for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
\r
1659 newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
\r
1666 private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,
\r
1667 final double min_distance_to_root ) {
\r
1668 final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();
\r
1669 final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );
\r
1670 for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {
\r
1671 if ( ext.getIndicator() != 0 ) {
\r
1672 throw new RuntimeException( "this should not have happened" );
\r
1674 ext.setIndicator( ( byte ) 1 );
\r
1681 * Calculates the distance between PhylogenyNodes n1 and n2.
\r
1682 * PRECONDITION: n1 is a descendant of n2.
\r
1685 * a descendant of n2
\r
1687 * @return distance between n1 and n2
\r
1689 private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1691 while ( n1 != n2 ) {
\r
1692 if ( n1.getDistanceToParent() > 0.0 ) {
\r
1693 d += n1.getDistanceToParent();
\r
1695 n1 = n1.getParent();
\r
1700 private static boolean match( final String s,
\r
1701 final String query,
\r
1702 final boolean case_sensitive,
\r
1703 final boolean partial,
\r
1704 final boolean regex ) {
\r
1705 if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
\r
1708 String my_s = s.trim();
\r
1709 String my_query = query.trim();
\r
1710 if ( !case_sensitive && !regex ) {
\r
1711 my_s = my_s.toLowerCase();
\r
1712 my_query = my_query.toLowerCase();
\r
1717 if ( case_sensitive ) {
\r
1718 p = Pattern.compile( my_query );
\r
1721 p = Pattern.compile( my_query, Pattern.CASE_INSENSITIVE );
\r
1724 catch ( final PatternSyntaxException e ) {
\r
1727 if ( p != null ) {
\r
1728 return p.matcher( my_s ).find();
\r
1734 else if ( partial ) {
\r
1735 return my_s.indexOf( my_query ) >= 0;
\r
1740 p = Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" );
\r
1742 catch ( final PatternSyntaxException e ) {
\r
1745 if ( p != null ) {
\r
1746 return p.matcher( my_s ).find();
\r
1754 private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {
\r
1755 PhylogenyNode n = node;
\r
1756 PhylogenyNode prev = node;
\r
1757 while ( min_distance_to_root < n.calculateDistanceToRoot() ) {
\r
1759 n = n.getParent();
\r
1764 public static enum DESCENDANT_SORT_PRIORITY {
\r
1765 NODE_NAME, SEQUENCE, TAXONOMY;
\r
1768 public static enum PhylogenyNodeField {
\r
1773 TAXONOMY_COMMON_NAME,
\r
1775 TAXONOMY_ID_UNIPROT_1,
\r
1776 TAXONOMY_ID_UNIPROT_2,
\r
1777 TAXONOMY_SCIENTIFIC_NAME;
\r
1780 public static void addMolecularSeqsToTree( final Phylogeny phy, final Msa msa ) {
\r
1781 for( int s = 0; s < msa.getNumberOfSequences(); ++s ) {
\r
1782 final org.forester.sequence.MolecularSequence seq = msa.getSequence( s );
\r
1783 final PhylogenyNode node = phy.getNode( seq.getIdentifier() );
\r
1784 final org.forester.phylogeny.data.Sequence new_seq = new Sequence();
\r
1785 new_seq.setMolecularSequenceAligned( true );
\r
1786 new_seq.setMolecularSequence( seq.getMolecularSequenceAsString() );
\r
1787 new_seq.setName( seq.getIdentifier() );
\r
1789 new_seq.setType( PhyloXmlUtil.SEQ_TYPE_PROTEIN );
\r
1791 catch ( final PhyloXmlDataFormatException ignore ) {
\r
1794 node.getNodeData().addSequence( new_seq );
\r
1798 final private static class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
\r
1801 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1802 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1803 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1804 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1805 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1806 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1808 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1809 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1810 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1811 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1814 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1815 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1816 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1817 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1818 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1820 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1821 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1822 return n1.getNodeData().getSequence().getGeneName()
\r
1823 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1825 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1826 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1827 return n1.getNodeData().getSequence().getSymbol()
\r
1828 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1831 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1832 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1838 final private static class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
\r
1841 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1842 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1843 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1844 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1845 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1846 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1848 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1849 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1850 return n1.getNodeData().getSequence().getGeneName()
\r
1851 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1853 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1854 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1855 return n1.getNodeData().getSequence().getSymbol()
\r
1856 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r
1859 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1860 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1861 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1862 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1863 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1865 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1866 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1867 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1868 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1871 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1872 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1878 final private static class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
\r
1881 public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
\r
1882 if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
\r
1883 return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
\r
1885 if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
\r
1886 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
\r
1887 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
\r
1888 return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
\r
1889 .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
\r
1891 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
\r
1892 && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
\r
1893 return n1.getNodeData().getTaxonomy().getTaxonomyCode()
\r
1894 .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
\r
1897 if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
\r
1898 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
\r
1899 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
\r
1900 return n1.getNodeData().getSequence().getName().toLowerCase()
\r
1901 .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
\r
1903 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
\r
1904 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
\r
1905 return n1.getNodeData().getSequence().getGeneName()
\r
1906 .compareTo( n2.getNodeData().getSequence().getGeneName() );
\r
1908 if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
\r
1909 && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
\r
1910 return n1.getNodeData().getSequence().getSymbol()
\r
1911 .compareTo( n2.getNodeData().getSequence().getSymbol() );
\r