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