2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.Mafft;
58 import org.forester.msa.Msa;
59 import org.forester.msa.MsaInferrer;
60 import org.forester.pccx.TestPccx;
61 import org.forester.phylogeny.Phylogeny;
62 import org.forester.phylogeny.PhylogenyBranch;
63 import org.forester.phylogeny.PhylogenyMethods;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.data.BinaryCharacters;
66 import org.forester.phylogeny.data.BranchWidth;
67 import org.forester.phylogeny.data.Confidence;
68 import org.forester.phylogeny.data.Distribution;
69 import org.forester.phylogeny.data.DomainArchitecture;
70 import org.forester.phylogeny.data.Event;
71 import org.forester.phylogeny.data.Identifier;
72 import org.forester.phylogeny.data.PhylogenyData;
73 import org.forester.phylogeny.data.PhylogenyDataUtil;
74 import org.forester.phylogeny.data.Polygon;
75 import org.forester.phylogeny.data.PropertiesMap;
76 import org.forester.phylogeny.data.Property;
77 import org.forester.phylogeny.data.Property.AppliesTo;
78 import org.forester.phylogeny.data.ProteinDomain;
79 import org.forester.phylogeny.data.Taxonomy;
80 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
81 import org.forester.phylogeny.factories.PhylogenyFactory;
82 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
83 import org.forester.sdi.SDI;
84 import org.forester.sdi.SDIR;
85 import org.forester.sdi.SDIse;
86 import org.forester.sdi.TaxonomyAssigner;
87 import org.forester.sdi.TestGSDI;
88 import org.forester.sequence.BasicSequence;
89 import org.forester.sequence.Sequence;
90 import org.forester.surfacing.Protein;
91 import org.forester.surfacing.TestSurfacing;
92 import org.forester.tools.ConfidenceAssessor;
93 import org.forester.tools.SupportCount;
94 import org.forester.tools.TreeSplitMatrix;
95 import org.forester.util.AsciiHistogram;
96 import org.forester.util.BasicDescriptiveStatistics;
97 import org.forester.util.BasicTable;
98 import org.forester.util.BasicTableParser;
99 import org.forester.util.DescriptiveStatistics;
100 import org.forester.util.ForesterConstants;
101 import org.forester.util.ForesterUtil;
102 import org.forester.util.GeneralTable;
103 import org.forester.ws.uniprot.DatabaseTools;
104 import org.forester.ws.uniprot.SequenceDatabaseEntry;
105 import org.forester.ws.uniprot.UniProtTaxonomy;
106 import org.forester.ws.uniprot.UniProtWsTools;
107 import org.forester.ws.wabi.TxSearch;
108 import org.forester.ws.wabi.TxSearch.RANKS;
109 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
110 import org.forester.ws.wabi.TxSearch.TAX_RANK;
112 @SuppressWarnings( "unused")
113 public final class Test {
115 private final static double ZERO_DIFF = 1.0E-9;
116 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
117 + ForesterUtil.getFileSeparator() + "test_data"
118 + ForesterUtil.getFileSeparator();
119 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
120 + ForesterUtil.getFileSeparator() + "resources"
121 + ForesterUtil.getFileSeparator();
122 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
123 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
124 + ForesterConstants.PHYLO_XML_VERSION + "/"
125 + ForesterConstants.PHYLO_XML_XSD;
126 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
127 + ForesterConstants.PHYLO_XML_VERSION + "/"
128 + ForesterConstants.PHYLO_XML_XSD;
130 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
131 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
135 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
136 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
137 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
140 public static boolean isEqual( final double a, final double b ) {
141 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
144 public static void main( final String[] args ) {
145 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
146 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
148 Locale.setDefault( Locale.US );
149 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
152 System.out.print( "[Test if directory with files for testing exists/is readable: " );
153 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
154 System.out.println( "OK.]" );
157 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
158 System.out.println( "Testing aborted." );
161 System.out.print( "[Test if resources directory exists/is readable: " );
162 if ( testDir( PATH_TO_RESOURCES ) ) {
163 System.out.println( "OK.]" );
166 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
167 System.out.println( "Testing aborted." );
170 final long start_time = new Date().getTime();
171 System.out.print( "Hmmscan output parser: " );
172 if ( testHmmscanOutputParser() ) {
173 System.out.println( "OK." );
177 System.out.println( "failed." );
180 System.out.print( "Basic node methods: " );
181 if ( Test.testBasicNodeMethods() ) {
182 System.out.println( "OK." );
186 System.out.println( "failed." );
189 System.out.print( "Basic node construction and parsing of NHX (node level): " );
190 if ( Test.testNHXNodeParsing() ) {
191 System.out.println( "OK." );
195 System.out.println( "failed." );
198 System.out.print( "NH parsing: " );
199 if ( Test.testNHParsing() ) {
200 System.out.println( "OK." );
204 System.out.println( "failed." );
207 System.out.print( "Conversion to NHX (node level): " );
208 if ( Test.testNHXconversion() ) {
209 System.out.println( "OK." );
213 System.out.println( "failed." );
216 System.out.print( "NHX parsing: " );
217 if ( Test.testNHXParsing() ) {
218 System.out.println( "OK." );
222 System.out.println( "failed." );
225 System.out.print( "NHX parsing with quotes: " );
226 if ( Test.testNHXParsingQuotes() ) {
227 System.out.println( "OK." );
231 System.out.println( "failed." );
234 System.out.print( "NHX parsing (MrBayes): " );
235 if ( Test.testNHXParsingMB() ) {
236 System.out.println( "OK." );
240 System.out.println( "failed." );
243 System.out.print( "Nexus characters parsing: " );
244 if ( Test.testNexusCharactersParsing() ) {
245 System.out.println( "OK." );
249 System.out.println( "failed." );
252 System.out.print( "Nexus tree parsing: " );
253 if ( Test.testNexusTreeParsing() ) {
254 System.out.println( "OK." );
258 System.out.println( "failed." );
261 System.out.print( "Nexus tree parsing (translating): " );
262 if ( Test.testNexusTreeParsingTranslating() ) {
263 System.out.println( "OK." );
267 System.out.println( "failed." );
270 System.out.print( "Nexus matrix parsing: " );
271 if ( Test.testNexusMatrixParsing() ) {
272 System.out.println( "OK." );
276 System.out.println( "failed." );
279 System.out.print( "Basic phyloXML parsing: " );
280 if ( Test.testBasicPhyloXMLparsing() ) {
281 System.out.println( "OK." );
285 System.out.println( "failed." );
288 System.out.print( "Basic phyloXML parsing (validating against schema): " );
289 if ( testBasicPhyloXMLparsingValidating() ) {
290 System.out.println( "OK." );
294 System.out.println( "failed." );
297 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
298 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
299 System.out.println( "OK." );
303 System.out.println( "failed." );
306 System.out.print( "phyloXML Distribution Element: " );
307 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
308 System.out.println( "OK." );
312 System.out.println( "failed." );
315 System.out.print( "Tol XML parsing: " );
316 if ( Test.testBasicTolXMLparsing() ) {
317 System.out.println( "OK." );
321 System.out.println( "failed." );
324 System.out.print( "Copying of node data: " );
325 if ( Test.testCopyOfNodeData() ) {
326 System.out.println( "OK." );
330 System.out.println( "failed." );
333 System.out.print( "Basic tree methods: " );
334 if ( Test.testBasicTreeMethods() ) {
335 System.out.println( "OK." );
339 System.out.println( "failed." );
342 System.out.print( "Postorder Iterator: " );
343 if ( Test.testPostOrderIterator() ) {
344 System.out.println( "OK." );
348 System.out.println( "failed." );
351 System.out.print( "Preorder Iterator: " );
352 if ( Test.testPreOrderIterator() ) {
353 System.out.println( "OK." );
357 System.out.println( "failed." );
360 System.out.print( "Levelorder Iterator: " );
361 if ( Test.testLevelOrderIterator() ) {
362 System.out.println( "OK." );
366 System.out.println( "failed." );
369 System.out.print( "Re-id methods: " );
370 if ( Test.testReIdMethods() ) {
371 System.out.println( "OK." );
375 System.out.println( "failed." );
378 System.out.print( "Methods on last external nodes: " );
379 if ( Test.testLastExternalNodeMethods() ) {
380 System.out.println( "OK." );
384 System.out.println( "failed." );
387 System.out.print( "Methods on external nodes: " );
388 if ( Test.testExternalNodeRelatedMethods() ) {
389 System.out.println( "OK." );
393 System.out.println( "failed." );
396 System.out.print( "Deletion of external nodes: " );
397 if ( Test.testDeletionOfExternalNodes() ) {
398 System.out.println( "OK." );
402 System.out.println( "failed." );
405 System.out.print( "Subtree deletion: " );
406 if ( Test.testSubtreeDeletion() ) {
407 System.out.println( "OK." );
411 System.out.println( "failed." );
414 System.out.print( "Phylogeny branch: " );
415 if ( Test.testPhylogenyBranch() ) {
416 System.out.println( "OK." );
420 System.out.println( "failed." );
423 System.out.print( "Rerooting: " );
424 if ( Test.testRerooting() ) {
425 System.out.println( "OK." );
429 System.out.println( "failed." );
432 System.out.print( "Mipoint rooting: " );
433 if ( Test.testMidpointrooting() ) {
434 System.out.println( "OK." );
438 System.out.println( "failed." );
441 System.out.print( "Support count: " );
442 if ( Test.testSupportCount() ) {
443 System.out.println( "OK." );
447 System.out.println( "failed." );
450 System.out.print( "Support transfer: " );
451 if ( Test.testSupportTransfer() ) {
452 System.out.println( "OK." );
456 System.out.println( "failed." );
459 System.out.print( "Finding of LCA: " );
460 if ( Test.testGetLCA() ) {
461 System.out.println( "OK." );
465 System.out.println( "failed." );
468 System.out.print( "Calculation of distance between nodes: " );
469 if ( Test.testGetDistance() ) {
470 System.out.println( "OK." );
474 System.out.println( "failed." );
477 System.out.print( "SDIse: " );
478 if ( Test.testSDIse() ) {
479 System.out.println( "OK." );
483 System.out.println( "failed." );
486 System.out.print( "Taxonomy assigner: " );
487 if ( Test.testTaxonomyAssigner() ) {
488 System.out.println( "OK." );
492 System.out.println( "failed." );
495 System.out.print( "SDIunrooted: " );
496 if ( Test.testSDIunrooted() ) {
497 System.out.println( "OK." );
501 System.out.println( "failed." );
504 System.out.print( "GSDI: " );
505 if ( TestGSDI.test() ) {
506 System.out.println( "OK." );
510 System.out.println( "failed." );
513 System.out.print( "Descriptive statistics: " );
514 if ( Test.testDescriptiveStatistics() ) {
515 System.out.println( "OK." );
519 System.out.println( "failed." );
522 System.out.print( "Data objects and methods: " );
523 if ( Test.testDataObjects() ) {
524 System.out.println( "OK." );
528 System.out.println( "failed." );
531 System.out.print( "Properties map: " );
532 if ( Test.testPropertiesMap() ) {
533 System.out.println( "OK." );
537 System.out.println( "failed." );
540 System.out.print( "Phylogeny reconstruction:" );
541 System.out.println();
542 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
543 System.out.println( "OK." );
547 System.out.println( "failed." );
550 System.out.print( "Analysis of domain architectures: " );
551 System.out.println();
552 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
553 System.out.println( "OK." );
557 System.out.println( "failed." );
560 System.out.print( "GO: " );
561 System.out.println();
562 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
563 System.out.println( "OK." );
567 System.out.println( "failed." );
570 System.out.print( "Modeling tools: " );
571 if ( TestPccx.test() ) {
572 System.out.println( "OK." );
576 System.out.println( "failed." );
579 System.out.print( "Split Matrix strict: " );
580 if ( Test.testSplitStrict() ) {
581 System.out.println( "OK." );
585 System.out.println( "failed." );
588 System.out.print( "Split Matrix: " );
589 if ( Test.testSplit() ) {
590 System.out.println( "OK." );
594 System.out.println( "failed." );
597 System.out.print( "Confidence Assessor: " );
598 if ( Test.testConfidenceAssessor() ) {
599 System.out.println( "OK." );
603 System.out.println( "failed." );
606 System.out.print( "Basic table: " );
607 if ( Test.testBasicTable() ) {
608 System.out.println( "OK." );
612 System.out.println( "failed." );
615 System.out.print( "General table: " );
616 if ( Test.testGeneralTable() ) {
617 System.out.println( "OK." );
621 System.out.println( "failed." );
624 System.out.print( "Amino acid sequence: " );
625 if ( Test.testAminoAcidSequence() ) {
626 System.out.println( "OK." );
630 System.out.println( "failed." );
633 System.out.print( "General MSA parser: " );
634 if ( Test.testGeneralMsaParser() ) {
635 System.out.println( "OK." );
639 System.out.println( "failed." );
642 System.out.print( "Fasta parser for msa: " );
643 if ( Test.testFastaParser() ) {
644 System.out.println( "OK." );
648 System.out.println( "failed." );
651 System.out.print( "Creation of balanced phylogeny: " );
652 if ( Test.testCreateBalancedPhylogeny() ) {
653 System.out.println( "OK." );
657 System.out.println( "failed." );
660 System.out.print( "EMBL Entry Retrieval: " );
661 if ( Test.testEmblEntryRetrieval() ) {
662 System.out.println( "OK." );
666 System.out.println( "failed." );
669 System.out.print( "Uniprot Entry Retrieval: " );
670 if ( Test.testUniprotEntryRetrieval() ) {
671 System.out.println( "OK." );
675 System.out.println( "failed." );
678 System.out.print( "Uniprot Taxonomy Search: " );
679 if ( Test.testUniprotTaxonomySearch() ) {
680 System.out.println( "OK." );
684 System.out.println( "failed." );
687 if ( Mafft.isInstalled() ) {
688 System.out.print( "MAFFT (external program): " );
689 if ( Test.testMafft() ) {
690 System.out.println( "OK." );
694 System.out.println( "failed [will not count towards failed tests]" );
697 System.out.print( "Next nodes with collapsed: " );
698 if ( Test.testNextNodeWithCollapsing() ) {
699 System.out.println( "OK." );
703 System.out.println( "failed." );
706 // System.out.print( "WABI TxSearch: " );
707 // if ( Test.testWabiTxSearch() ) {
708 // System.out.println( "OK." );
713 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
715 System.out.println();
716 final Runtime rt = java.lang.Runtime.getRuntime();
717 final long free_memory = rt.freeMemory() / 1000000;
718 final long total_memory = rt.totalMemory() / 1000000;
719 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
720 + free_memory + "MB, total memory: " + total_memory + "MB)" );
721 System.out.println();
722 System.out.println( "Successful tests: " + succeeded );
723 System.out.println( "Failed tests: " + failed );
724 System.out.println();
726 System.out.println( "OK." );
729 System.out.println( "Not OK." );
731 // System.out.println();
732 // Development.setTime( true );
734 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
735 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
736 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
737 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
738 // "multifurcations_ex_1.nhx";
739 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
740 // final Phylogeny t1 = factory.create( new File( domains ), new
741 // NHXParser() )[ 0 ];
742 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
744 // catch ( final Exception e ) {
745 // e.printStackTrace();
747 // t1.getRoot().preorderPrint();
748 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
752 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
753 // + "\\AtNBSpos.nhx" ) );
755 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
756 // new NHXParser() );
757 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
758 // + "\\AtNBSpos.nhx" ) );
760 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
761 // new NHXParser() );
764 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
765 // + "\\big_tree.nhx" ) );
766 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
767 // + "\\big_tree.nhx" ) );
769 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
770 // new NHXParser() );
772 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
773 // new NHXParser() );
775 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
776 // + "\\big_tree.nhx" ) );
777 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
778 // + "\\big_tree.nhx" ) );
781 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
782 // new NHXParser() );
784 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
785 // new NHXParser() );
787 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
788 // + "\\AtNBSpos.nhx" ) );
790 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
791 // new NHXParser() );
794 // catch ( IOException e ) {
795 // // TODO Auto-generated catch block
796 // e.printStackTrace();
800 private static boolean testBasicNodeMethods() {
802 if ( PhylogenyNode.getNodeCount() != 0 ) {
805 final PhylogenyNode n1 = new PhylogenyNode();
806 final PhylogenyNode n2 = PhylogenyNode
807 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
808 final PhylogenyNode n3 = PhylogenyNode
809 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
810 final PhylogenyNode n4 = PhylogenyNode
811 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
812 if ( n1.isHasAssignedEvent() ) {
815 if ( PhylogenyNode.getNodeCount() != 4 ) {
818 if ( n3.getIndicator() != 0 ) {
821 if ( n3.getNumberOfExternalNodes() != 1 ) {
824 if ( !n3.isExternal() ) {
827 if ( !n3.isRoot() ) {
830 if ( !n4.getName().equals( "n4" ) ) {
834 catch ( final Exception e ) {
835 e.printStackTrace( System.out );
841 private static boolean testBasicPhyloXMLparsing() {
843 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
844 final PhyloXmlParser xml_parser = new PhyloXmlParser();
845 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
847 if ( xml_parser.getErrorCount() > 0 ) {
848 System.out.println( xml_parser.getErrorMessages().toString() );
851 if ( phylogenies_0.length != 4 ) {
854 final Phylogeny t1 = phylogenies_0[ 0 ];
855 final Phylogeny t2 = phylogenies_0[ 1 ];
856 final Phylogeny t3 = phylogenies_0[ 2 ];
857 final Phylogeny t4 = phylogenies_0[ 3 ];
858 if ( t1.getNumberOfExternalNodes() != 1 ) {
861 if ( !t1.isRooted() ) {
864 if ( t1.isRerootable() ) {
867 if ( !t1.getType().equals( "gene_tree" ) ) {
870 if ( t2.getNumberOfExternalNodes() != 2 ) {
873 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
876 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
879 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
882 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
885 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
888 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
891 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
892 .startsWith( "actgtgggggt" ) ) {
895 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
896 .startsWith( "ctgtgatgcat" ) ) {
899 if ( t3.getNumberOfExternalNodes() != 4 ) {
902 if ( !t1.getName().equals( "t1" ) ) {
905 if ( !t2.getName().equals( "t2" ) ) {
908 if ( !t3.getName().equals( "t3" ) ) {
911 if ( !t4.getName().equals( "t4" ) ) {
914 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
917 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
920 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
923 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
924 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
927 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
930 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
933 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
936 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
937 .equals( "apoptosis" ) ) {
940 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
941 .equals( "GO:0006915" ) ) {
944 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
945 .equals( "UniProtKB" ) ) {
948 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
949 .equals( "experimental" ) ) {
952 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
953 .equals( "function" ) ) {
956 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
960 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
961 .getType().equals( "ml" ) ) {
964 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
965 .equals( "apoptosis" ) ) {
968 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
969 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
972 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
973 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
976 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
977 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
980 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
981 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
984 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
985 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
988 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
989 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
992 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
993 .equals( "GO:0005829" ) ) {
996 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
997 .equals( "intracellular organelle" ) ) {
1000 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1003 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1004 .equals( "UniProt link" ) ) ) {
1007 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1010 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1013 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1016 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1019 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1022 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1025 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1028 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1031 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1034 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1037 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1038 // .equals( "B" ) ) {
1041 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1044 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1047 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1050 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1051 // .getConfidence() != 2144 ) {
1054 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1055 // .equals( "pfam" ) ) {
1058 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1061 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1064 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1067 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1070 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1071 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1075 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1078 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1081 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1084 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1087 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1090 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1093 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1096 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1098 // if ( xml_parser.getErrorCount() > 0 ) {
1099 // System.out.println( xml_parser.getErrorMessages().toString() );
1102 // if ( phylogenies_1.length != 2 ) {
1105 // final Phylogeny a = phylogenies_1[ 0 ];
1106 // if ( !a.getName().equals( "tree 4" ) ) {
1109 // if ( a.getNumberOfExternalNodes() != 3 ) {
1112 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1115 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1119 catch ( final Exception e ) {
1120 e.printStackTrace( System.out );
1126 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1128 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1129 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1130 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1131 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1134 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1136 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1138 if ( xml_parser.getErrorCount() > 0 ) {
1139 System.out.println( xml_parser.getErrorMessages().toString() );
1142 if ( phylogenies_0.length != 4 ) {
1145 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1146 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1147 if ( phylogenies_t1.length != 1 ) {
1150 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1151 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1154 if ( !t1_rt.isRooted() ) {
1157 if ( t1_rt.isRerootable() ) {
1160 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1163 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1164 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1165 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1166 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1169 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1172 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1175 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1178 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1179 .startsWith( "actgtgggggt" ) ) {
1182 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1183 .startsWith( "ctgtgatgcat" ) ) {
1186 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1187 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1188 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1189 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1190 if ( phylogenies_1.length != 1 ) {
1193 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1194 if ( !t3_rt.getName().equals( "t3" ) ) {
1197 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1200 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1203 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1206 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1209 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1210 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1213 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1216 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1219 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1220 .equals( "UniProtKB" ) ) {
1223 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1224 .equals( "apoptosis" ) ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1228 .equals( "GO:0006915" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1232 .equals( "UniProtKB" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1236 .equals( "experimental" ) ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1240 .equals( "function" ) ) {
1243 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1244 .getValue() != 1 ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1248 .getType().equals( "ml" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1252 .equals( "apoptosis" ) ) {
1255 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1256 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1260 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1264 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1267 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1268 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1271 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1272 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1275 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1276 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1279 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1280 .equals( "GO:0005829" ) ) {
1283 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1284 .equals( "intracellular organelle" ) ) {
1287 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1290 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1291 .equals( "UniProt link" ) ) ) {
1294 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1297 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1300 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1301 .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
1304 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1307 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1310 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1313 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1316 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1317 .equals( "ncbi" ) ) {
1320 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1323 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1324 .getName().equals( "B" ) ) {
1327 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1328 .getFrom() != 21 ) {
1331 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1334 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1335 .getLength() != 24 ) {
1338 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1339 .getConfidence() != 2144 ) {
1342 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1343 .equals( "pfam" ) ) {
1346 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1349 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1352 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1355 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1358 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1359 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1362 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1365 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1368 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1371 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1374 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1377 if ( taxbb.getSynonyms().size() != 2 ) {
1380 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1383 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1386 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1389 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1392 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1395 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1396 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1400 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1403 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1406 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1409 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1412 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1415 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1418 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1422 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1425 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1426 .equalsIgnoreCase( "435" ) ) {
1429 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1432 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1433 .equalsIgnoreCase( "443.7" ) ) {
1436 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1439 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1442 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1443 .equalsIgnoreCase( "433" ) ) {
1447 catch ( final Exception e ) {
1448 e.printStackTrace( System.out );
1454 private static boolean testBasicPhyloXMLparsingValidating() {
1456 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1457 PhyloXmlParser xml_parser = null;
1459 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1461 catch ( final Exception e ) {
1462 // Do nothing -- means were not running from jar.
1464 if ( xml_parser == null ) {
1465 xml_parser = new PhyloXmlParser();
1466 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1467 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1470 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1473 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1475 if ( xml_parser.getErrorCount() > 0 ) {
1476 System.out.println( xml_parser.getErrorMessages().toString() );
1479 if ( phylogenies_0.length != 4 ) {
1482 final Phylogeny t1 = phylogenies_0[ 0 ];
1483 final Phylogeny t2 = phylogenies_0[ 1 ];
1484 final Phylogeny t3 = phylogenies_0[ 2 ];
1485 final Phylogeny t4 = phylogenies_0[ 3 ];
1486 if ( !t1.getName().equals( "t1" ) ) {
1489 if ( !t2.getName().equals( "t2" ) ) {
1492 if ( !t3.getName().equals( "t3" ) ) {
1495 if ( !t4.getName().equals( "t4" ) ) {
1498 if ( t1.getNumberOfExternalNodes() != 1 ) {
1501 if ( t2.getNumberOfExternalNodes() != 2 ) {
1504 if ( t3.getNumberOfExternalNodes() != 4 ) {
1507 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1508 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1509 if ( xml_parser.getErrorCount() > 0 ) {
1510 System.out.println( "errors:" );
1511 System.out.println( xml_parser.getErrorMessages().toString() );
1514 if ( phylogenies_1.length != 4 ) {
1517 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1519 if ( xml_parser.getErrorCount() > 0 ) {
1520 System.out.println( "errors:" );
1521 System.out.println( xml_parser.getErrorMessages().toString() );
1524 if ( phylogenies_2.length != 1 ) {
1527 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1530 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1532 if ( xml_parser.getErrorCount() > 0 ) {
1533 System.out.println( xml_parser.getErrorMessages().toString() );
1536 if ( phylogenies_3.length != 2 ) {
1539 final Phylogeny a = phylogenies_3[ 0 ];
1540 if ( !a.getName().equals( "tree 4" ) ) {
1543 if ( a.getNumberOfExternalNodes() != 3 ) {
1546 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1549 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1552 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1554 if ( xml_parser.getErrorCount() > 0 ) {
1555 System.out.println( xml_parser.getErrorMessages().toString() );
1558 if ( phylogenies_4.length != 1 ) {
1561 final Phylogeny s = phylogenies_4[ 0 ];
1562 if ( s.getNumberOfExternalNodes() != 6 ) {
1565 s.getNode( "first" );
1567 s.getNode( "\"<a'b&c'd\">\"" );
1568 s.getNode( "'''\"" );
1569 s.getNode( "\"\"\"" );
1570 s.getNode( "dick & doof" );
1572 catch ( final Exception e ) {
1573 e.printStackTrace( System.out );
1579 private static boolean testBasicTable() {
1581 final BasicTable<String> t0 = new BasicTable<String>();
1582 if ( t0.getNumberOfColumns() != 0 ) {
1585 if ( t0.getNumberOfRows() != 0 ) {
1588 t0.setValue( 3, 2, "23" );
1589 t0.setValue( 10, 1, "error" );
1590 t0.setValue( 10, 1, "110" );
1591 t0.setValue( 9, 1, "19" );
1592 t0.setValue( 1, 10, "101" );
1593 t0.setValue( 10, 10, "1010" );
1594 t0.setValue( 100, 10, "10100" );
1595 t0.setValue( 0, 0, "00" );
1596 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1599 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1602 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1605 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1608 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1611 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1614 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1617 if ( t0.getNumberOfColumns() != 101 ) {
1620 if ( t0.getNumberOfRows() != 11 ) {
1623 if ( t0.getValueAsString( 49, 4 ) != null ) {
1626 final String l = ForesterUtil.getLineSeparator();
1627 final StringBuffer source = new StringBuffer();
1628 source.append( "" + l );
1629 source.append( "# 1 1 1 1 1 1 1 1" + l );
1630 source.append( " 00 01 02 03" + l );
1631 source.append( " 10 11 12 13 " + l );
1632 source.append( "20 21 22 23 " + l );
1633 source.append( " 30 31 32 33" + l );
1634 source.append( "40 41 42 43" + l );
1635 source.append( " # 1 1 1 1 1 " + l );
1636 source.append( "50 51 52 53 54" + l );
1637 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1638 if ( t1.getNumberOfColumns() != 5 ) {
1641 if ( t1.getNumberOfRows() != 6 ) {
1644 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1647 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1650 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1653 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1656 final StringBuffer source1 = new StringBuffer();
1657 source1.append( "" + l );
1658 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1659 source1.append( " 00; 01 ;02;03" + l );
1660 source1.append( " 10; 11; 12; 13 " + l );
1661 source1.append( "20; 21; 22; 23 " + l );
1662 source1.append( " 30; 31; 32; 33" + l );
1663 source1.append( "40;41;42;43" + l );
1664 source1.append( " # 1 1 1 1 1 " + l );
1665 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1666 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1667 if ( t2.getNumberOfColumns() != 5 ) {
1670 if ( t2.getNumberOfRows() != 6 ) {
1673 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1676 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1679 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1682 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1685 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1688 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1691 final StringBuffer source2 = new StringBuffer();
1692 source2.append( "" + l );
1693 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1694 source2.append( " 00; 01 ;02;03" + l );
1695 source2.append( " 10; 11; 12; 13 " + l );
1696 source2.append( "20; 21; 22; 23 " + l );
1697 source2.append( " " + l );
1698 source2.append( " 30; 31; 32; 33" + l );
1699 source2.append( "40;41;42;43" + l );
1700 source2.append( " comment: 1 1 1 1 1 " + l );
1701 source2.append( ";;;50 ; 52; 53;;54 " + l );
1702 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1707 if ( tl.size() != 2 ) {
1710 final BasicTable<String> t3 = tl.get( 0 );
1711 final BasicTable<String> t4 = tl.get( 1 );
1712 if ( t3.getNumberOfColumns() != 4 ) {
1715 if ( t3.getNumberOfRows() != 3 ) {
1718 if ( t4.getNumberOfColumns() != 4 ) {
1721 if ( t4.getNumberOfRows() != 3 ) {
1724 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1727 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1731 catch ( final Exception e ) {
1732 e.printStackTrace( System.out );
1738 private static boolean testBasicTolXMLparsing() {
1740 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1741 final TolParser parser = new TolParser();
1742 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1743 if ( parser.getErrorCount() > 0 ) {
1744 System.out.println( parser.getErrorMessages().toString() );
1747 if ( phylogenies_0.length != 1 ) {
1750 final Phylogeny t1 = phylogenies_0[ 0 ];
1751 if ( t1.getNumberOfExternalNodes() != 5 ) {
1754 if ( !t1.isRooted() ) {
1757 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1760 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1763 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1766 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1769 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1770 if ( parser.getErrorCount() > 0 ) {
1771 System.out.println( parser.getErrorMessages().toString() );
1774 if ( phylogenies_1.length != 1 ) {
1777 final Phylogeny t2 = phylogenies_1[ 0 ];
1778 if ( t2.getNumberOfExternalNodes() != 664 ) {
1781 if ( !t2.isRooted() ) {
1784 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1787 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1790 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1793 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1796 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1799 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1800 .equals( "Aquifex" ) ) {
1803 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1804 if ( parser.getErrorCount() > 0 ) {
1805 System.out.println( parser.getErrorMessages().toString() );
1808 if ( phylogenies_2.length != 1 ) {
1811 final Phylogeny t3 = phylogenies_2[ 0 ];
1812 if ( t3.getNumberOfExternalNodes() != 184 ) {
1815 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1818 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1821 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1824 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1825 if ( parser.getErrorCount() > 0 ) {
1826 System.out.println( parser.getErrorMessages().toString() );
1829 if ( phylogenies_3.length != 1 ) {
1832 final Phylogeny t4 = phylogenies_3[ 0 ];
1833 if ( t4.getNumberOfExternalNodes() != 1 ) {
1836 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1839 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1842 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1845 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1846 if ( parser.getErrorCount() > 0 ) {
1847 System.out.println( parser.getErrorMessages().toString() );
1850 if ( phylogenies_4.length != 1 ) {
1853 final Phylogeny t5 = phylogenies_4[ 0 ];
1854 if ( t5.getNumberOfExternalNodes() != 13 ) {
1857 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1860 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1863 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1867 catch ( final Exception e ) {
1868 e.printStackTrace( System.out );
1874 private static boolean testBasicTreeMethods() {
1876 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1877 final Phylogeny t1 = factory.create();
1878 if ( !t1.isEmpty() ) {
1881 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1882 if ( t2.getNumberOfExternalNodes() != 4 ) {
1885 if ( t2.getHeight() != 8.5 ) {
1888 if ( !t2.isCompletelyBinary() ) {
1891 if ( t2.isEmpty() ) {
1894 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1895 if ( t3.getNumberOfExternalNodes() != 5 ) {
1898 if ( t3.getHeight() != 11 ) {
1901 if ( t3.isCompletelyBinary() ) {
1904 final PhylogenyNode n = t3.getNode( "ABC" );
1905 PhylogenyNodeIterator it;
1906 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1909 for( it.reset(); it.hasNext(); ) {
1912 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1913 if ( !it2.next().getName().equals( "A" ) ) {
1916 if ( !it2.next().getName().equals( "B" ) ) {
1919 if ( !it2.next().getName().equals( "C" ) ) {
1922 if ( it2.hasNext() ) {
1925 final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
1926 if ( t4.getNumberOfExternalNodes() != 9 ) {
1929 if ( t4.getHeight() != 11 ) {
1932 if ( t4.isCompletelyBinary() ) {
1935 final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1936 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1937 if ( t5.getNumberOfExternalNodes() != 8 ) {
1940 if ( t5.getHeight() != 15 ) {
1943 final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1944 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1945 if ( t6.getHeight() != 15 ) {
1948 final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
1949 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1950 if ( t7.getHeight() != 15 ) {
1953 final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
1954 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1955 if ( t8.getNumberOfExternalNodes() != 10 ) {
1958 if ( t8.getHeight() != 15 ) {
1961 final char[] a9 = new char[] {};
1962 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1963 if ( t9.getHeight() != 0 ) {
1966 final char[] a10 = new char[] { 'a', ':', '6' };
1967 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1968 if ( t10.getHeight() != 6 ) {
1972 catch ( final Exception e ) {
1973 e.printStackTrace( System.out );
1979 private static boolean testConfidenceAssessor() {
1981 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1982 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1983 final Phylogeny[] ev0 = factory
1984 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1986 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1987 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1990 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1993 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1994 final Phylogeny[] ev1 = factory
1995 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1997 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1998 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2001 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2004 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2005 final Phylogeny[] ev_b = factory
2006 .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
2008 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2009 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2010 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2013 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2017 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2018 final Phylogeny[] ev1x = factory
2019 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
2021 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2022 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2025 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2028 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2029 final Phylogeny[] ev_bx = factory
2030 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
2032 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2033 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2036 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2040 final Phylogeny[] t2 = factory
2041 .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
2043 final Phylogeny[] ev2 = factory
2044 .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);",
2046 for( final Phylogeny target : t2 ) {
2047 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2050 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2051 new NHXParser() )[ 0 ];
2052 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2053 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2054 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2057 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2060 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2064 catch ( final Exception e ) {
2065 e.printStackTrace();
2071 private static boolean testCopyOfNodeData() {
2073 final PhylogenyNode n1 = PhylogenyNode
2074 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2075 final PhylogenyNode n2 = n1.copyNodeData();
2076 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2080 catch ( final Exception e ) {
2081 e.printStackTrace();
2087 private static boolean testDataObjects() {
2089 final Confidence s0 = new Confidence();
2090 final Confidence s1 = new Confidence();
2091 if ( !s0.isEqual( s1 ) ) {
2094 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2095 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2096 if ( s2.isEqual( s1 ) ) {
2099 if ( !s2.isEqual( s3 ) ) {
2102 final Confidence s4 = ( Confidence ) s3.copy();
2103 if ( !s4.isEqual( s3 ) ) {
2110 final Taxonomy t1 = new Taxonomy();
2111 final Taxonomy t2 = new Taxonomy();
2112 final Taxonomy t3 = new Taxonomy();
2113 final Taxonomy t4 = new Taxonomy();
2114 final Taxonomy t5 = new Taxonomy();
2115 t1.setIdentifier( new Identifier( "ecoli" ) );
2116 t1.setTaxonomyCode( "ECOLI" );
2117 t1.setScientificName( "E. coli" );
2118 t1.setCommonName( "coli" );
2119 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2120 if ( !t1.isEqual( t0 ) ) {
2123 t2.setIdentifier( new Identifier( "ecoli" ) );
2124 t2.setTaxonomyCode( "other" );
2125 t2.setScientificName( "what" );
2126 t2.setCommonName( "something" );
2127 if ( !t1.isEqual( t2 ) ) {
2130 t2.setIdentifier( new Identifier( "nemve" ) );
2131 if ( t1.isEqual( t2 ) ) {
2134 t1.setIdentifier( null );
2135 t3.setTaxonomyCode( "ECOLI" );
2136 t3.setScientificName( "what" );
2137 t3.setCommonName( "something" );
2138 if ( !t1.isEqual( t3 ) ) {
2141 t1.setIdentifier( null );
2142 t1.setTaxonomyCode( "" );
2143 t4.setScientificName( "E. ColI" );
2144 t4.setCommonName( "something" );
2145 if ( !t1.isEqual( t4 ) ) {
2148 t4.setScientificName( "B. subtilis" );
2149 t4.setCommonName( "something" );
2150 if ( t1.isEqual( t4 ) ) {
2153 t1.setIdentifier( null );
2154 t1.setTaxonomyCode( "" );
2155 t1.setScientificName( "" );
2156 t5.setCommonName( "COLI" );
2157 if ( !t1.isEqual( t5 ) ) {
2160 t5.setCommonName( "vibrio" );
2161 if ( t1.isEqual( t5 ) ) {
2166 final Identifier id0 = new Identifier( "123", "pfam" );
2167 final Identifier id1 = ( Identifier ) id0.copy();
2168 if ( !id1.isEqual( id1 ) ) {
2171 if ( !id1.isEqual( id0 ) ) {
2174 if ( !id0.isEqual( id1 ) ) {
2181 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2182 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2183 if ( !pd1.isEqual( pd1 ) ) {
2186 if ( !pd1.isEqual( pd0 ) ) {
2191 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2192 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2193 if ( !pd3.isEqual( pd3 ) ) {
2196 if ( !pd2.isEqual( pd3 ) ) {
2199 if ( !pd0.isEqual( pd3 ) ) {
2204 // DomainArchitecture
2205 // ------------------
2206 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2207 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2208 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2209 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2210 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2211 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2216 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2217 if ( ds0.getNumberOfDomains() != 4 ) {
2220 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2221 if ( !ds0.isEqual( ds0 ) ) {
2224 if ( !ds0.isEqual( ds1 ) ) {
2227 if ( ds1.getNumberOfDomains() != 4 ) {
2230 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2235 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2236 if ( ds0.isEqual( ds2 ) ) {
2242 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2243 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2244 System.out.println( ds3.toNHX() );
2247 if ( ds3.getNumberOfDomains() != 3 ) {
2252 final Event e1 = new Event( Event.EventType.fusion );
2253 if ( e1.isDuplication() ) {
2256 if ( !e1.isFusion() ) {
2259 if ( !e1.asText().toString().equals( "fusion" ) ) {
2262 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2265 final Event e11 = new Event( Event.EventType.fusion );
2266 if ( !e11.isEqual( e1 ) ) {
2269 if ( !e11.toNHX().toString().equals( "" ) ) {
2272 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2273 if ( e2.isDuplication() ) {
2276 if ( !e2.isSpeciationOrDuplication() ) {
2279 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2282 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2285 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2288 if ( e11.isEqual( e2 ) ) {
2291 final Event e2c = ( Event ) e2.copy();
2292 if ( !e2c.isEqual( e2 ) ) {
2295 Event e3 = new Event( 1, 2, 3 );
2296 if ( e3.isDuplication() ) {
2299 if ( e3.isSpeciation() ) {
2302 if ( e3.isGeneLoss() ) {
2305 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2308 final Event e3c = ( Event ) e3.copy();
2309 final Event e3cc = ( Event ) e3c.copy();
2310 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2314 if ( !e3c.isEqual( e3cc ) ) {
2317 Event e4 = new Event( 1, 2, 3 );
2318 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2321 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2324 final Event e4c = ( Event ) e4.copy();
2326 final Event e4cc = ( Event ) e4c.copy();
2327 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2330 if ( !e4c.isEqual( e4cc ) ) {
2333 final Event e5 = new Event();
2334 if ( !e5.isUnassigned() ) {
2337 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2340 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2343 final Event e6 = new Event( 1, 0, 0 );
2344 if ( !e6.asText().toString().equals( "duplication" ) ) {
2347 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2350 final Event e7 = new Event( 0, 1, 0 );
2351 if ( !e7.asText().toString().equals( "speciation" ) ) {
2354 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2357 final Event e8 = new Event( 0, 0, 1 );
2358 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2361 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2365 catch ( final Exception e ) {
2366 e.printStackTrace( System.out );
2372 private static boolean testDeletionOfExternalNodes() {
2374 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2375 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2376 final PhylogenyWriter w = new PhylogenyWriter();
2377 if ( t0.isEmpty() ) {
2380 if ( t0.getNumberOfExternalNodes() != 1 ) {
2383 t0.deleteSubtree( t0.getNode( "A" ), false );
2384 if ( t0.getNumberOfExternalNodes() != 0 ) {
2387 if ( !t0.isEmpty() ) {
2390 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2391 if ( t1.getNumberOfExternalNodes() != 2 ) {
2394 t1.deleteSubtree( t1.getNode( "A" ), false );
2395 if ( t1.getNumberOfExternalNodes() != 1 ) {
2398 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2401 t1.deleteSubtree( t1.getNode( "B" ), false );
2402 if ( t1.getNumberOfExternalNodes() != 1 ) {
2405 t1.deleteSubtree( t1.getNode( "r" ), false );
2406 if ( !t1.isEmpty() ) {
2409 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2410 if ( t2.getNumberOfExternalNodes() != 3 ) {
2413 t2.deleteSubtree( t2.getNode( "B" ), false );
2414 if ( t2.getNumberOfExternalNodes() != 2 ) {
2417 t2.toNewHampshireX();
2418 PhylogenyNode n = t2.getNode( "A" );
2419 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2422 t2.deleteSubtree( t2.getNode( "A" ), false );
2423 if ( t2.getNumberOfExternalNodes() != 2 ) {
2426 t2.deleteSubtree( t2.getNode( "C" ), true );
2427 if ( t2.getNumberOfExternalNodes() != 1 ) {
2430 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2431 if ( t3.getNumberOfExternalNodes() != 4 ) {
2434 t3.deleteSubtree( t3.getNode( "B" ), true );
2435 if ( t3.getNumberOfExternalNodes() != 3 ) {
2438 n = t3.getNode( "A" );
2439 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2442 n = n.getNextExternalNode();
2443 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2446 t3.deleteSubtree( t3.getNode( "A" ), true );
2447 if ( t3.getNumberOfExternalNodes() != 2 ) {
2450 n = t3.getNode( "C" );
2451 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2454 t3.deleteSubtree( t3.getNode( "C" ), true );
2455 if ( t3.getNumberOfExternalNodes() != 1 ) {
2458 t3.deleteSubtree( t3.getNode( "D" ), true );
2459 if ( t3.getNumberOfExternalNodes() != 0 ) {
2462 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2463 if ( t4.getNumberOfExternalNodes() != 6 ) {
2466 t4.deleteSubtree( t4.getNode( "B2" ), true );
2467 if ( t4.getNumberOfExternalNodes() != 5 ) {
2470 String s = w.toNewHampshire( t4, false, true ).toString();
2471 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2474 t4.deleteSubtree( t4.getNode( "B11" ), true );
2475 if ( t4.getNumberOfExternalNodes() != 4 ) {
2478 t4.deleteSubtree( t4.getNode( "C" ), true );
2479 if ( t4.getNumberOfExternalNodes() != 3 ) {
2482 n = t4.getNode( "A" );
2483 n = n.getNextExternalNode();
2484 if ( !n.getName().equals( "B12" ) ) {
2487 n = n.getNextExternalNode();
2488 if ( !n.getName().equals( "D" ) ) {
2491 s = w.toNewHampshire( t4, false, true ).toString();
2492 if ( !s.equals( "((A,B12),D);" ) ) {
2495 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2496 t5.deleteSubtree( t5.getNode( "A" ), true );
2497 if ( t5.getNumberOfExternalNodes() != 5 ) {
2500 s = w.toNewHampshire( t5, false, true ).toString();
2501 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2504 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2505 t6.deleteSubtree( t6.getNode( "B11" ), true );
2506 if ( t6.getNumberOfExternalNodes() != 5 ) {
2509 s = w.toNewHampshire( t6, false, false ).toString();
2510 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2513 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2514 t7.deleteSubtree( t7.getNode( "B12" ), true );
2515 if ( t7.getNumberOfExternalNodes() != 5 ) {
2518 s = w.toNewHampshire( t7, false, true ).toString();
2519 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2522 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2523 t8.deleteSubtree( t8.getNode( "B2" ), true );
2524 if ( t8.getNumberOfExternalNodes() != 5 ) {
2527 s = w.toNewHampshire( t8, false, false ).toString();
2528 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2531 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2532 t9.deleteSubtree( t9.getNode( "C" ), true );
2533 if ( t9.getNumberOfExternalNodes() != 5 ) {
2536 s = w.toNewHampshire( t9, false, true ).toString();
2537 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2540 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2541 t10.deleteSubtree( t10.getNode( "D" ), true );
2542 if ( t10.getNumberOfExternalNodes() != 5 ) {
2545 s = w.toNewHampshire( t10, false, true ).toString();
2546 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2549 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2550 t11.deleteSubtree( t11.getNode( "A" ), true );
2551 if ( t11.getNumberOfExternalNodes() != 2 ) {
2554 s = w.toNewHampshire( t11, false, true ).toString();
2555 if ( !s.equals( "(B,C);" ) ) {
2558 t11.deleteSubtree( t11.getNode( "C" ), true );
2559 if ( t11.getNumberOfExternalNodes() != 1 ) {
2562 s = w.toNewHampshire( t11, false, false ).toString();
2563 if ( !s.equals( "B;" ) ) {
2566 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2567 t12.deleteSubtree( t12.getNode( "B2" ), true );
2568 if ( t12.getNumberOfExternalNodes() != 8 ) {
2571 s = w.toNewHampshire( t12, false, true ).toString();
2572 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2575 t12.deleteSubtree( t12.getNode( "B3" ), true );
2576 if ( t12.getNumberOfExternalNodes() != 7 ) {
2579 s = w.toNewHampshire( t12, false, true ).toString();
2580 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2583 t12.deleteSubtree( t12.getNode( "C3" ), true );
2584 if ( t12.getNumberOfExternalNodes() != 6 ) {
2587 s = w.toNewHampshire( t12, false, true ).toString();
2588 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2591 t12.deleteSubtree( t12.getNode( "A1" ), true );
2592 if ( t12.getNumberOfExternalNodes() != 5 ) {
2595 s = w.toNewHampshire( t12, false, true ).toString();
2596 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2599 t12.deleteSubtree( t12.getNode( "B1" ), true );
2600 if ( t12.getNumberOfExternalNodes() != 4 ) {
2603 s = w.toNewHampshire( t12, false, true ).toString();
2604 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2607 t12.deleteSubtree( t12.getNode( "A3" ), true );
2608 if ( t12.getNumberOfExternalNodes() != 3 ) {
2611 s = w.toNewHampshire( t12, false, true ).toString();
2612 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2615 t12.deleteSubtree( t12.getNode( "A2" ), true );
2616 if ( t12.getNumberOfExternalNodes() != 2 ) {
2619 s = w.toNewHampshire( t12, false, true ).toString();
2620 if ( !s.equals( "(C1,C2);" ) ) {
2623 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2624 t13.deleteSubtree( t13.getNode( "D" ), true );
2625 if ( t13.getNumberOfExternalNodes() != 4 ) {
2628 s = w.toNewHampshire( t13, false, true ).toString();
2629 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2632 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2633 t14.deleteSubtree( t14.getNode( "E" ), true );
2634 if ( t14.getNumberOfExternalNodes() != 5 ) {
2637 s = w.toNewHampshire( t14, false, true ).toString();
2638 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2641 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2642 t15.deleteSubtree( t15.getNode( "B2" ), true );
2643 if ( t15.getNumberOfExternalNodes() != 11 ) {
2646 t15.deleteSubtree( t15.getNode( "B1" ), true );
2647 if ( t15.getNumberOfExternalNodes() != 10 ) {
2650 t15.deleteSubtree( t15.getNode( "B3" ), true );
2651 if ( t15.getNumberOfExternalNodes() != 9 ) {
2654 t15.deleteSubtree( t15.getNode( "B4" ), true );
2655 if ( t15.getNumberOfExternalNodes() != 8 ) {
2658 t15.deleteSubtree( t15.getNode( "A1" ), true );
2659 if ( t15.getNumberOfExternalNodes() != 7 ) {
2662 t15.deleteSubtree( t15.getNode( "C4" ), true );
2663 if ( t15.getNumberOfExternalNodes() != 6 ) {
2667 catch ( final Exception e ) {
2668 e.printStackTrace( System.out );
2674 private static boolean testDescriptiveStatistics() {
2676 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2677 dss1.addValue( 82 );
2678 dss1.addValue( 78 );
2679 dss1.addValue( 70 );
2680 dss1.addValue( 58 );
2681 dss1.addValue( 42 );
2682 if ( dss1.getN() != 5 ) {
2685 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2688 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2691 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2694 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2697 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2700 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2703 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2706 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2709 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2712 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2715 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2718 dss1.addValue( 123 );
2719 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2722 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2725 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2728 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2729 dss2.addValue( -1.85 );
2730 dss2.addValue( 57.5 );
2731 dss2.addValue( 92.78 );
2732 dss2.addValue( 57.78 );
2733 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2736 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2739 final double[] a = dss2.getDataAsDoubleArray();
2740 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2743 dss2.addValue( -100 );
2744 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2747 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2750 final double[] ds = new double[ 14 ];
2765 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2766 if ( bins.length != 4 ) {
2769 if ( bins[ 0 ] != 2 ) {
2772 if ( bins[ 1 ] != 3 ) {
2775 if ( bins[ 2 ] != 4 ) {
2778 if ( bins[ 3 ] != 5 ) {
2781 final double[] ds1 = new double[ 9 ];
2791 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2792 if ( bins1.length != 4 ) {
2795 if ( bins1[ 0 ] != 2 ) {
2798 if ( bins1[ 1 ] != 3 ) {
2801 if ( bins1[ 2 ] != 0 ) {
2804 if ( bins1[ 3 ] != 4 ) {
2807 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2808 if ( bins1_1.length != 3 ) {
2811 if ( bins1_1[ 0 ] != 3 ) {
2814 if ( bins1_1[ 1 ] != 2 ) {
2817 if ( bins1_1[ 2 ] != 4 ) {
2820 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2821 if ( bins1_2.length != 3 ) {
2824 if ( bins1_2[ 0 ] != 2 ) {
2827 if ( bins1_2[ 1 ] != 2 ) {
2830 if ( bins1_2[ 2 ] != 2 ) {
2833 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2847 dss3.addValue( 10 );
2848 dss3.addValue( 10 );
2849 dss3.addValue( 10 );
2850 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2851 histo.toStringBuffer( 10, '=', 40, 5 );
2852 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2854 catch ( final Exception e ) {
2855 e.printStackTrace( System.out );
2861 private static boolean testDir( final String file ) {
2863 final File f = new File( file );
2864 if ( !f.exists() ) {
2867 if ( !f.isDirectory() ) {
2870 if ( !f.canRead() ) {
2874 catch ( final Exception e ) {
2880 private static boolean testExternalNodeRelatedMethods() {
2882 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2883 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2884 PhylogenyNode n = t1.getNode( "A" );
2885 n = n.getNextExternalNode();
2886 if ( !n.getName().equals( "B" ) ) {
2889 n = n.getNextExternalNode();
2890 if ( !n.getName().equals( "C" ) ) {
2893 n = n.getNextExternalNode();
2894 if ( !n.getName().equals( "D" ) ) {
2897 n = t1.getNode( "B" );
2898 while ( !n.isLastExternalNode() ) {
2899 n = n.getNextExternalNode();
2901 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2902 n = t2.getNode( "A" );
2903 n = n.getNextExternalNode();
2904 if ( !n.getName().equals( "B" ) ) {
2907 n = n.getNextExternalNode();
2908 if ( !n.getName().equals( "C" ) ) {
2911 n = n.getNextExternalNode();
2912 if ( !n.getName().equals( "D" ) ) {
2915 n = t2.getNode( "B" );
2916 while ( !n.isLastExternalNode() ) {
2917 n = n.getNextExternalNode();
2919 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2920 n = t3.getNode( "A" );
2921 n = n.getNextExternalNode();
2922 if ( !n.getName().equals( "B" ) ) {
2925 n = n.getNextExternalNode();
2926 if ( !n.getName().equals( "C" ) ) {
2929 n = n.getNextExternalNode();
2930 if ( !n.getName().equals( "D" ) ) {
2933 n = n.getNextExternalNode();
2934 if ( !n.getName().equals( "E" ) ) {
2937 n = n.getNextExternalNode();
2938 if ( !n.getName().equals( "F" ) ) {
2941 n = n.getNextExternalNode();
2942 if ( !n.getName().equals( "G" ) ) {
2945 n = n.getNextExternalNode();
2946 if ( !n.getName().equals( "H" ) ) {
2949 n = t3.getNode( "B" );
2950 while ( !n.isLastExternalNode() ) {
2951 n = n.getNextExternalNode();
2953 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2954 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2955 final PhylogenyNode node = iter.next();
2957 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2958 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2959 final PhylogenyNode node = iter.next();
2962 catch ( final Exception e ) {
2963 e.printStackTrace( System.out );
2969 private static boolean testGeneralTable() {
2971 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2972 t0.setValue( 3, 2, "23" );
2973 t0.setValue( 10, 1, "error" );
2974 t0.setValue( 10, 1, "110" );
2975 t0.setValue( 9, 1, "19" );
2976 t0.setValue( 1, 10, "101" );
2977 t0.setValue( 10, 10, "1010" );
2978 t0.setValue( 100, 10, "10100" );
2979 t0.setValue( 0, 0, "00" );
2980 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2983 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2986 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2989 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2992 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2995 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2998 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3001 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3004 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3007 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3008 t1.setValue( "3", "2", "23" );
3009 t1.setValue( "10", "1", "error" );
3010 t1.setValue( "10", "1", "110" );
3011 t1.setValue( "9", "1", "19" );
3012 t1.setValue( "1", "10", "101" );
3013 t1.setValue( "10", "10", "1010" );
3014 t1.setValue( "100", "10", "10100" );
3015 t1.setValue( "0", "0", "00" );
3016 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3017 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3020 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3023 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3026 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3029 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3032 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3035 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3038 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3041 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3044 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3048 catch ( final Exception e ) {
3049 e.printStackTrace( System.out );
3055 private static boolean testGetDistance() {
3057 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3058 final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
3059 new NHXParser() )[ 0 ];
3060 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3061 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3064 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3067 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3070 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3073 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3076 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3079 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3082 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3085 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3088 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3091 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3094 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3097 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3100 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3103 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3106 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3109 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3112 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3115 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3118 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3121 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3124 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3127 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3130 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3133 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3136 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3139 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3142 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3145 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3148 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3151 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3154 final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
3155 new NHXParser() )[ 0 ];
3156 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3159 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3162 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3165 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3168 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3171 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3174 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3177 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3180 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3183 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3186 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3190 catch ( final Exception e ) {
3191 e.printStackTrace( System.out );
3197 private static boolean testGetLCA() {
3199 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3200 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3201 new NHXParser() )[ 0 ];
3202 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3203 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3204 if ( !A.getName().equals( "A" ) ) {
3207 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3208 if ( !gh.getName().equals( "gh" ) ) {
3211 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3212 if ( !ab.getName().equals( "ab" ) ) {
3215 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3216 if ( !ab2.getName().equals( "ab" ) ) {
3219 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3220 if ( !gh2.getName().equals( "gh" ) ) {
3223 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3224 if ( !gh3.getName().equals( "gh" ) ) {
3227 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3228 if ( !abc.getName().equals( "abc" ) ) {
3231 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3232 if ( !abc2.getName().equals( "abc" ) ) {
3235 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3236 if ( !abcd.getName().equals( "abcd" ) ) {
3239 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3240 if ( !abcd2.getName().equals( "abcd" ) ) {
3243 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3244 if ( !abcdef.getName().equals( "abcdef" ) ) {
3247 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3248 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3251 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3252 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3255 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3256 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3259 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3260 if ( !abcde.getName().equals( "abcde" ) ) {
3263 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3264 if ( !abcde2.getName().equals( "abcde" ) ) {
3267 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3268 if ( !r.getName().equals( "abcdefgh" ) ) {
3271 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3272 if ( !r2.getName().equals( "abcdefgh" ) ) {
3275 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3276 if ( !r3.getName().equals( "abcdefgh" ) ) {
3279 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3280 if ( !abcde3.getName().equals( "abcde" ) ) {
3283 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3284 if ( !abcde4.getName().equals( "abcde" ) ) {
3287 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3288 if ( !ab3.getName().equals( "ab" ) ) {
3291 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3292 if ( !ab4.getName().equals( "ab" ) ) {
3295 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3296 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3297 if ( !cd.getName().equals( "cd" ) ) {
3300 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3301 if ( !cd2.getName().equals( "cd" ) ) {
3304 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3305 if ( !cde.getName().equals( "cde" ) ) {
3308 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3309 if ( !cde2.getName().equals( "cde" ) ) {
3312 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3313 if ( !cdef.getName().equals( "cdef" ) ) {
3316 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3317 if ( !cdef2.getName().equals( "cdef" ) ) {
3320 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3321 if ( !cdef3.getName().equals( "cdef" ) ) {
3324 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3325 if ( !rt.getName().equals( "r" ) ) {
3328 final Phylogeny p3 = factory
3329 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3330 new NHXParser() )[ 0 ];
3331 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3332 if ( !bc_3.getName().equals( "bc" ) ) {
3335 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3336 if ( !ac_3.getName().equals( "abc" ) ) {
3339 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3340 if ( !ad_3.getName().equals( "abcde" ) ) {
3343 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3344 if ( !af_3.getName().equals( "abcdef" ) ) {
3347 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3348 if ( !ag_3.getName().equals( "" ) ) {
3351 if ( !ag_3.isRoot() ) {
3354 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3355 if ( !al_3.getName().equals( "" ) ) {
3358 if ( !al_3.isRoot() ) {
3361 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3362 if ( !kl_3.getName().equals( "" ) ) {
3365 if ( !kl_3.isRoot() ) {
3368 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3369 if ( !fl_3.getName().equals( "" ) ) {
3372 if ( !fl_3.isRoot() ) {
3375 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3376 if ( !gk_3.getName().equals( "ghijk" ) ) {
3379 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3380 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3381 if ( !r_4.getName().equals( "r" ) ) {
3384 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3385 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3386 if ( !r_5.getName().equals( "root" ) ) {
3389 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3390 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3391 if ( !r_6.getName().equals( "rot" ) ) {
3394 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3395 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3396 if ( !r_7.getName().equals( "rott" ) ) {
3400 catch ( final Exception e ) {
3401 e.printStackTrace( System.out );
3407 private static boolean testHmmscanOutputParser() {
3408 final String test_dir = Test.PATH_TO_TEST_DATA;
3410 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3411 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3413 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3414 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3415 final List<Protein> proteins = parser2.parse();
3416 if ( parser2.getProteinsEncountered() != 4 ) {
3419 if ( proteins.size() != 4 ) {
3422 if ( parser2.getDomainsEncountered() != 69 ) {
3425 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3428 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3431 final Protein p1 = proteins.get( 0 );
3432 if ( p1.getNumberOfProteinDomains() != 15 ) {
3435 final Protein p2 = proteins.get( 1 );
3436 if ( p2.getNumberOfProteinDomains() != 51 ) {
3439 final Protein p3 = proteins.get( 2 );
3440 if ( p3.getNumberOfProteinDomains() != 2 ) {
3443 final Protein p4 = proteins.get( 3 );
3444 if ( p4.getNumberOfProteinDomains() != 1 ) {
3447 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3450 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3453 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3456 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3459 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3462 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3465 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3468 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3471 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3475 catch ( final Exception e ) {
3476 e.printStackTrace( System.out );
3482 private static boolean testLastExternalNodeMethods() {
3484 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3485 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3486 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3487 final PhylogenyNode n1 = t0.getNode( "A" );
3488 if ( n1.isLastExternalNode() ) {
3491 final PhylogenyNode n2 = t0.getNode( "B" );
3492 if ( n2.isLastExternalNode() ) {
3495 final PhylogenyNode n3 = t0.getNode( "C" );
3496 if ( n3.isLastExternalNode() ) {
3499 final PhylogenyNode n4 = t0.getNode( "D" );
3500 if ( !n4.isLastExternalNode() ) {
3504 catch ( final Exception e ) {
3505 e.printStackTrace( System.out );
3511 private static boolean testLevelOrderIterator() {
3513 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3514 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3515 PhylogenyNodeIterator it0;
3516 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3519 for( it0.reset(); it0.hasNext(); ) {
3522 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3523 if ( !it.next().getName().equals( "r" ) ) {
3526 if ( !it.next().getName().equals( "ab" ) ) {
3529 if ( !it.next().getName().equals( "cd" ) ) {
3532 if ( !it.next().getName().equals( "A" ) ) {
3535 if ( !it.next().getName().equals( "B" ) ) {
3538 if ( !it.next().getName().equals( "C" ) ) {
3541 if ( !it.next().getName().equals( "D" ) ) {
3544 if ( it.hasNext() ) {
3547 final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r",
3548 new NHXParser() )[ 0 ];
3549 PhylogenyNodeIterator it2;
3550 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3553 for( it2.reset(); it2.hasNext(); ) {
3556 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3557 if ( !it3.next().getName().equals( "r" ) ) {
3560 if ( !it3.next().getName().equals( "abc" ) ) {
3563 if ( !it3.next().getName().equals( "defg" ) ) {
3566 if ( !it3.next().getName().equals( "A" ) ) {
3569 if ( !it3.next().getName().equals( "B" ) ) {
3572 if ( !it3.next().getName().equals( "C" ) ) {
3575 if ( !it3.next().getName().equals( "D" ) ) {
3578 if ( !it3.next().getName().equals( "E" ) ) {
3581 if ( !it3.next().getName().equals( "F" ) ) {
3584 if ( !it3.next().getName().equals( "G" ) ) {
3587 if ( !it3.next().getName().equals( "1" ) ) {
3590 if ( !it3.next().getName().equals( "2" ) ) {
3593 if ( !it3.next().getName().equals( "3" ) ) {
3596 if ( !it3.next().getName().equals( "4" ) ) {
3599 if ( !it3.next().getName().equals( "5" ) ) {
3602 if ( !it3.next().getName().equals( "6" ) ) {
3605 if ( !it3.next().getName().equals( "f1" ) ) {
3608 if ( !it3.next().getName().equals( "f2" ) ) {
3611 if ( !it3.next().getName().equals( "f3" ) ) {
3614 if ( !it3.next().getName().equals( "a" ) ) {
3617 if ( !it3.next().getName().equals( "b" ) ) {
3620 if ( !it3.next().getName().equals( "f21" ) ) {
3623 if ( !it3.next().getName().equals( "X" ) ) {
3626 if ( !it3.next().getName().equals( "Y" ) ) {
3629 if ( !it3.next().getName().equals( "Z" ) ) {
3632 if ( it3.hasNext() ) {
3635 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3636 PhylogenyNodeIterator it4;
3637 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3640 for( it4.reset(); it4.hasNext(); ) {
3643 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3644 if ( !it5.next().getName().equals( "r" ) ) {
3647 if ( !it5.next().getName().equals( "A" ) ) {
3650 if ( !it5.next().getName().equals( "B" ) ) {
3653 if ( !it5.next().getName().equals( "C" ) ) {
3656 if ( !it5.next().getName().equals( "D" ) ) {
3659 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3660 PhylogenyNodeIterator it6;
3661 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3664 for( it6.reset(); it6.hasNext(); ) {
3667 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3668 if ( !it7.next().getName().equals( "A" ) ) {
3671 if ( it.hasNext() ) {
3675 catch ( final Exception e ) {
3676 e.printStackTrace( System.out );
3682 private static boolean testMidpointrooting() {
3684 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3685 final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5",
3686 new NHXParser() )[ 0 ];
3687 if ( !t1.isRooted() ) {
3690 PhylogenyMethods.midpointRoot( t1 );
3691 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3694 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3697 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3700 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3703 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3706 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3709 t1.reRoot( t1.getNode( "A" ) );
3710 PhylogenyMethods.midpointRoot( t1 );
3711 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3714 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3717 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3720 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3723 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3726 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3730 catch ( final Exception e ) {
3731 e.printStackTrace( System.out );
3737 private static boolean testNexusCharactersParsing() {
3739 final NexusCharactersParser parser = new NexusCharactersParser();
3740 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3742 String[] labels = parser.getCharStateLabels();
3743 if ( labels.length != 7 ) {
3746 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3749 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3752 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3755 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3758 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3761 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3764 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3767 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3769 labels = parser.getCharStateLabels();
3770 if ( labels.length != 7 ) {
3773 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3776 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3779 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3782 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3785 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3788 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3791 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3795 catch ( final Exception e ) {
3796 e.printStackTrace( System.out );
3802 private static boolean testNexusMatrixParsing() {
3804 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3805 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3807 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3808 if ( m.getNumberOfCharacters() != 9 ) {
3811 if ( m.getNumberOfIdentifiers() != 5 ) {
3814 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3817 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3820 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3823 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3826 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3829 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3832 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3835 // if ( labels.length != 7 ) {
3838 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3841 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3844 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3847 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3850 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3853 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3856 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3859 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3861 // labels = parser.getCharStateLabels();
3862 // if ( labels.length != 7 ) {
3865 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3868 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3871 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3874 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3877 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3880 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3883 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3887 catch ( final Exception e ) {
3888 e.printStackTrace( System.out );
3894 private static boolean testNexusTreeParsing() {
3896 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3897 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3898 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3899 if ( phylogenies.length != 1 ) {
3902 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3905 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3909 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3910 if ( phylogenies.length != 1 ) {
3913 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3916 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3920 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3921 if ( phylogenies.length != 1 ) {
3924 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3927 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3930 if ( phylogenies[ 0 ].isRooted() ) {
3934 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3935 if ( phylogenies.length != 18 ) {
3938 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3941 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3944 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3947 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3950 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3953 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3956 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3959 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3962 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3965 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3968 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3971 if ( phylogenies[ 8 ].isRooted() ) {
3974 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3977 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3980 if ( !phylogenies[ 9 ].isRooted() ) {
3983 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3986 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3989 if ( !phylogenies[ 10 ].isRooted() ) {
3992 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3995 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3998 if ( phylogenies[ 11 ].isRooted() ) {
4001 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4004 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4007 if ( !phylogenies[ 12 ].isRooted() ) {
4010 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4013 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4016 if ( !phylogenies[ 13 ].isRooted() ) {
4019 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4022 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4025 if ( !phylogenies[ 14 ].isRooted() ) {
4028 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4031 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4034 if ( phylogenies[ 15 ].isRooted() ) {
4037 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4040 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4043 if ( !phylogenies[ 16 ].isRooted() ) {
4046 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4049 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4052 if ( phylogenies[ 17 ].isRooted() ) {
4055 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4059 catch ( final Exception e ) {
4060 e.printStackTrace( System.out );
4066 private static boolean testNexusTreeParsingTranslating() {
4068 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4069 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4070 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4071 if ( phylogenies.length != 1 ) {
4074 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4077 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4080 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4083 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4086 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4087 .equals( "Aranaeus" ) ) {
4091 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4092 if ( phylogenies.length != 3 ) {
4095 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4098 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4101 if ( phylogenies[ 0 ].isRooted() ) {
4104 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4107 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4110 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4111 .equals( "Aranaeus" ) ) {
4114 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4117 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4120 if ( phylogenies[ 1 ].isRooted() ) {
4123 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4126 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4129 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4130 .equals( "Aranaeus" ) ) {
4133 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4136 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4139 if ( !phylogenies[ 2 ].isRooted() ) {
4142 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4145 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4148 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4149 .equals( "Aranaeus" ) ) {
4153 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4154 if ( phylogenies.length != 3 ) {
4157 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4160 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4163 if ( phylogenies[ 0 ].isRooted() ) {
4166 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4169 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4172 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4173 .equals( "Aranaeus" ) ) {
4176 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4179 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4182 if ( phylogenies[ 1 ].isRooted() ) {
4185 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4188 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4191 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4192 .equals( "Aranaeus" ) ) {
4195 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4198 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4201 if ( !phylogenies[ 2 ].isRooted() ) {
4204 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4207 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4210 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4211 .equals( "Aranaeus" ) ) {
4215 catch ( final Exception e ) {
4216 e.printStackTrace( System.out );
4222 private static boolean testNHParsing() {
4224 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4225 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4226 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4229 final NHXParser nhxp = new NHXParser();
4230 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4231 nhxp.setReplaceUnderscores( true );
4232 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4233 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4236 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4239 final Phylogeny p1b = factory
4240 .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
4241 new NHXParser() )[ 0 ];
4242 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4245 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4248 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4249 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4250 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4251 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4252 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4253 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4254 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4255 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4256 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4257 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4258 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4259 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4260 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4262 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4265 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4268 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4271 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4274 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4275 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4276 final String p16_S = "((A,B),C)";
4277 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4278 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4281 final String p17_S = "(C,(A,B))";
4282 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4283 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4286 final String p18_S = "((A,B),(C,D))";
4287 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4288 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4291 final String p19_S = "(((A,B),C),D)";
4292 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4293 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4296 final String p20_S = "(A,(B,(C,D)))";
4297 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4298 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4301 final String p21_S = "(A,(B,(C,(D,E))))";
4302 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4303 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4306 final String p22_S = "((((A,B),C),D),E)";
4307 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4308 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4311 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4312 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4313 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4316 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4317 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4318 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4321 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4322 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4323 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4324 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4327 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4330 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4331 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4332 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4333 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4334 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4335 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4336 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4337 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4338 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4339 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4342 final String p26_S = "(A,B)ab";
4343 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4344 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4347 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4348 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4350 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4353 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4354 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4355 final String p28_S3 = "(A,B)ab";
4356 final String p28_S4 = "((((A,B),C),D),;E;)";
4357 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4359 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4362 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4365 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4368 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4371 final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
4372 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4373 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4376 final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
4377 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4378 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4381 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4382 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4383 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4386 final String p33_S = "A";
4387 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4388 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4391 final String p34_S = "B;";
4392 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4393 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4396 final String p35_S = "B:0.2";
4397 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4398 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4401 final String p36_S = "(A)";
4402 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4403 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4406 final String p37_S = "((A))";
4407 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4408 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4411 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4412 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4413 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4416 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4417 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4418 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4421 final String p40_S = "(A,B,C)";
4422 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4423 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4426 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4427 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4428 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4431 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4432 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4433 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4436 final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
4437 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4438 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4441 final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
4442 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4443 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4446 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4447 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4448 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4451 final String p46_S = "";
4452 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4453 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4457 catch ( final Exception e ) {
4458 e.printStackTrace( System.out );
4464 private static boolean testNHXconversion() {
4466 final PhylogenyNode n1 = new PhylogenyNode();
4467 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4468 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4469 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4470 final PhylogenyNode n5 = PhylogenyNode
4471 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4472 final PhylogenyNode n6 = PhylogenyNode
4473 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4474 if ( !n1.toNewHampshireX().equals( "" ) ) {
4477 if ( !n2.toNewHampshireX().equals( "" ) ) {
4480 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4483 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4486 if ( !n5.toNewHampshireX()
4487 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56.0:W=2.0:C=10.20.30]" ) ) {
4490 if ( !n6.toNewHampshireX()
4491 .equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100.0:W=2.0:C=0.0.0]" ) ) {
4495 catch ( final Exception e ) {
4496 e.printStackTrace( System.out );
4502 private static boolean testNHXNodeParsing() {
4504 final PhylogenyNode n1 = new PhylogenyNode();
4505 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4506 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4507 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4508 final PhylogenyNode n5 = PhylogenyNode
4509 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
4510 if ( !n3.getName().equals( "n3" ) ) {
4513 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4516 if ( n3.isDuplication() ) {
4519 if ( n3.isHasAssignedEvent() ) {
4522 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4525 if ( !n4.getName().equals( "n4" ) ) {
4528 if ( n4.getDistanceToParent() != 0.01 ) {
4531 if ( !n5.getName().equals( "n5" ) ) {
4534 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4537 if ( n5.getDistanceToParent() != 0.1 ) {
4540 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4543 if ( !n5.isDuplication() ) {
4546 if ( !n5.isHasAssignedEvent() ) {
4549 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4552 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4555 final PhylogenyNode n8 = PhylogenyNode
4556 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4557 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4558 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4561 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4564 final PhylogenyNode n9 = PhylogenyNode
4565 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4566 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4567 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4570 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4573 final PhylogenyNode n10 = PhylogenyNode
4574 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4575 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4578 final PhylogenyNode n20 = PhylogenyNode
4579 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4580 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4583 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4586 final PhylogenyNode n20x = PhylogenyNode
4587 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4588 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4591 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4594 final PhylogenyNode n20xx = PhylogenyNode
4595 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4596 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4599 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4602 final PhylogenyNode n20xxx = PhylogenyNode
4603 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4604 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4607 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4610 final PhylogenyNode n20xxxx = PhylogenyNode
4611 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4612 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4615 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4618 final PhylogenyNode n21 = PhylogenyNode
4619 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4620 if ( !n21.getName().equals( "n21_PIG" ) ) {
4623 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4626 final PhylogenyNode n21x = PhylogenyNode
4627 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4628 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4631 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4634 final PhylogenyNode n22 = PhylogenyNode
4635 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4636 if ( !n22.getName().equals( "n22/PIG" ) ) {
4639 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4642 final PhylogenyNode n23 = PhylogenyNode
4643 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4644 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4647 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4650 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4651 final PhylogenyNode a = PhylogenyNode
4652 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4653 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4654 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4657 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4660 final PhylogenyNode b = PhylogenyNode
4661 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4662 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4663 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4666 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4669 final PhylogenyNode c = PhylogenyNode
4670 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4671 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4672 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4675 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4678 final PhylogenyNode d = PhylogenyNode
4679 .createInstanceFromNhxString( "n10_RAT1/1-2",
4680 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4681 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4684 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4687 final PhylogenyNode e = PhylogenyNode
4688 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4689 if ( !e.getName().equals( "n10_RAT1" ) ) {
4692 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4696 final PhylogenyNode n11 = PhylogenyNode
4697 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4698 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4699 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4702 if ( n11.getDistanceToParent() != 0.4 ) {
4705 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4708 final PhylogenyNode n12 = PhylogenyNode
4709 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4710 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4711 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4714 if ( n12.getDistanceToParent() != 0.4 ) {
4717 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4720 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4721 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4722 if ( !tvu1.getRef().equals( "tag1" ) ) {
4725 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4728 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4731 if ( !tvu1.getValue().equals( "value1" ) ) {
4734 if ( !tvu3.getRef().equals( "tag3" ) ) {
4737 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4740 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4743 if ( !tvu3.getValue().equals( "value3" ) ) {
4746 if ( n1.getName().compareTo( "" ) != 0 ) {
4749 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4752 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4755 if ( n2.getName().compareTo( "" ) != 0 ) {
4758 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4761 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4764 final PhylogenyNode n00 = PhylogenyNode
4765 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
4766 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4769 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4772 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4775 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4778 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4781 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4784 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4787 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4790 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4791 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4794 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4795 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4798 final PhylogenyNode n13 = PhylogenyNode
4799 .createInstanceFromNhxString( "blah_12345/1-2",
4800 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4801 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4804 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4807 final PhylogenyNode n14 = PhylogenyNode
4808 .createInstanceFromNhxString( "blah_12X45/1-2",
4809 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4810 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4813 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4816 final PhylogenyNode n15 = PhylogenyNode
4817 .createInstanceFromNhxString( "something_wicked[123]",
4818 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4819 if ( !n15.getName().equals( "something_wicked" ) ) {
4822 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4825 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4828 final PhylogenyNode n16 = PhylogenyNode
4829 .createInstanceFromNhxString( "something_wicked2[9]",
4830 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4831 if ( !n16.getName().equals( "something_wicked2" ) ) {
4834 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4837 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4840 final PhylogenyNode n17 = PhylogenyNode
4841 .createInstanceFromNhxString( "something_wicked3[a]",
4842 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4843 if ( !n17.getName().equals( "something_wicked3" ) ) {
4846 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4849 final PhylogenyNode n18 = PhylogenyNode
4850 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4851 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4854 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4857 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4861 catch ( final Exception e ) {
4862 e.printStackTrace( System.out );
4868 private static boolean testNHXParsing() {
4870 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4871 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4872 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4875 final String p2_S = "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]";
4876 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4877 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4880 final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
4881 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4882 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4885 final Phylogeny[] p3 = factory
4886 .create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]",
4888 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4891 final Phylogeny[] p4 = factory
4892 .create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]",
4894 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4897 final Phylogeny[] p5 = factory
4898 .create( "[] ( [][ ][ ] ([((( &&NHXcomment only![[[[[[]([]((((A:0.2[&&NHX:S=q[comment )))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]",
4900 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4903 final String p6_S_C = "(A[][][][1][22][333][4444][55555][666666][&&NHX:S=Aspecies],B[))],C,(AA,BB,CC,(CCC,DDD,EEE,[comment](FFFF,GGGG)x)y,D[comment]D,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
4904 final String p6_S_WO_C = "(A[&&NHX:S=Aspecies],B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
4905 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4906 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4909 final String p7_S_C = "(((A [&&NHX:S=species_a], B [&&NHX:S=Vstorri] , C , D),(A,B,C,D[comment])[],[c][]([xxx]A[comment],[comment]B[comment][comment],[comment][comment]C[comment][comment],[comment][comment]D[comment][comment])[comment][comment],[comment] [comment](A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C[comment][comment][comment][comment][comment] [comment],D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),[comment][comment]((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
4910 final String p7_S_WO_C = "(((A[&&NHX:S=species_a],B[&&NHX:S=Vstorri],C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
4911 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4912 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4915 final String p8_S_C = "[cmt](((([]([))))))](((((A[&&NHX:S= [a comment] a])))))))[too many comments!:)])),(((((((((B[&&NHX[ a comment in a bad place]:S =b])))))[] [] )))),(((((((((C[&&NHX:S=c]) ))[,,, ])))))))";
4916 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4917 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4918 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4921 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4922 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) {
4925 final Phylogeny p10 = factory
4926 .create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]",
4927 new NHXParser() )[ 0 ];
4928 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) {
4932 catch ( final Exception e ) {
4933 e.printStackTrace( System.out );
4939 private static boolean testNHXParsingQuotes() {
4941 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4942 final NHXParser p = new NHXParser();
4943 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4944 if ( phylogenies_0.length != 5 ) {
4947 final Phylogeny phy = phylogenies_0[ 4 ];
4948 if ( phy.getNumberOfExternalNodes() != 7 ) {
4951 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4954 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4957 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4958 .getScientificName().equals( "hsapiens" ) ) {
4961 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4964 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4967 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4970 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4973 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4976 final NHXParser p1p = new NHXParser();
4977 p1p.setIgnoreQuotes( true );
4978 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4979 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4982 final NHXParser p2p = new NHXParser();
4983 p1p.setIgnoreQuotes( false );
4984 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4985 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4988 final NHXParser p3p = new NHXParser();
4989 p3p.setIgnoreQuotes( false );
4990 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4991 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4994 final NHXParser p4p = new NHXParser();
4995 p4p.setIgnoreQuotes( false );
4996 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4997 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5000 final Phylogeny p10 = factory
5001 .create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]",
5002 new NHXParser() )[ 0 ];
5003 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]";
5004 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5007 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5008 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5012 final Phylogeny p12 = factory
5013 .create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]",
5014 new NHXParser() )[ 0 ];
5015 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]";
5016 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5019 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5020 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5023 final String p12_clean_str_nh = "(('A B':0.2,'BB B':0.03):0.5,'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1;";
5024 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5027 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5028 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5032 catch ( final Exception e ) {
5033 e.printStackTrace( System.out );
5039 private static boolean testNHXParsingMB() {
5041 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5042 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5043 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5044 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5045 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5046 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5047 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5048 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5049 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5050 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5051 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5054 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5057 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5058 0.1100000000000000e+00 ) ) {
5061 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5064 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5067 final Phylogeny p2 = factory
5068 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5069 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5070 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5071 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5072 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5073 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5074 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5075 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5076 + "7.369400000000000e-02}])",
5077 new NHXParser() )[ 0 ];
5078 if ( p2.getNode( "1" ) == null ) {
5081 if ( p2.getNode( "2" ) == null ) {
5085 catch ( final Exception e ) {
5086 e.printStackTrace( System.out );
5093 private static boolean testPhylogenyBranch() {
5095 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5096 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5097 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5098 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5099 if ( !a1b1.equals( a1b1 ) ) {
5102 if ( !a1b1.equals( b1a1 ) ) {
5105 if ( !b1a1.equals( a1b1 ) ) {
5108 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5109 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5110 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5111 if ( a1_b1.equals( b1_a1 ) ) {
5114 if ( a1_b1.equals( a1_b1_ ) ) {
5117 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5118 if ( !a1_b1.equals( b1_a1_ ) ) {
5121 if ( a1_b1_.equals( b1_a1_ ) ) {
5124 if ( !a1_b1_.equals( b1_a1 ) ) {
5128 catch ( final Exception e ) {
5129 e.printStackTrace( System.out );
5135 private static boolean testPhyloXMLparsingOfDistributionElement() {
5137 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5138 PhyloXmlParser xml_parser = null;
5140 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5142 catch ( final Exception e ) {
5143 // Do nothing -- means were not running from jar.
5145 if ( xml_parser == null ) {
5146 xml_parser = new PhyloXmlParser();
5147 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5148 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5151 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5154 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5156 if ( xml_parser.getErrorCount() > 0 ) {
5157 System.out.println( xml_parser.getErrorMessages().toString() );
5160 if ( phylogenies_0.length != 1 ) {
5163 final Phylogeny t1 = phylogenies_0[ 0 ];
5164 PhylogenyNode n = null;
5165 Distribution d = null;
5166 n = t1.getNode( "root node" );
5167 if ( !n.getNodeData().isHasDistribution() ) {
5170 if ( n.getNodeData().getDistributions().size() != 1 ) {
5173 d = n.getNodeData().getDistribution();
5174 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5177 if ( d.getPoints().size() != 1 ) {
5180 if ( d.getPolygons() != null ) {
5183 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5186 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5189 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5192 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5195 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5198 n = t1.getNode( "node a" );
5199 if ( !n.getNodeData().isHasDistribution() ) {
5202 if ( n.getNodeData().getDistributions().size() != 2 ) {
5205 d = n.getNodeData().getDistribution( 1 );
5206 if ( !d.getDesc().equals( "San Diego" ) ) {
5209 if ( d.getPoints().size() != 1 ) {
5212 if ( d.getPolygons() != null ) {
5215 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5218 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5221 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5224 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5227 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5230 n = t1.getNode( "node bb" );
5231 if ( !n.getNodeData().isHasDistribution() ) {
5234 if ( n.getNodeData().getDistributions().size() != 1 ) {
5237 d = n.getNodeData().getDistribution( 0 );
5238 if ( d.getPoints().size() != 3 ) {
5241 if ( d.getPolygons().size() != 2 ) {
5244 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5247 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5250 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5253 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5256 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5259 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5262 Polygon p = d.getPolygons().get( 0 );
5263 if ( p.getPoints().size() != 3 ) {
5266 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5269 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5272 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5275 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5278 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5281 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5284 p = d.getPolygons().get( 1 );
5285 if ( p.getPoints().size() != 3 ) {
5288 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5291 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5294 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5298 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5299 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5300 if ( rt.length != 1 ) {
5303 final Phylogeny t1_rt = rt[ 0 ];
5304 n = t1_rt.getNode( "root node" );
5305 if ( !n.getNodeData().isHasDistribution() ) {
5308 if ( n.getNodeData().getDistributions().size() != 1 ) {
5311 d = n.getNodeData().getDistribution();
5312 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5315 if ( d.getPoints().size() != 1 ) {
5318 if ( d.getPolygons() != null ) {
5321 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5324 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5327 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5330 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5333 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5336 n = t1_rt.getNode( "node a" );
5337 if ( !n.getNodeData().isHasDistribution() ) {
5340 if ( n.getNodeData().getDistributions().size() != 2 ) {
5343 d = n.getNodeData().getDistribution( 1 );
5344 if ( !d.getDesc().equals( "San Diego" ) ) {
5347 if ( d.getPoints().size() != 1 ) {
5350 if ( d.getPolygons() != null ) {
5353 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5356 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5359 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5362 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5365 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5368 n = t1_rt.getNode( "node bb" );
5369 if ( !n.getNodeData().isHasDistribution() ) {
5372 if ( n.getNodeData().getDistributions().size() != 1 ) {
5375 d = n.getNodeData().getDistribution( 0 );
5376 if ( d.getPoints().size() != 3 ) {
5379 if ( d.getPolygons().size() != 2 ) {
5382 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5385 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5388 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5391 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5394 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5397 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5400 p = d.getPolygons().get( 0 );
5401 if ( p.getPoints().size() != 3 ) {
5404 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5407 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5410 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5413 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5416 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5419 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5422 p = d.getPolygons().get( 1 );
5423 if ( p.getPoints().size() != 3 ) {
5426 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5429 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5432 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5436 catch ( final Exception e ) {
5437 e.printStackTrace( System.out );
5443 private static boolean testPostOrderIterator() {
5445 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5446 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5447 PhylogenyNodeIterator it0;
5448 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5451 for( it0.reset(); it0.hasNext(); ) {
5454 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5455 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5456 if ( !it.next().getName().equals( "A" ) ) {
5459 if ( !it.next().getName().equals( "B" ) ) {
5462 if ( !it.next().getName().equals( "ab" ) ) {
5465 if ( !it.next().getName().equals( "C" ) ) {
5468 if ( !it.next().getName().equals( "D" ) ) {
5471 if ( !it.next().getName().equals( "cd" ) ) {
5474 if ( !it.next().getName().equals( "abcd" ) ) {
5477 if ( !it.next().getName().equals( "E" ) ) {
5480 if ( !it.next().getName().equals( "F" ) ) {
5483 if ( !it.next().getName().equals( "ef" ) ) {
5486 if ( !it.next().getName().equals( "G" ) ) {
5489 if ( !it.next().getName().equals( "H" ) ) {
5492 if ( !it.next().getName().equals( "gh" ) ) {
5495 if ( !it.next().getName().equals( "efgh" ) ) {
5498 if ( !it.next().getName().equals( "r" ) ) {
5501 if ( it.hasNext() ) {
5505 catch ( final Exception e ) {
5506 e.printStackTrace( System.out );
5512 private static boolean testPreOrderIterator() {
5514 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5515 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5516 PhylogenyNodeIterator it0;
5517 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5520 for( it0.reset(); it0.hasNext(); ) {
5523 PhylogenyNodeIterator it = t0.iteratorPreorder();
5524 if ( !it.next().getName().equals( "r" ) ) {
5527 if ( !it.next().getName().equals( "ab" ) ) {
5530 if ( !it.next().getName().equals( "A" ) ) {
5533 if ( !it.next().getName().equals( "B" ) ) {
5536 if ( !it.next().getName().equals( "cd" ) ) {
5539 if ( !it.next().getName().equals( "C" ) ) {
5542 if ( !it.next().getName().equals( "D" ) ) {
5545 if ( it.hasNext() ) {
5548 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5549 it = t1.iteratorPreorder();
5550 if ( !it.next().getName().equals( "r" ) ) {
5553 if ( !it.next().getName().equals( "abcd" ) ) {
5556 if ( !it.next().getName().equals( "ab" ) ) {
5559 if ( !it.next().getName().equals( "A" ) ) {
5562 if ( !it.next().getName().equals( "B" ) ) {
5565 if ( !it.next().getName().equals( "cd" ) ) {
5568 if ( !it.next().getName().equals( "C" ) ) {
5571 if ( !it.next().getName().equals( "D" ) ) {
5574 if ( !it.next().getName().equals( "efgh" ) ) {
5577 if ( !it.next().getName().equals( "ef" ) ) {
5580 if ( !it.next().getName().equals( "E" ) ) {
5583 if ( !it.next().getName().equals( "F" ) ) {
5586 if ( !it.next().getName().equals( "gh" ) ) {
5589 if ( !it.next().getName().equals( "G" ) ) {
5592 if ( !it.next().getName().equals( "H" ) ) {
5595 if ( it.hasNext() ) {
5599 catch ( final Exception e ) {
5600 e.printStackTrace( System.out );
5606 private static boolean testPropertiesMap() {
5608 final PropertiesMap pm = new PropertiesMap();
5609 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5610 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5611 final Property p2 = new Property( "something:else",
5613 "improbable:research",
5616 pm.addProperty( p0 );
5617 pm.addProperty( p1 );
5618 pm.addProperty( p2 );
5619 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5622 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5625 if ( pm.getProperties().size() != 3 ) {
5628 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5631 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5634 if ( pm.getProperties().size() != 3 ) {
5637 pm.removeProperty( "dimensions:diameter" );
5638 if ( pm.getProperties().size() != 2 ) {
5641 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5644 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5648 catch ( final Exception e ) {
5649 e.printStackTrace( System.out );
5655 private static boolean testReIdMethods() {
5657 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5658 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5659 final int count = PhylogenyNode.getNodeCount();
5661 if ( p.getNode( "r" ).getId() != count ) {
5664 if ( p.getNode( "A" ).getId() != count + 1 ) {
5667 if ( p.getNode( "B" ).getId() != count + 1 ) {
5670 if ( p.getNode( "C" ).getId() != count + 1 ) {
5673 if ( p.getNode( "1" ).getId() != count + 2 ) {
5676 if ( p.getNode( "2" ).getId() != count + 2 ) {
5679 if ( p.getNode( "3" ).getId() != count + 2 ) {
5682 if ( p.getNode( "4" ).getId() != count + 2 ) {
5685 if ( p.getNode( "5" ).getId() != count + 2 ) {
5688 if ( p.getNode( "6" ).getId() != count + 2 ) {
5691 if ( p.getNode( "a" ).getId() != count + 3 ) {
5694 if ( p.getNode( "b" ).getId() != count + 3 ) {
5697 if ( p.getNode( "X" ).getId() != count + 4 ) {
5700 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5703 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5707 catch ( final Exception e ) {
5708 e.printStackTrace( System.out );
5714 private static boolean testRerooting() {
5716 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5717 final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:5)CD:3[&&NHX:B=10])ABCD:0.5",
5718 new NHXParser() )[ 0 ];
5719 if ( !t1.isRooted() ) {
5722 t1.reRoot( t1.getNode( "D" ) );
5723 t1.reRoot( t1.getNode( "CD" ) );
5724 t1.reRoot( t1.getNode( "A" ) );
5725 t1.reRoot( t1.getNode( "B" ) );
5726 t1.reRoot( t1.getNode( "AB" ) );
5727 t1.reRoot( t1.getNode( "D" ) );
5728 t1.reRoot( t1.getNode( "C" ) );
5729 t1.reRoot( t1.getNode( "CD" ) );
5730 t1.reRoot( t1.getNode( "A" ) );
5731 t1.reRoot( t1.getNode( "B" ) );
5732 t1.reRoot( t1.getNode( "AB" ) );
5733 t1.reRoot( t1.getNode( "D" ) );
5734 t1.reRoot( t1.getNode( "D" ) );
5735 t1.reRoot( t1.getNode( "C" ) );
5736 t1.reRoot( t1.getNode( "A" ) );
5737 t1.reRoot( t1.getNode( "B" ) );
5738 t1.reRoot( t1.getNode( "AB" ) );
5739 t1.reRoot( t1.getNode( "C" ) );
5740 t1.reRoot( t1.getNode( "D" ) );
5741 t1.reRoot( t1.getNode( "CD" ) );
5742 t1.reRoot( t1.getNode( "D" ) );
5743 t1.reRoot( t1.getNode( "A" ) );
5744 t1.reRoot( t1.getNode( "B" ) );
5745 t1.reRoot( t1.getNode( "AB" ) );
5746 t1.reRoot( t1.getNode( "C" ) );
5747 t1.reRoot( t1.getNode( "D" ) );
5748 t1.reRoot( t1.getNode( "CD" ) );
5749 t1.reRoot( t1.getNode( "D" ) );
5750 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5753 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5756 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5759 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5762 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5765 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5768 final Phylogeny t2 = factory.create( "(((A:1,B:2)AB:10[&&NHX:B=55],C)ABC:3[&&NHX:B=33],D:5)ABCD:0.5",
5769 new NHXParser() )[ 0 ];
5770 t2.reRoot( t2.getNode( "A" ) );
5771 t2.reRoot( t2.getNode( "D" ) );
5772 t2.reRoot( t2.getNode( "ABC" ) );
5773 t2.reRoot( t2.getNode( "A" ) );
5774 t2.reRoot( t2.getNode( "B" ) );
5775 t2.reRoot( t2.getNode( "D" ) );
5776 t2.reRoot( t2.getNode( "C" ) );
5777 t2.reRoot( t2.getNode( "ABC" ) );
5778 t2.reRoot( t2.getNode( "A" ) );
5779 t2.reRoot( t2.getNode( "B" ) );
5780 t2.reRoot( t2.getNode( "AB" ) );
5781 t2.reRoot( t2.getNode( "AB" ) );
5782 t2.reRoot( t2.getNode( "D" ) );
5783 t2.reRoot( t2.getNode( "C" ) );
5784 t2.reRoot( t2.getNode( "B" ) );
5785 t2.reRoot( t2.getNode( "AB" ) );
5786 t2.reRoot( t2.getNode( "D" ) );
5787 t2.reRoot( t2.getNode( "D" ) );
5788 t2.reRoot( t2.getNode( "ABC" ) );
5789 t2.reRoot( t2.getNode( "A" ) );
5790 t2.reRoot( t2.getNode( "B" ) );
5791 t2.reRoot( t2.getNode( "AB" ) );
5792 t2.reRoot( t2.getNode( "D" ) );
5793 t2.reRoot( t2.getNode( "C" ) );
5794 t2.reRoot( t2.getNode( "ABC" ) );
5795 t2.reRoot( t2.getNode( "A" ) );
5796 t2.reRoot( t2.getNode( "B" ) );
5797 t2.reRoot( t2.getNode( "AB" ) );
5798 t2.reRoot( t2.getNode( "D" ) );
5799 t2.reRoot( t2.getNode( "D" ) );
5800 t2.reRoot( t2.getNode( "C" ) );
5801 t2.reRoot( t2.getNode( "A" ) );
5802 t2.reRoot( t2.getNode( "B" ) );
5803 t2.reRoot( t2.getNode( "AB" ) );
5804 t2.reRoot( t2.getNode( "C" ) );
5805 t2.reRoot( t2.getNode( "D" ) );
5806 t2.reRoot( t2.getNode( "ABC" ) );
5807 t2.reRoot( t2.getNode( "D" ) );
5808 t2.reRoot( t2.getNode( "A" ) );
5809 t2.reRoot( t2.getNode( "B" ) );
5810 t2.reRoot( t2.getNode( "AB" ) );
5811 t2.reRoot( t2.getNode( "C" ) );
5812 t2.reRoot( t2.getNode( "D" ) );
5813 t2.reRoot( t2.getNode( "ABC" ) );
5814 t2.reRoot( t2.getNode( "D" ) );
5815 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5818 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5821 t2.reRoot( t2.getNode( "ABC" ) );
5822 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5825 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5828 t2.reRoot( t2.getNode( "AB" ) );
5829 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5832 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5835 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5838 t2.reRoot( t2.getNode( "AB" ) );
5839 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5842 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5845 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5848 t2.reRoot( t2.getNode( "D" ) );
5849 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5852 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5855 t2.reRoot( t2.getNode( "ABC" ) );
5856 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5859 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5862 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5863 new NHXParser() )[ 0 ];
5864 t3.reRoot( t3.getNode( "B" ) );
5865 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5868 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5871 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5874 t3.reRoot( t3.getNode( "B" ) );
5875 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5878 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5881 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5884 t3.reRoot( t3.getRoot() );
5885 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5888 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5891 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5895 catch ( final Exception e ) {
5896 e.printStackTrace( System.out );
5902 private static boolean testSDIse() {
5904 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5905 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5906 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5907 gene1.setRooted( true );
5908 species1.setRooted( true );
5909 final SDI sdi = new SDIse( gene1, species1 );
5910 if ( !gene1.getRoot().isDuplication() ) {
5913 final Phylogeny species2 = factory
5914 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5915 new NHXParser() )[ 0 ];
5916 final Phylogeny gene2 = factory
5917 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5918 new NHXParser() )[ 0 ];
5919 species2.setRooted( true );
5920 gene2.setRooted( true );
5921 final SDI sdi2 = new SDIse( gene2, species2 );
5922 if ( sdi2.getDuplicationsSum() != 0 ) {
5925 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5928 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5931 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5934 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5937 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5940 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5943 final Phylogeny species3 = factory
5944 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5945 new NHXParser() )[ 0 ];
5946 final Phylogeny gene3 = factory
5947 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5948 new NHXParser() )[ 0 ];
5949 species3.setRooted( true );
5950 gene3.setRooted( true );
5951 final SDI sdi3 = new SDIse( gene3, species3 );
5952 if ( sdi3.getDuplicationsSum() != 1 ) {
5955 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5958 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5961 final Phylogeny species4 = factory
5962 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5963 new NHXParser() )[ 0 ];
5964 final Phylogeny gene4 = factory
5965 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5966 new NHXParser() )[ 0 ];
5967 species4.setRooted( true );
5968 gene4.setRooted( true );
5969 final SDI sdi4 = new SDIse( gene4, species4 );
5970 if ( sdi4.getDuplicationsSum() != 1 ) {
5973 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5976 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5979 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5982 if ( species4.getNumberOfExternalNodes() != 6 ) {
5985 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5988 final Phylogeny species5 = factory
5989 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5990 new NHXParser() )[ 0 ];
5991 final Phylogeny gene5 = factory
5992 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5993 new NHXParser() )[ 0 ];
5994 species5.setRooted( true );
5995 gene5.setRooted( true );
5996 final SDI sdi5 = new SDIse( gene5, species5 );
5997 if ( sdi5.getDuplicationsSum() != 2 ) {
6000 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6003 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6006 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6009 if ( species5.getNumberOfExternalNodes() != 6 ) {
6012 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6015 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6016 // Conjecture for Comparing Molecular Phylogenies"
6017 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6018 final Phylogeny species6 = factory
6019 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6020 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6021 new NHXParser() )[ 0 ];
6022 final Phylogeny gene6 = factory
6023 .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1,"
6024 + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
6025 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
6026 new NHXParser() )[ 0 ];
6027 species6.setRooted( true );
6028 gene6.setRooted( true );
6029 final SDI sdi6 = new SDIse( gene6, species6 );
6030 if ( sdi6.getDuplicationsSum() != 3 ) {
6033 if ( !gene6.getNode( "r" ).isDuplication() ) {
6036 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6039 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6042 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6045 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6048 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6051 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6054 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6057 sdi6.computeMappingCostL();
6058 if ( sdi6.computeMappingCostL() != 17 ) {
6061 if ( species6.getNumberOfExternalNodes() != 9 ) {
6064 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6067 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6068 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6069 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6070 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6071 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6072 species7.setRooted( true );
6073 final Phylogeny gene7_1 = Test
6074 .createPhylogeny( "((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
6075 gene7_1.setRooted( true );
6076 final SDI sdi7 = new SDIse( gene7_1, species7 );
6077 if ( sdi7.getDuplicationsSum() != 0 ) {
6080 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6083 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6086 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6089 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6092 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6095 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6098 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6101 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6104 final Phylogeny gene7_2 = Test
6105 .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
6106 gene7_2.setRooted( true );
6107 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6108 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6111 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6114 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6117 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6120 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6123 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6126 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6129 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6132 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6135 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6139 catch ( final Exception e ) {
6145 private static boolean testSDIunrooted() {
6147 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6148 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6149 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6150 final Iterator<PhylogenyBranch> iter = l.iterator();
6151 PhylogenyBranch br = iter.next();
6152 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6155 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6159 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6162 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6166 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6169 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6173 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6176 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6180 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6183 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6187 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6190 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6194 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6197 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6201 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6204 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6208 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6211 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6215 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6218 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6222 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6225 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6229 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6232 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6236 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6239 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6243 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6246 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6250 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6253 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6256 if ( iter.hasNext() ) {
6259 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6260 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6261 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6263 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6266 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6270 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6273 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6277 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6280 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6283 if ( iter1.hasNext() ) {
6286 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6287 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6288 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6290 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6293 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6297 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6300 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6304 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6307 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6310 if ( iter2.hasNext() ) {
6313 final Phylogeny species0 = factory
6314 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6315 new NHXParser() )[ 0 ];
6316 final Phylogeny gene1 = factory
6317 .create( "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])",
6318 new NHXParser() )[ 0 ];
6319 species0.setRooted( true );
6320 gene1.setRooted( true );
6321 final SDIR sdi_unrooted = new SDIR();
6322 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6323 if ( sdi_unrooted.getCount() != 1 ) {
6326 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6329 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6332 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6335 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6338 final Phylogeny gene2 = factory
6339 .create( "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])",
6340 new NHXParser() )[ 0 ];
6341 gene2.setRooted( true );
6342 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6343 if ( sdi_unrooted.getCount() != 1 ) {
6346 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6349 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6352 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6355 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6358 final Phylogeny species6 = factory
6359 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6360 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6361 new NHXParser() )[ 0 ];
6362 final Phylogeny gene6 = factory
6363 .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
6364 + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
6365 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6366 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6367 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6368 new NHXParser() )[ 0 ];
6369 species6.setRooted( true );
6370 gene6.setRooted( true );
6371 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6372 if ( sdi_unrooted.getCount() != 1 ) {
6375 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6378 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6381 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6384 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6387 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6390 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6393 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6396 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6399 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6402 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6405 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6408 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6412 final Phylogeny species7 = factory
6413 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6414 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6415 new NHXParser() )[ 0 ];
6416 final Phylogeny gene7 = factory
6417 .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
6418 + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
6419 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6420 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6421 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6422 new NHXParser() )[ 0 ];
6423 species7.setRooted( true );
6424 gene7.setRooted( true );
6425 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6426 if ( sdi_unrooted.getCount() != 1 ) {
6429 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6432 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6435 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6438 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6441 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6444 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6447 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6450 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6453 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6456 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6459 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6462 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6466 final Phylogeny species8 = factory
6467 .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
6468 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6469 new NHXParser() )[ 0 ];
6470 final Phylogeny gene8 = factory
6471 .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
6472 + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
6473 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6474 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6475 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6476 new NHXParser() )[ 0 ];
6477 species8.setRooted( true );
6478 gene8.setRooted( true );
6479 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6480 if ( sdi_unrooted.getCount() != 1 ) {
6483 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6486 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6489 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6492 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6495 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6498 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6501 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6504 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6507 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6510 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6513 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6516 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6521 catch ( final Exception e ) {
6522 e.printStackTrace( System.out );
6528 private static boolean testSplit() {
6530 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6531 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6532 //Archaeopteryx.createApplication( p0 );
6533 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6534 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6535 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6536 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6537 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6538 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6539 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6540 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6541 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6542 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6543 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6544 // System.out.println( s0.toString() );
6546 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6549 if ( s0.match( query_nodes ) ) {
6552 query_nodes = new HashSet<PhylogenyNode>();
6553 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6554 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6560 if ( !s0.match( query_nodes ) ) {
6564 query_nodes = new HashSet<PhylogenyNode>();
6565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6568 if ( !s0.match( query_nodes ) ) {
6572 query_nodes = new HashSet<PhylogenyNode>();
6573 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6574 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6575 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6577 if ( !s0.match( query_nodes ) ) {
6581 query_nodes = new HashSet<PhylogenyNode>();
6582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6583 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6584 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6586 if ( !s0.match( query_nodes ) ) {
6590 query_nodes = new HashSet<PhylogenyNode>();
6591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6594 if ( !s0.match( query_nodes ) ) {
6598 query_nodes = new HashSet<PhylogenyNode>();
6599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6601 if ( !s0.match( query_nodes ) ) {
6605 query_nodes = new HashSet<PhylogenyNode>();
6606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6611 if ( !s0.match( query_nodes ) ) {
6615 query_nodes = new HashSet<PhylogenyNode>();
6616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6619 if ( !s0.match( query_nodes ) ) {
6623 query_nodes = new HashSet<PhylogenyNode>();
6624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6628 if ( !s0.match( query_nodes ) ) {
6632 query_nodes = new HashSet<PhylogenyNode>();
6633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6635 if ( s0.match( query_nodes ) ) {
6639 query_nodes = new HashSet<PhylogenyNode>();
6640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6644 if ( s0.match( query_nodes ) ) {
6648 query_nodes = new HashSet<PhylogenyNode>();
6649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6654 if ( s0.match( query_nodes ) ) {
6658 query_nodes = new HashSet<PhylogenyNode>();
6659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6662 if ( s0.match( query_nodes ) ) {
6666 query_nodes = new HashSet<PhylogenyNode>();
6667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6669 if ( s0.match( query_nodes ) ) {
6673 query_nodes = new HashSet<PhylogenyNode>();
6674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6676 if ( s0.match( query_nodes ) ) {
6680 query_nodes = new HashSet<PhylogenyNode>();
6681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6683 if ( s0.match( query_nodes ) ) {
6687 query_nodes = new HashSet<PhylogenyNode>();
6688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6690 if ( s0.match( query_nodes ) ) {
6694 query_nodes = new HashSet<PhylogenyNode>();
6695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6697 if ( s0.match( query_nodes ) ) {
6701 query_nodes = new HashSet<PhylogenyNode>();
6702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6704 if ( s0.match( query_nodes ) ) {
6708 query_nodes = new HashSet<PhylogenyNode>();
6709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6712 if ( s0.match( query_nodes ) ) {
6716 query_nodes = new HashSet<PhylogenyNode>();
6717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6718 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6720 if ( s0.match( query_nodes ) ) {
6724 query_nodes = new HashSet<PhylogenyNode>();
6725 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6728 if ( s0.match( query_nodes ) ) {
6732 query_nodes = new HashSet<PhylogenyNode>();
6733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6734 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6735 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6736 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6737 if ( s0.match( query_nodes ) ) {
6741 // query_nodes = new HashSet<PhylogenyNode>();
6742 // query_nodes.add( new PhylogenyNode( "X" ) );
6743 // query_nodes.add( new PhylogenyNode( "Y" ) );
6744 // query_nodes.add( new PhylogenyNode( "A" ) );
6745 // query_nodes.add( new PhylogenyNode( "B" ) );
6746 // query_nodes.add( new PhylogenyNode( "C" ) );
6747 // query_nodes.add( new PhylogenyNode( "D" ) );
6748 // query_nodes.add( new PhylogenyNode( "E" ) );
6749 // query_nodes.add( new PhylogenyNode( "F" ) );
6750 // query_nodes.add( new PhylogenyNode( "G" ) );
6751 // if ( !s0.match( query_nodes ) ) {
6754 // query_nodes = new HashSet<PhylogenyNode>();
6755 // query_nodes.add( new PhylogenyNode( "X" ) );
6756 // query_nodes.add( new PhylogenyNode( "Y" ) );
6757 // query_nodes.add( new PhylogenyNode( "A" ) );
6758 // query_nodes.add( new PhylogenyNode( "B" ) );
6759 // query_nodes.add( new PhylogenyNode( "C" ) );
6760 // if ( !s0.match( query_nodes ) ) {
6764 // query_nodes = new HashSet<PhylogenyNode>();
6765 // query_nodes.add( new PhylogenyNode( "X" ) );
6766 // query_nodes.add( new PhylogenyNode( "Y" ) );
6767 // query_nodes.add( new PhylogenyNode( "D" ) );
6768 // query_nodes.add( new PhylogenyNode( "E" ) );
6769 // query_nodes.add( new PhylogenyNode( "F" ) );
6770 // query_nodes.add( new PhylogenyNode( "G" ) );
6771 // if ( !s0.match( query_nodes ) ) {
6775 // query_nodes = new HashSet<PhylogenyNode>();
6776 // query_nodes.add( new PhylogenyNode( "X" ) );
6777 // query_nodes.add( new PhylogenyNode( "Y" ) );
6778 // query_nodes.add( new PhylogenyNode( "A" ) );
6779 // query_nodes.add( new PhylogenyNode( "B" ) );
6780 // query_nodes.add( new PhylogenyNode( "C" ) );
6781 // query_nodes.add( new PhylogenyNode( "D" ) );
6782 // if ( !s0.match( query_nodes ) ) {
6786 // query_nodes = new HashSet<PhylogenyNode>();
6787 // query_nodes.add( new PhylogenyNode( "X" ) );
6788 // query_nodes.add( new PhylogenyNode( "Y" ) );
6789 // query_nodes.add( new PhylogenyNode( "E" ) );
6790 // query_nodes.add( new PhylogenyNode( "F" ) );
6791 // query_nodes.add( new PhylogenyNode( "G" ) );
6792 // if ( !s0.match( query_nodes ) ) {
6796 // query_nodes = new HashSet<PhylogenyNode>();
6797 // query_nodes.add( new PhylogenyNode( "X" ) );
6798 // query_nodes.add( new PhylogenyNode( "Y" ) );
6799 // query_nodes.add( new PhylogenyNode( "F" ) );
6800 // query_nodes.add( new PhylogenyNode( "G" ) );
6801 // if ( !s0.match( query_nodes ) ) {
6805 query_nodes = new HashSet<PhylogenyNode>();
6806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6807 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6808 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6809 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6810 if ( s0.match( query_nodes ) ) {
6814 query_nodes = new HashSet<PhylogenyNode>();
6815 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6816 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6817 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6818 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6819 if ( s0.match( query_nodes ) ) {
6822 ///////////////////////////
6824 query_nodes = new HashSet<PhylogenyNode>();
6825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6827 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6828 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6829 if ( s0.match( query_nodes ) ) {
6833 query_nodes = new HashSet<PhylogenyNode>();
6834 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6835 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6836 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6837 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6838 if ( s0.match( query_nodes ) ) {
6842 query_nodes = new HashSet<PhylogenyNode>();
6843 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6844 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6845 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6846 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6847 if ( s0.match( query_nodes ) ) {
6851 query_nodes = new HashSet<PhylogenyNode>();
6852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6854 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6855 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6856 if ( s0.match( query_nodes ) ) {
6860 query_nodes = new HashSet<PhylogenyNode>();
6861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6863 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6864 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6865 if ( s0.match( query_nodes ) ) {
6869 query_nodes = new HashSet<PhylogenyNode>();
6870 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6873 if ( s0.match( query_nodes ) ) {
6877 query_nodes = new HashSet<PhylogenyNode>();
6878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6881 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6882 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6883 if ( s0.match( query_nodes ) ) {
6887 query_nodes = new HashSet<PhylogenyNode>();
6888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6890 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6891 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6892 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6893 if ( s0.match( query_nodes ) ) {
6897 query_nodes = new HashSet<PhylogenyNode>();
6898 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6899 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6900 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6901 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6903 if ( s0.match( query_nodes ) ) {
6907 query_nodes = new HashSet<PhylogenyNode>();
6908 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6909 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6910 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6911 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6914 if ( s0.match( query_nodes ) ) {
6918 catch ( final Exception e ) {
6919 e.printStackTrace();
6925 private static boolean testSplitStrict() {
6927 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6928 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6929 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6930 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6931 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6932 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6933 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6934 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6935 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6936 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6937 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6938 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6941 if ( s0.match( query_nodes ) ) {
6944 query_nodes = new HashSet<PhylogenyNode>();
6945 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6952 if ( !s0.match( query_nodes ) ) {
6956 query_nodes = new HashSet<PhylogenyNode>();
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6960 if ( !s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6969 if ( !s0.match( query_nodes ) ) {
6973 query_nodes = new HashSet<PhylogenyNode>();
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6978 if ( !s0.match( query_nodes ) ) {
6982 query_nodes = new HashSet<PhylogenyNode>();
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6986 if ( !s0.match( query_nodes ) ) {
6990 query_nodes = new HashSet<PhylogenyNode>();
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6993 if ( !s0.match( query_nodes ) ) {
6997 query_nodes = new HashSet<PhylogenyNode>();
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7003 if ( !s0.match( query_nodes ) ) {
7007 query_nodes = new HashSet<PhylogenyNode>();
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7010 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7011 if ( !s0.match( query_nodes ) ) {
7015 query_nodes = new HashSet<PhylogenyNode>();
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7019 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7020 if ( !s0.match( query_nodes ) ) {
7024 query_nodes = new HashSet<PhylogenyNode>();
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7027 if ( s0.match( query_nodes ) ) {
7031 query_nodes = new HashSet<PhylogenyNode>();
7032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7036 if ( s0.match( query_nodes ) ) {
7040 query_nodes = new HashSet<PhylogenyNode>();
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7046 if ( s0.match( query_nodes ) ) {
7050 query_nodes = new HashSet<PhylogenyNode>();
7051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7054 if ( s0.match( query_nodes ) ) {
7058 query_nodes = new HashSet<PhylogenyNode>();
7059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7061 if ( s0.match( query_nodes ) ) {
7065 query_nodes = new HashSet<PhylogenyNode>();
7066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7068 if ( s0.match( query_nodes ) ) {
7072 query_nodes = new HashSet<PhylogenyNode>();
7073 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7075 if ( s0.match( query_nodes ) ) {
7079 query_nodes = new HashSet<PhylogenyNode>();
7080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7082 if ( s0.match( query_nodes ) ) {
7086 query_nodes = new HashSet<PhylogenyNode>();
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7089 if ( s0.match( query_nodes ) ) {
7093 query_nodes = new HashSet<PhylogenyNode>();
7094 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7096 if ( s0.match( query_nodes ) ) {
7100 query_nodes = new HashSet<PhylogenyNode>();
7101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7104 if ( s0.match( query_nodes ) ) {
7108 query_nodes = new HashSet<PhylogenyNode>();
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7112 if ( s0.match( query_nodes ) ) {
7116 query_nodes = new HashSet<PhylogenyNode>();
7117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7120 if ( s0.match( query_nodes ) ) {
7124 query_nodes = new HashSet<PhylogenyNode>();
7125 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7126 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7129 if ( s0.match( query_nodes ) ) {
7133 catch ( final Exception e ) {
7134 e.printStackTrace();
7140 private static boolean testSubtreeDeletion() {
7142 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7143 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7144 t1.deleteSubtree( t1.getNode( "A" ), false );
7145 if ( t1.getNumberOfExternalNodes() != 5 ) {
7148 t1.toNewHampshireX();
7149 t1.deleteSubtree( t1.getNode( "E" ), false );
7150 if ( t1.getNumberOfExternalNodes() != 4 ) {
7153 t1.toNewHampshireX();
7154 t1.deleteSubtree( t1.getNode( "F" ), false );
7155 if ( t1.getNumberOfExternalNodes() != 3 ) {
7158 t1.toNewHampshireX();
7159 t1.deleteSubtree( t1.getNode( "D" ), false );
7160 t1.toNewHampshireX();
7161 if ( t1.getNumberOfExternalNodes() != 3 ) {
7164 t1.deleteSubtree( t1.getNode( "def" ), false );
7165 t1.toNewHampshireX();
7166 if ( t1.getNumberOfExternalNodes() != 2 ) {
7169 t1.deleteSubtree( t1.getNode( "B" ), false );
7170 t1.toNewHampshireX();
7171 if ( t1.getNumberOfExternalNodes() != 1 ) {
7174 t1.deleteSubtree( t1.getNode( "C" ), false );
7175 t1.toNewHampshireX();
7176 if ( t1.getNumberOfExternalNodes() != 1 ) {
7179 t1.deleteSubtree( t1.getNode( "abc" ), false );
7180 t1.toNewHampshireX();
7181 if ( t1.getNumberOfExternalNodes() != 1 ) {
7184 t1.deleteSubtree( t1.getNode( "r" ), false );
7185 if ( t1.getNumberOfExternalNodes() != 0 ) {
7188 if ( !t1.isEmpty() ) {
7191 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7192 t2.deleteSubtree( t2.getNode( "A" ), false );
7193 t2.toNewHampshireX();
7194 if ( t2.getNumberOfExternalNodes() != 5 ) {
7197 t2.deleteSubtree( t2.getNode( "abc" ), false );
7198 t2.toNewHampshireX();
7199 if ( t2.getNumberOfExternalNodes() != 3 ) {
7202 t2.deleteSubtree( t2.getNode( "def" ), false );
7203 t2.toNewHampshireX();
7204 if ( t2.getNumberOfExternalNodes() != 1 ) {
7208 catch ( final Exception e ) {
7209 e.printStackTrace( System.out );
7215 private static boolean testSupportCount() {
7217 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7218 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7219 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7220 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7221 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7222 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7223 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7225 SupportCount.count( t0_1, phylogenies_1, true, false );
7226 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7227 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7228 + "(((((A,B),C),D),E),((F,G),X))"
7229 + "(((((A,Y),B),C),D),((F,G),E))"
7230 + "(((((A,B),C),D),E),(F,G))"
7231 + "(((((A,B),C),D),E),(F,G))"
7232 + "(((((A,B),C),D),E),(F,G))"
7233 + "(((((A,B),C),D),E),(F,G),Z)"
7234 + "(((((A,B),C),D),E),(F,G))"
7235 + "((((((A,B),C),D),E),F),G)"
7236 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7238 SupportCount.count( t0_2, phylogenies_2, true, false );
7239 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7240 while ( it.hasNext() ) {
7241 final PhylogenyNode n = it.next();
7242 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7246 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7247 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7248 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7249 SupportCount.count( t0_3, phylogenies_3, true, false );
7250 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7251 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7254 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7257 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7260 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7263 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7266 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7269 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7272 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7275 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7278 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7281 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7282 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7283 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7284 SupportCount.count( t0_4, phylogenies_4, true, false );
7285 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7286 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7289 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7292 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7295 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7298 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7301 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7304 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7307 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7310 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7313 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7316 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7317 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7318 double d = SupportCount.compare( b1, a, true, true, true );
7319 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7322 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7323 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7324 d = SupportCount.compare( b2, a, true, true, true );
7325 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7328 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7329 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7330 d = SupportCount.compare( b3, a, true, true, true );
7331 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7334 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7335 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7336 d = SupportCount.compare( b4, a, true, true, false );
7337 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7341 catch ( final Exception e ) {
7342 e.printStackTrace( System.out );
7348 private static boolean testSupportTransfer() {
7350 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7351 final Phylogeny p1 = factory.create( "(((A,B)ab:97,C)abc:57,((D,E)de:10,(F,G)fg:50,(H,I)hi:64)defghi)",
7352 new NHXParser() )[ 0 ];
7353 final Phylogeny p2 = factory
7354 .create( "(((A:0.1,B:0.3)ab:0.4,C)abc:0.5,((D,E)de,(F,G)fg,(H,I)hi:0.59)defghi)", new NHXParser() )[ 0 ];
7355 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7358 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7361 support_transfer.moveBranchLengthsToBootstrap( p1 );
7362 support_transfer.transferSupportValues( p1, p2 );
7363 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7366 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7369 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7372 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7375 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7378 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7381 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7384 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7388 catch ( final Exception e ) {
7389 e.printStackTrace( System.out );
7395 private static boolean testTaxonomyAssigner() {
7397 String s0_str = "(((([&&NHX:S=A],[&&NHX:S=B])[&&NHX:S=AB],[&&NHX:S=C])[&&NHX:S=ABC],[&&NHX:S=D])[&&NHX:S=ABCD],[&&NHX:S=E])[&&NHX:S=ABCDE]";
7398 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7399 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7400 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7401 s0.setRooted( true );
7402 g0.setRooted( true );
7403 TaxonomyAssigner.execute( g0, s0 );
7404 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7407 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7410 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7413 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7414 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7415 g0.setRooted( true );
7416 TaxonomyAssigner.execute( g0, s0 );
7417 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7420 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7423 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7426 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7427 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7428 g0.setRooted( true );
7429 TaxonomyAssigner.execute( g0, s0 );
7430 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7433 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7436 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7439 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7440 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7441 g0.setRooted( true );
7442 TaxonomyAssigner.execute( g0, s0 );
7443 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7446 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7449 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7452 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7453 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7454 g0.setRooted( true );
7455 TaxonomyAssigner.execute( g0, s0 );
7456 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7459 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7462 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7465 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7466 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7467 g0.setRooted( true );
7468 TaxonomyAssigner.execute( g0, s0 );
7469 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7472 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7475 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7478 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7479 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7480 g0.setRooted( true );
7481 TaxonomyAssigner.execute( g0, s0 );
7482 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7485 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7488 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7491 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7492 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7493 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7494 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7495 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7496 s0.setRooted( true );
7497 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7498 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7499 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7500 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7501 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7502 g0.setRooted( true );
7503 TaxonomyAssigner.execute( g0, s0 );
7504 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7507 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7510 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7513 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7516 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7519 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7520 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7521 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7522 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7523 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7524 g0.setRooted( true );
7525 TaxonomyAssigner.execute( g0, s0 );
7526 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7529 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7532 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7535 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7538 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7541 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7542 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7543 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7544 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7545 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7546 g0.setRooted( true );
7547 TaxonomyAssigner.execute( g0, s0 );
7548 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7551 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7554 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7557 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7560 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7563 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7564 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7565 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7566 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7567 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7568 g0.setRooted( true );
7569 TaxonomyAssigner.execute( g0, s0 );
7570 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7573 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7576 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7579 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7582 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7585 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7586 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7587 g0.setRooted( true );
7588 TaxonomyAssigner.execute( g0, s0 );
7589 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7592 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7595 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7598 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7599 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7600 g0.setRooted( true );
7601 TaxonomyAssigner.execute( g0, s0 );
7602 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7605 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7608 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7611 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7612 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7613 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7614 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7615 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7616 g0.setRooted( true );
7617 TaxonomyAssigner.execute( g0, s0 );
7618 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7621 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7624 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7627 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7630 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7633 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7636 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7639 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7640 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7641 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7642 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7643 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7644 g0.setRooted( true );
7645 TaxonomyAssigner.execute( g0, s0 );
7646 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7649 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7652 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7655 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7658 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7661 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7664 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7667 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7668 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7669 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7670 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7671 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7672 g0.setRooted( true );
7673 TaxonomyAssigner.execute( g0, s0 );
7674 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7677 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7680 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7683 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7686 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7689 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7692 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7695 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7696 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7697 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7698 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7699 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7700 g0.setRooted( true );
7701 TaxonomyAssigner.execute( g0, s0 );
7702 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7705 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7708 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7711 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7714 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7717 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7720 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7723 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7724 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7725 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7726 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7727 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7728 s0.setRooted( true );
7729 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7730 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7731 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7732 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7733 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7734 g0.setRooted( true );
7735 TaxonomyAssigner.execute( g0, s0 );
7736 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7739 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7743 catch ( final Exception e ) {
7744 e.printStackTrace( System.out );
7750 private static boolean testUniprotTaxonomySearch() {
7752 List<UniProtTaxonomy> results = UniProtWsTools
7753 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7754 if ( results.size() != 1 ) {
7757 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7760 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7763 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7766 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7769 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7773 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7774 if ( results.size() != 1 ) {
7777 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7780 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7783 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7786 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7789 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7793 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7794 if ( results.size() != 1 ) {
7797 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7800 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7803 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7806 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7809 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7813 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7814 if ( results.size() != 1 ) {
7817 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7820 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7823 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7826 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7829 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7832 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7835 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7838 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7839 .equals( "Nematostella vectensis" ) ) {
7840 System.out.println( results.get( 0 ).getLineage() );
7844 catch ( final IOException e ) {
7845 System.out.println();
7846 System.out.println( "the following might be due to absence internet connection:" );
7847 e.printStackTrace( System.out );
7850 catch ( final Exception e ) {
7856 private static boolean testEmblEntryRetrieval() {
7857 //The format for GenBank Accession numbers are:
7858 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7859 //Protein: 3 letters + 5 numerals
7860 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7861 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7864 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7867 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7870 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7873 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7876 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7879 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7882 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7885 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7888 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7891 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7894 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7897 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7903 private static boolean testUniprotEntryRetrieval() {
7904 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7907 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7910 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7913 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7916 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7919 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7922 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7925 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7928 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7931 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7934 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7937 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7940 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7944 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7945 if ( !entry.getAccession().equals( "P12345" ) ) {
7948 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7951 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7954 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7957 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7961 catch ( final IOException e ) {
7962 System.out.println();
7963 System.out.println( "the following might be due to absence internet connection:" );
7964 e.printStackTrace( System.out );
7967 catch ( final Exception e ) {
7973 private static boolean testWabiTxSearch() {
7976 result = TxSearch.searchSimple( "nematostella" );
7977 result = TxSearch.getTxId( "nematostella" );
7978 if ( !result.equals( "45350" ) ) {
7981 result = TxSearch.getTxName( "45350" );
7982 if ( !result.equals( "Nematostella" ) ) {
7985 result = TxSearch.getTxId( "nematostella vectensis" );
7986 if ( !result.equals( "45351" ) ) {
7989 result = TxSearch.getTxName( "45351" );
7990 if ( !result.equals( "Nematostella vectensis" ) ) {
7993 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7994 if ( !result.equals( "536089" ) ) {
7997 result = TxSearch.getTxName( "536089" );
7998 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8001 final List<String> queries = new ArrayList<String>();
8002 queries.add( "Campylobacter coli" );
8003 queries.add( "Escherichia coli" );
8004 queries.add( "Arabidopsis" );
8005 queries.add( "Trichoplax" );
8006 queries.add( "Samanea saman" );
8007 queries.add( "Kluyveromyces marxianus" );
8008 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8009 queries.add( "Bornavirus parrot/PDD/2008" );
8010 final List<RANKS> ranks = new ArrayList<RANKS>();
8011 ranks.add( RANKS.SUPERKINGDOM );
8012 ranks.add( RANKS.KINGDOM );
8013 ranks.add( RANKS.FAMILY );
8014 ranks.add( RANKS.GENUS );
8015 ranks.add( RANKS.TRIBE );
8016 result = TxSearch.searchLineage( queries, ranks );
8017 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8018 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8020 catch ( final Exception e ) {
8021 System.out.println();
8022 System.out.println( "the following might be due to absence internet connection:" );
8023 e.printStackTrace( System.out );
8029 private static boolean testAminoAcidSequence() {
8031 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8032 if ( aa1.getLength() != 13 ) {
8035 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8038 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8041 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8044 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8045 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8048 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8049 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8052 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8053 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8057 catch ( final Exception e ) {
8058 e.printStackTrace();
8064 private static boolean testCreateBalancedPhylogeny() {
8066 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8067 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8070 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8073 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8074 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8077 if ( p1.getNumberOfExternalNodes() != 100 ) {
8081 catch ( final Exception e ) {
8082 e.printStackTrace();
8088 private static boolean testFastaParser() {
8090 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8093 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8096 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8097 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8100 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8103 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8106 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8109 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8112 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8116 catch ( final Exception e ) {
8117 e.printStackTrace();
8123 private static boolean testGeneralMsaParser() {
8125 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8126 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8127 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
8128 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8129 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8130 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8131 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8132 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8133 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8134 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8137 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8140 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8143 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8144 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8147 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8150 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8153 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8154 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8157 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8160 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8164 catch ( final Exception e ) {
8165 e.printStackTrace();
8171 private static boolean testMafft() {
8173 final List<String> opts = new ArrayList<String>();
8174 opts.add( "--maxiterate" );
8176 opts.add( "--localpair" );
8177 opts.add( "--quiet" );
8179 final MsaInferrer mafft = Mafft.createInstance();
8180 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
8181 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8185 catch ( final Exception e ) {
8186 e.printStackTrace( System.out );
8192 private static boolean testNextNodeWithCollapsing() {
8194 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8196 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8197 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8198 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8199 t0.getNode( "cd" ).setCollapse( true );
8200 t0.getNode( "cde" ).setCollapse( true );
8201 n = t0.getFirstExternalNode();
8202 while ( n != null ) {
8204 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8206 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8209 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8212 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8215 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8218 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8221 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8225 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8226 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8227 t1.getNode( "ab" ).setCollapse( true );
8228 t1.getNode( "cd" ).setCollapse( true );
8229 t1.getNode( "cde" ).setCollapse( true );
8230 n = t1.getNode( "ab" );
8231 ext = new ArrayList<PhylogenyNode>();
8232 while ( n != null ) {
8234 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8236 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8239 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8242 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8245 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8248 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8254 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8255 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8256 t2.getNode( "ab" ).setCollapse( true );
8257 t2.getNode( "cd" ).setCollapse( true );
8258 t2.getNode( "cde" ).setCollapse( true );
8259 t2.getNode( "c" ).setCollapse( true );
8260 t2.getNode( "d" ).setCollapse( true );
8261 t2.getNode( "e" ).setCollapse( true );
8262 t2.getNode( "gh" ).setCollapse( true );
8263 n = t2.getNode( "ab" );
8264 ext = new ArrayList<PhylogenyNode>();
8265 while ( n != null ) {
8267 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8269 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8272 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8275 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8278 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8284 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8285 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8286 t3.getNode( "ab" ).setCollapse( true );
8287 t3.getNode( "cd" ).setCollapse( true );
8288 t3.getNode( "cde" ).setCollapse( true );
8289 t3.getNode( "c" ).setCollapse( true );
8290 t3.getNode( "d" ).setCollapse( true );
8291 t3.getNode( "e" ).setCollapse( true );
8292 t3.getNode( "gh" ).setCollapse( true );
8293 t3.getNode( "fgh" ).setCollapse( true );
8294 n = t3.getNode( "ab" );
8295 ext = new ArrayList<PhylogenyNode>();
8296 while ( n != null ) {
8298 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8300 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8303 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8306 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8312 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8313 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8314 t4.getNode( "ab" ).setCollapse( true );
8315 t4.getNode( "cd" ).setCollapse( true );
8316 t4.getNode( "cde" ).setCollapse( true );
8317 t4.getNode( "c" ).setCollapse( true );
8318 t4.getNode( "d" ).setCollapse( true );
8319 t4.getNode( "e" ).setCollapse( true );
8320 t4.getNode( "gh" ).setCollapse( true );
8321 t4.getNode( "fgh" ).setCollapse( true );
8322 t4.getNode( "abcdefgh" ).setCollapse( true );
8323 n = t4.getNode( "abcdefgh" );
8324 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8329 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8330 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8332 n = t5.getFirstExternalNode();
8333 while ( n != null ) {
8335 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8337 if ( ext.size() != 8 ) {
8340 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8343 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8346 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8349 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8352 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8355 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8358 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8361 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8366 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8367 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8369 t6.getNode( "ab" ).setCollapse( true );
8370 n = t6.getNode( "ab" );
8371 while ( n != null ) {
8373 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8375 if ( ext.size() != 7 ) {
8378 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8381 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8384 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8387 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8390 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8393 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8396 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8401 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8402 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8404 t7.getNode( "cd" ).setCollapse( true );
8405 n = t7.getNode( "a" );
8406 while ( n != null ) {
8408 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8410 if ( ext.size() != 7 ) {
8413 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8416 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8419 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8422 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8425 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8428 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8431 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8436 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8437 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8439 t8.getNode( "cd" ).setCollapse( true );
8440 t8.getNode( "c" ).setCollapse( true );
8441 t8.getNode( "d" ).setCollapse( true );
8442 n = t8.getNode( "a" );
8443 while ( n != null ) {
8445 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8447 if ( ext.size() != 7 ) {
8450 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8453 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8456 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8457 System.out.println( "2 fail" );
8460 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8463 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8466 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8469 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8474 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8475 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8477 t9.getNode( "gh" ).setCollapse( true );
8478 n = t9.getNode( "a" );
8479 while ( n != null ) {
8481 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8483 if ( ext.size() != 7 ) {
8486 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8489 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8492 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8495 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8498 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8501 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8504 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8509 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8510 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8512 t10.getNode( "gh" ).setCollapse( true );
8513 t10.getNode( "g" ).setCollapse( true );
8514 t10.getNode( "h" ).setCollapse( true );
8515 n = t10.getNode( "a" );
8516 while ( n != null ) {
8518 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8520 if ( ext.size() != 7 ) {
8523 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8526 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8529 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8532 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8535 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8538 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8541 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8546 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8547 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8549 t11.getNode( "gh" ).setCollapse( true );
8550 t11.getNode( "fgh" ).setCollapse( true );
8551 n = t11.getNode( "a" );
8552 while ( n != null ) {
8554 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8556 if ( ext.size() != 6 ) {
8559 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8562 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8565 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8568 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8571 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8574 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8579 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8580 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8582 t12.getNode( "gh" ).setCollapse( true );
8583 t12.getNode( "fgh" ).setCollapse( true );
8584 t12.getNode( "g" ).setCollapse( true );
8585 t12.getNode( "h" ).setCollapse( true );
8586 t12.getNode( "f" ).setCollapse( true );
8587 n = t12.getNode( "a" );
8588 while ( n != null ) {
8590 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8592 if ( ext.size() != 6 ) {
8595 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8598 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8601 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8604 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8607 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8610 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8615 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8616 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8618 t13.getNode( "ab" ).setCollapse( true );
8619 t13.getNode( "b" ).setCollapse( true );
8620 t13.getNode( "fgh" ).setCollapse( true );
8621 t13.getNode( "gh" ).setCollapse( true );
8622 n = t13.getNode( "ab" );
8623 while ( n != null ) {
8625 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8627 if ( ext.size() != 5 ) {
8630 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8633 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8636 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8639 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8642 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8647 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8648 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8650 t14.getNode( "ab" ).setCollapse( true );
8651 t14.getNode( "a" ).setCollapse( true );
8652 t14.getNode( "fgh" ).setCollapse( true );
8653 t14.getNode( "gh" ).setCollapse( true );
8654 n = t14.getNode( "ab" );
8655 while ( n != null ) {
8657 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8659 if ( ext.size() != 5 ) {
8662 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8665 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8668 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8671 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8674 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8679 final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8680 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8682 t15.getNode( "ab" ).setCollapse( true );
8683 t15.getNode( "a" ).setCollapse( true );
8684 t15.getNode( "fgh" ).setCollapse( true );
8685 t15.getNode( "gh" ).setCollapse( true );
8686 n = t15.getNode( "ab" );
8687 while ( n != null ) {
8689 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8691 if ( ext.size() != 6 ) {
8694 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8697 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8700 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8703 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8706 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8709 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8714 final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8715 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8717 t16.getNode( "ab" ).setCollapse( true );
8718 t16.getNode( "a" ).setCollapse( true );
8719 t16.getNode( "fgh" ).setCollapse( true );
8720 t16.getNode( "gh" ).setCollapse( true );
8721 t16.getNode( "cd" ).setCollapse( true );
8722 t16.getNode( "cde" ).setCollapse( true );
8723 t16.getNode( "d" ).setCollapse( true );
8724 t16.getNode( "x" ).setCollapse( true );
8725 n = t16.getNode( "ab" );
8726 while ( n != null ) {
8728 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8730 if ( ext.size() != 4 ) {
8733 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8736 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8739 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8742 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8746 catch ( final Exception e ) {
8747 e.printStackTrace( System.out );