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.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
56 import org.forester.io.parsers.tol.TolParser;
57 import org.forester.io.parsers.util.ParserUtils;
58 import org.forester.io.writers.PhylogenyWriter;
59 import org.forester.msa.BasicMsa;
60 import org.forester.msa.Mafft;
61 import org.forester.msa.Msa;
62 import org.forester.msa.MsaInferrer;
63 import org.forester.msa.MsaMethods;
64 import org.forester.pccx.TestPccx;
65 import org.forester.phylogeny.Phylogeny;
66 import org.forester.phylogeny.PhylogenyBranch;
67 import org.forester.phylogeny.PhylogenyMethods;
68 import org.forester.phylogeny.PhylogenyNode;
69 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
70 import org.forester.phylogeny.data.BinaryCharacters;
71 import org.forester.phylogeny.data.BranchWidth;
72 import org.forester.phylogeny.data.Confidence;
73 import org.forester.phylogeny.data.Distribution;
74 import org.forester.phylogeny.data.DomainArchitecture;
75 import org.forester.phylogeny.data.Event;
76 import org.forester.phylogeny.data.Identifier;
77 import org.forester.phylogeny.data.PhylogenyData;
78 import org.forester.phylogeny.data.PhylogenyDataUtil;
79 import org.forester.phylogeny.data.Polygon;
80 import org.forester.phylogeny.data.PropertiesMap;
81 import org.forester.phylogeny.data.Property;
82 import org.forester.phylogeny.data.Property.AppliesTo;
83 import org.forester.phylogeny.data.ProteinDomain;
84 import org.forester.phylogeny.data.Taxonomy;
85 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
86 import org.forester.phylogeny.factories.PhylogenyFactory;
87 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
88 import org.forester.protein.Protein;
89 import org.forester.rio.TestRIO;
90 import org.forester.sdi.SDI;
91 import org.forester.sdi.SDIR;
92 import org.forester.sdi.TestGSDI;
93 import org.forester.sequence.BasicSequence;
94 import org.forester.sequence.Sequence;
95 import org.forester.surfacing.TestSurfacing;
96 import org.forester.tools.ConfidenceAssessor;
97 import org.forester.tools.SupportCount;
98 import org.forester.tools.TreeSplitMatrix;
99 import org.forester.util.AsciiHistogram;
100 import org.forester.util.BasicDescriptiveStatistics;
101 import org.forester.util.BasicTable;
102 import org.forester.util.BasicTableParser;
103 import org.forester.util.DescriptiveStatistics;
104 import org.forester.util.ForesterConstants;
105 import org.forester.util.ForesterUtil;
106 import org.forester.util.GeneralTable;
107 import org.forester.util.SequenceIdParser;
108 import org.forester.ws.seqdb.SequenceDatabaseEntry;
109 import org.forester.ws.seqdb.SequenceDbWsTools;
110 import org.forester.ws.seqdb.UniProtTaxonomy;
111 import org.forester.ws.wabi.TxSearch;
112 import org.forester.ws.wabi.TxSearch.RANKS;
113 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
114 import org.forester.ws.wabi.TxSearch.TAX_RANK;
116 @SuppressWarnings( "unused")
117 public final class Test {
119 private final static double ZERO_DIFF = 1.0E-9;
120 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "test_data"
122 + ForesterUtil.getFileSeparator();
123 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "resources"
125 + ForesterUtil.getFileSeparator();
126 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
127 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
130 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
134 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
135 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
139 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
140 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
143 public static boolean isEqual( final double a, final double b ) {
144 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
147 public static void main( final String[] args ) {
148 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
149 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
151 Locale.setDefault( Locale.US );
152 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
155 System.out.print( "[Test if directory with files for testing exists/is readable: " );
156 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
157 System.out.println( "OK.]" );
160 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
161 System.out.println( "Testing aborted." );
164 System.out.print( "[Test if resources directory exists/is readable: " );
165 if ( testDir( PATH_TO_RESOURCES ) ) {
166 System.out.println( "OK.]" );
169 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
170 System.out.println( "Testing aborted." );
173 final long start_time = new Date().getTime();
174 System.out.print( "Sequence id parsing: " );
175 if ( testSequenceIdParsing() ) {
176 System.out.println( "OK." );
180 System.out.println( "failed." );
183 System.out.print( "Hmmscan output parser: " );
184 if ( testHmmscanOutputParser() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node methods: " );
193 if ( Test.testBasicNodeMethods() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "Taxonomy code extraction: " );
202 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "Taxonomy extraction (general): " );
211 if ( Test.testTaxonomyExtraction() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "Basic node construction and parsing of NHX (node level): " );
220 if ( Test.testNHXNodeParsing() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NH parsing: " );
229 if ( Test.testNHParsing() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
238 System.out.print( "Conversion to NHX (node level): " );
239 if ( Test.testNHXconversion() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "NHX parsing: " );
248 if ( Test.testNHXParsing() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "NHX parsing with quotes: " );
257 if ( Test.testNHXParsingQuotes() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "NHX parsing (MrBayes): " );
266 if ( Test.testNHXParsingMB() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "Nexus characters parsing: " );
275 if ( Test.testNexusCharactersParsing() ) {
276 System.out.println( "OK." );
280 System.out.println( "failed." );
283 System.out.print( "Nexus tree parsing: " );
284 if ( Test.testNexusTreeParsing() ) {
285 System.out.println( "OK." );
289 System.out.println( "failed." );
292 System.out.print( "Nexus tree parsing (translating): " );
293 if ( Test.testNexusTreeParsingTranslating() ) {
294 System.out.println( "OK." );
298 System.out.println( "failed." );
301 System.out.print( "Nexus matrix parsing: " );
302 if ( Test.testNexusMatrixParsing() ) {
303 System.out.println( "OK." );
307 System.out.println( "failed." );
310 System.out.print( "Basic phyloXML parsing: " );
311 if ( Test.testBasicPhyloXMLparsing() ) {
312 System.out.println( "OK." );
316 System.out.println( "failed." );
319 System.out.print( "Basic phyloXML parsing (validating against schema): " );
320 if ( testBasicPhyloXMLparsingValidating() ) {
321 System.out.println( "OK." );
325 System.out.println( "failed." );
328 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
329 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
330 System.out.println( "OK." );
334 System.out.println( "failed." );
337 System.out.print( "phyloXML Distribution Element: " );
338 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
339 System.out.println( "OK." );
343 System.out.println( "failed." );
346 System.out.print( "Tol XML parsing: " );
347 if ( Test.testBasicTolXMLparsing() ) {
348 System.out.println( "OK." );
352 System.out.println( "failed." );
355 System.out.print( "Copying of node data: " );
356 if ( Test.testCopyOfNodeData() ) {
357 System.out.println( "OK." );
361 System.out.println( "failed." );
364 System.out.print( "Basic tree methods: " );
365 if ( Test.testBasicTreeMethods() ) {
366 System.out.println( "OK." );
370 System.out.println( "failed." );
373 System.out.print( "Postorder Iterator: " );
374 if ( Test.testPostOrderIterator() ) {
375 System.out.println( "OK." );
379 System.out.println( "failed." );
382 System.out.print( "Preorder Iterator: " );
383 if ( Test.testPreOrderIterator() ) {
384 System.out.println( "OK." );
388 System.out.println( "failed." );
391 System.out.print( "Levelorder Iterator: " );
392 if ( Test.testLevelOrderIterator() ) {
393 System.out.println( "OK." );
397 System.out.println( "failed." );
400 System.out.print( "Re-id methods: " );
401 if ( Test.testReIdMethods() ) {
402 System.out.println( "OK." );
406 System.out.println( "failed." );
409 System.out.print( "Methods on last external nodes: " );
410 if ( Test.testLastExternalNodeMethods() ) {
411 System.out.println( "OK." );
415 System.out.println( "failed." );
418 System.out.print( "Methods on external nodes: " );
419 if ( Test.testExternalNodeRelatedMethods() ) {
420 System.out.println( "OK." );
424 System.out.println( "failed." );
427 System.out.print( "Deletion of external nodes: " );
428 if ( Test.testDeletionOfExternalNodes() ) {
429 System.out.println( "OK." );
433 System.out.println( "failed." );
436 System.out.print( "Subtree deletion: " );
437 if ( Test.testSubtreeDeletion() ) {
438 System.out.println( "OK." );
442 System.out.println( "failed." );
445 System.out.print( "Phylogeny branch: " );
446 if ( Test.testPhylogenyBranch() ) {
447 System.out.println( "OK." );
451 System.out.println( "failed." );
454 System.out.print( "Rerooting: " );
455 if ( Test.testRerooting() ) {
456 System.out.println( "OK." );
460 System.out.println( "failed." );
463 System.out.print( "Mipoint rooting: " );
464 if ( Test.testMidpointrooting() ) {
465 System.out.println( "OK." );
469 System.out.println( "failed." );
472 System.out.print( "Node removal: " );
473 if ( Test.testNodeRemoval() ) {
474 System.out.println( "OK." );
478 System.out.println( "failed." );
481 System.out.print( "Support count: " );
482 if ( Test.testSupportCount() ) {
483 System.out.println( "OK." );
487 System.out.println( "failed." );
490 System.out.print( "Support transfer: " );
491 if ( Test.testSupportTransfer() ) {
492 System.out.println( "OK." );
496 System.out.println( "failed." );
499 System.out.print( "Finding of LCA: " );
500 if ( Test.testGetLCA() ) {
501 System.out.println( "OK." );
505 System.out.println( "failed." );
508 System.out.print( "Finding of LCA 2: " );
509 if ( Test.testGetLCA2() ) {
510 System.out.println( "OK." );
514 System.out.println( "failed." );
517 System.out.print( "Calculation of distance between nodes: " );
518 if ( Test.testGetDistance() ) {
519 System.out.println( "OK." );
523 System.out.println( "failed." );
526 System.out.print( "Descriptive statistics: " );
527 if ( Test.testDescriptiveStatistics() ) {
528 System.out.println( "OK." );
532 System.out.println( "failed." );
535 System.out.print( "Data objects and methods: " );
536 if ( Test.testDataObjects() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
544 System.out.print( "Properties map: " );
545 if ( Test.testPropertiesMap() ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "SDIse: " );
554 if ( Test.testSDIse() ) {
555 System.out.println( "OK." );
559 System.out.println( "failed." );
562 System.out.print( "SDIunrooted: " );
563 if ( Test.testSDIunrooted() ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "GSDI: " );
572 if ( TestGSDI.test() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "RIO: " );
581 if ( TestRIO.test() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "Phylogeny reconstruction:" );
590 System.out.println();
591 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
592 System.out.println( "OK." );
596 System.out.println( "failed." );
599 System.out.print( "Analysis of domain architectures: " );
600 System.out.println();
601 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
602 System.out.println( "OK." );
606 System.out.println( "failed." );
609 System.out.print( "GO: " );
610 System.out.println();
611 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
612 System.out.println( "OK." );
616 System.out.println( "failed." );
619 System.out.print( "Modeling tools: " );
620 if ( TestPccx.test() ) {
621 System.out.println( "OK." );
625 System.out.println( "failed." );
628 System.out.print( "Split Matrix strict: " );
629 if ( Test.testSplitStrict() ) {
630 System.out.println( "OK." );
634 System.out.println( "failed." );
637 System.out.print( "Split Matrix: " );
638 if ( Test.testSplit() ) {
639 System.out.println( "OK." );
643 System.out.println( "failed." );
646 System.out.print( "Confidence Assessor: " );
647 if ( Test.testConfidenceAssessor() ) {
648 System.out.println( "OK." );
652 System.out.println( "failed." );
655 System.out.print( "Basic table: " );
656 if ( Test.testBasicTable() ) {
657 System.out.println( "OK." );
661 System.out.println( "failed." );
664 System.out.print( "General table: " );
665 if ( Test.testGeneralTable() ) {
666 System.out.println( "OK." );
670 System.out.println( "failed." );
673 System.out.print( "Amino acid sequence: " );
674 if ( Test.testAminoAcidSequence() ) {
675 System.out.println( "OK." );
679 System.out.println( "failed." );
682 System.out.print( "General MSA parser: " );
683 if ( Test.testGeneralMsaParser() ) {
684 System.out.println( "OK." );
688 System.out.println( "failed." );
691 System.out.print( "Fasta parser for msa: " );
692 if ( Test.testFastaParser() ) {
693 System.out.println( "OK." );
697 System.out.println( "failed." );
700 System.out.print( "Creation of balanced phylogeny: " );
701 if ( Test.testCreateBalancedPhylogeny() ) {
702 System.out.println( "OK." );
706 System.out.println( "failed." );
709 System.out.print( "EMBL Entry Retrieval: " );
710 if ( Test.testEmblEntryRetrieval() ) {
711 System.out.println( "OK." );
715 System.out.println( "failed." );
718 System.out.print( "Uniprot Entry Retrieval: " );
719 if ( Test.testUniprotEntryRetrieval() ) {
720 System.out.println( "OK." );
724 System.out.println( "failed." );
727 System.out.print( "Uniprot Taxonomy Search: " );
728 if ( Test.testUniprotTaxonomySearch() ) {
729 System.out.println( "OK." );
733 System.out.println( "failed." );
738 final String os = ForesterUtil.OS_NAME.toLowerCase();
739 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
740 path = "/usr/local/bin/mafft";
742 else if ( os.indexOf( "win" ) >= 0 ) {
743 path = "C:\\Program Files\\mafft-win\\mafft.bat";
746 path = "/home/czmasek/bin/mafft";
748 if ( !MsaInferrer.isInstalled( path ) ) {
751 if ( !MsaInferrer.isInstalled( path ) ) {
752 path = "/usr/local/bin/mafft";
754 if ( MsaInferrer.isInstalled( path ) ) {
755 System.out.print( "MAFFT (external program): " );
756 if ( Test.testMafft( path ) ) {
757 System.out.println( "OK." );
761 System.out.println( "failed [will not count towards failed tests]" );
765 System.out.print( "Next nodes with collapsed: " );
766 if ( Test.testNextNodeWithCollapsing() ) {
767 System.out.println( "OK." );
771 System.out.println( "failed." );
774 System.out.print( "Simple MSA quality: " );
775 if ( Test.testMsaQualityMethod() ) {
776 System.out.println( "OK." );
780 System.out.println( "failed." );
783 System.out.println();
784 final Runtime rt = java.lang.Runtime.getRuntime();
785 final long free_memory = rt.freeMemory() / 1000000;
786 final long total_memory = rt.totalMemory() / 1000000;
787 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
788 + free_memory + "MB, total memory: " + total_memory + "MB)" );
789 System.out.println();
790 System.out.println( "Successful tests: " + succeeded );
791 System.out.println( "Failed tests: " + failed );
792 System.out.println();
794 System.out.println( "OK." );
797 System.out.println( "Not OK." );
801 private static boolean testExtractTaxonomyCodeFromNodeName() {
803 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
806 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
809 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
812 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
813 .equals( "MOUSE" ) ) {
816 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
817 .equals( "MOUSE" ) ) {
820 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
821 .equals( "MOUSE" ) ) {
824 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
827 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
830 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
834 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
838 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
842 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
845 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
848 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
851 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
855 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
856 .equals( "MOUSE" ) ) {
859 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
860 .equals( "MOUSE" ) ) {
864 catch ( final Exception e ) {
865 e.printStackTrace( System.out );
871 private static boolean testBasicNodeMethods() {
873 if ( PhylogenyNode.getNodeCount() != 0 ) {
876 final PhylogenyNode n1 = new PhylogenyNode();
877 final PhylogenyNode n2 = PhylogenyNode
878 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
879 final PhylogenyNode n3 = PhylogenyNode
880 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
881 final PhylogenyNode n4 = PhylogenyNode
882 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
883 if ( n1.isHasAssignedEvent() ) {
886 if ( PhylogenyNode.getNodeCount() != 4 ) {
889 if ( n3.getIndicator() != 0 ) {
892 if ( n3.getNumberOfExternalNodes() != 1 ) {
895 if ( !n3.isExternal() ) {
898 if ( !n3.isRoot() ) {
901 if ( !n4.getName().equals( "n4" ) ) {
905 catch ( final Exception e ) {
906 e.printStackTrace( System.out );
912 private static boolean testBasicPhyloXMLparsing() {
914 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
915 final PhyloXmlParser xml_parser = new PhyloXmlParser();
916 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
918 if ( xml_parser.getErrorCount() > 0 ) {
919 System.out.println( xml_parser.getErrorMessages().toString() );
922 if ( phylogenies_0.length != 4 ) {
925 final Phylogeny t1 = phylogenies_0[ 0 ];
926 final Phylogeny t2 = phylogenies_0[ 1 ];
927 final Phylogeny t3 = phylogenies_0[ 2 ];
928 final Phylogeny t4 = phylogenies_0[ 3 ];
929 if ( t1.getNumberOfExternalNodes() != 1 ) {
932 if ( !t1.isRooted() ) {
935 if ( t1.isRerootable() ) {
938 if ( !t1.getType().equals( "gene_tree" ) ) {
941 if ( t2.getNumberOfExternalNodes() != 2 ) {
944 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
947 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
950 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
953 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
956 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
959 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
962 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
963 .startsWith( "actgtgggggt" ) ) {
966 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
967 .startsWith( "ctgtgatgcat" ) ) {
970 if ( t3.getNumberOfExternalNodes() != 4 ) {
973 if ( !t1.getName().equals( "t1" ) ) {
976 if ( !t2.getName().equals( "t2" ) ) {
979 if ( !t3.getName().equals( "t3" ) ) {
982 if ( !t4.getName().equals( "t4" ) ) {
985 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
988 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
991 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
994 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
995 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
998 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1001 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1004 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1007 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1008 .equals( "apoptosis" ) ) {
1011 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1012 .equals( "GO:0006915" ) ) {
1015 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1016 .equals( "UniProtKB" ) ) {
1019 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1020 .equals( "experimental" ) ) {
1023 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1024 .equals( "function" ) ) {
1027 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1028 .getValue() != 1 ) {
1031 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1032 .getType().equals( "ml" ) ) {
1035 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1036 .equals( "apoptosis" ) ) {
1039 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1040 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1043 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1044 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1047 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1048 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1051 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1052 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1055 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1056 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1059 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1060 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1063 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1064 .equals( "GO:0005829" ) ) {
1067 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1068 .equals( "intracellular organelle" ) ) {
1071 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1074 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1075 .equals( "UniProt link" ) ) ) {
1078 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1082 catch ( final Exception e ) {
1083 e.printStackTrace( System.out );
1089 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1091 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1092 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1093 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1094 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1097 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1099 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1101 if ( xml_parser.getErrorCount() > 0 ) {
1102 System.out.println( xml_parser.getErrorMessages().toString() );
1105 if ( phylogenies_0.length != 4 ) {
1108 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1109 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1110 if ( phylogenies_t1.length != 1 ) {
1113 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1114 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1117 if ( !t1_rt.isRooted() ) {
1120 if ( t1_rt.isRerootable() ) {
1123 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1126 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1127 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1128 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1129 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1132 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1135 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1138 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1141 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1142 .startsWith( "actgtgggggt" ) ) {
1145 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1146 .startsWith( "ctgtgatgcat" ) ) {
1149 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1150 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1151 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1152 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1153 if ( phylogenies_1.length != 1 ) {
1156 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1157 if ( !t3_rt.getName().equals( "t3" ) ) {
1160 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1163 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1166 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1169 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1172 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1173 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1176 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1179 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1182 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1183 .equals( "UniProtKB" ) ) {
1186 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1187 .equals( "apoptosis" ) ) {
1190 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1191 .equals( "GO:0006915" ) ) {
1194 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1195 .equals( "UniProtKB" ) ) {
1198 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1199 .equals( "experimental" ) ) {
1202 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1203 .equals( "function" ) ) {
1206 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1207 .getValue() != 1 ) {
1210 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1211 .getType().equals( "ml" ) ) {
1214 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1215 .equals( "apoptosis" ) ) {
1218 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1219 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1222 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1223 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1226 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1227 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1230 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1231 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1234 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1235 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1238 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1239 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1242 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1243 .equals( "GO:0005829" ) ) {
1246 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1247 .equals( "intracellular organelle" ) ) {
1250 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1253 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1254 .equals( "UniProt link" ) ) ) {
1257 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1260 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1264 .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." ) ) ) {
1267 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1270 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1273 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1276 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1279 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1280 .equals( "ncbi" ) ) {
1283 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1286 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1287 .getName().equals( "B" ) ) {
1290 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1291 .getFrom() != 21 ) {
1294 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1297 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1298 .getLength() != 24 ) {
1301 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1302 .getConfidence() != 2144 ) {
1305 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1306 .equals( "pfam" ) ) {
1309 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1312 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1315 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1318 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1321 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1322 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1325 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1328 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1331 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1334 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1337 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1340 if ( taxbb.getSynonyms().size() != 2 ) {
1343 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1346 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1349 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1352 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1355 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1358 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1359 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1363 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1366 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1369 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1372 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1375 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1378 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1381 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1385 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1388 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1389 .equalsIgnoreCase( "435" ) ) {
1392 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1395 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1396 .equalsIgnoreCase( "443.7" ) ) {
1399 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1402 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1405 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1406 .equalsIgnoreCase( "433" ) ) {
1410 catch ( final Exception e ) {
1411 e.printStackTrace( System.out );
1417 private static boolean testBasicPhyloXMLparsingValidating() {
1419 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1420 PhyloXmlParser xml_parser = null;
1422 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1424 catch ( final Exception e ) {
1425 // Do nothing -- means were not running from jar.
1427 if ( xml_parser == null ) {
1428 xml_parser = new PhyloXmlParser();
1429 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1430 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1433 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1436 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1438 if ( xml_parser.getErrorCount() > 0 ) {
1439 System.out.println( xml_parser.getErrorMessages().toString() );
1442 if ( phylogenies_0.length != 4 ) {
1445 final Phylogeny t1 = phylogenies_0[ 0 ];
1446 final Phylogeny t2 = phylogenies_0[ 1 ];
1447 final Phylogeny t3 = phylogenies_0[ 2 ];
1448 final Phylogeny t4 = phylogenies_0[ 3 ];
1449 if ( !t1.getName().equals( "t1" ) ) {
1452 if ( !t2.getName().equals( "t2" ) ) {
1455 if ( !t3.getName().equals( "t3" ) ) {
1458 if ( !t4.getName().equals( "t4" ) ) {
1461 if ( t1.getNumberOfExternalNodes() != 1 ) {
1464 if ( t2.getNumberOfExternalNodes() != 2 ) {
1467 if ( t3.getNumberOfExternalNodes() != 4 ) {
1470 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1471 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1472 if ( xml_parser.getErrorCount() > 0 ) {
1473 System.out.println( "errors:" );
1474 System.out.println( xml_parser.getErrorMessages().toString() );
1477 if ( phylogenies_1.length != 4 ) {
1480 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1482 if ( xml_parser.getErrorCount() > 0 ) {
1483 System.out.println( "errors:" );
1484 System.out.println( xml_parser.getErrorMessages().toString() );
1487 if ( phylogenies_2.length != 1 ) {
1490 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1493 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1495 if ( xml_parser.getErrorCount() > 0 ) {
1496 System.out.println( xml_parser.getErrorMessages().toString() );
1499 if ( phylogenies_3.length != 2 ) {
1502 final Phylogeny a = phylogenies_3[ 0 ];
1503 if ( !a.getName().equals( "tree 4" ) ) {
1506 if ( a.getNumberOfExternalNodes() != 3 ) {
1509 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1512 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1515 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1517 if ( xml_parser.getErrorCount() > 0 ) {
1518 System.out.println( xml_parser.getErrorMessages().toString() );
1521 if ( phylogenies_4.length != 1 ) {
1524 final Phylogeny s = phylogenies_4[ 0 ];
1525 if ( s.getNumberOfExternalNodes() != 6 ) {
1528 s.getNode( "first" );
1530 s.getNode( "\"<a'b&c'd\">\"" );
1531 s.getNode( "'''\"" );
1532 s.getNode( "\"\"\"" );
1533 s.getNode( "dick & doof" );
1535 catch ( final Exception e ) {
1536 e.printStackTrace( System.out );
1542 private static boolean testBasicTable() {
1544 final BasicTable<String> t0 = new BasicTable<String>();
1545 if ( t0.getNumberOfColumns() != 0 ) {
1548 if ( t0.getNumberOfRows() != 0 ) {
1551 t0.setValue( 3, 2, "23" );
1552 t0.setValue( 10, 1, "error" );
1553 t0.setValue( 10, 1, "110" );
1554 t0.setValue( 9, 1, "19" );
1555 t0.setValue( 1, 10, "101" );
1556 t0.setValue( 10, 10, "1010" );
1557 t0.setValue( 100, 10, "10100" );
1558 t0.setValue( 0, 0, "00" );
1559 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1562 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1565 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1568 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1571 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1574 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1577 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1580 if ( t0.getNumberOfColumns() != 101 ) {
1583 if ( t0.getNumberOfRows() != 11 ) {
1586 if ( t0.getValueAsString( 49, 4 ) != null ) {
1589 final String l = ForesterUtil.getLineSeparator();
1590 final StringBuffer source = new StringBuffer();
1591 source.append( "" + l );
1592 source.append( "# 1 1 1 1 1 1 1 1" + l );
1593 source.append( " 00 01 02 03" + l );
1594 source.append( " 10 11 12 13 " + l );
1595 source.append( "20 21 22 23 " + l );
1596 source.append( " 30 31 32 33" + l );
1597 source.append( "40 41 42 43" + l );
1598 source.append( " # 1 1 1 1 1 " + l );
1599 source.append( "50 51 52 53 54" + l );
1600 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1601 if ( t1.getNumberOfColumns() != 5 ) {
1604 if ( t1.getNumberOfRows() != 6 ) {
1607 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1610 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1613 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1616 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1619 final StringBuffer source1 = new StringBuffer();
1620 source1.append( "" + l );
1621 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1622 source1.append( " 00; 01 ;02;03" + l );
1623 source1.append( " 10; 11; 12; 13 " + l );
1624 source1.append( "20; 21; 22; 23 " + l );
1625 source1.append( " 30; 31; 32; 33" + l );
1626 source1.append( "40;41;42;43" + l );
1627 source1.append( " # 1 1 1 1 1 " + l );
1628 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1629 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1630 if ( t2.getNumberOfColumns() != 5 ) {
1633 if ( t2.getNumberOfRows() != 6 ) {
1636 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1639 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1642 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1645 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1648 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1651 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1654 final StringBuffer source2 = new StringBuffer();
1655 source2.append( "" + l );
1656 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1657 source2.append( " 00; 01 ;02;03" + l );
1658 source2.append( " 10; 11; 12; 13 " + l );
1659 source2.append( "20; 21; 22; 23 " + l );
1660 source2.append( " " + l );
1661 source2.append( " 30; 31; 32; 33" + l );
1662 source2.append( "40;41;42;43" + l );
1663 source2.append( " comment: 1 1 1 1 1 " + l );
1664 source2.append( ";;;50 ; 52; 53;;54 " + l );
1665 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1671 if ( tl.size() != 2 ) {
1674 final BasicTable<String> t3 = tl.get( 0 );
1675 final BasicTable<String> t4 = tl.get( 1 );
1676 if ( t3.getNumberOfColumns() != 4 ) {
1679 if ( t3.getNumberOfRows() != 3 ) {
1682 if ( t4.getNumberOfColumns() != 4 ) {
1685 if ( t4.getNumberOfRows() != 3 ) {
1688 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1691 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1695 catch ( final Exception e ) {
1696 e.printStackTrace( System.out );
1702 private static boolean testBasicTolXMLparsing() {
1704 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1705 final TolParser parser = new TolParser();
1706 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1707 if ( parser.getErrorCount() > 0 ) {
1708 System.out.println( parser.getErrorMessages().toString() );
1711 if ( phylogenies_0.length != 1 ) {
1714 final Phylogeny t1 = phylogenies_0[ 0 ];
1715 if ( t1.getNumberOfExternalNodes() != 5 ) {
1718 if ( !t1.isRooted() ) {
1721 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1724 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1727 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1730 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1733 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1734 if ( parser.getErrorCount() > 0 ) {
1735 System.out.println( parser.getErrorMessages().toString() );
1738 if ( phylogenies_1.length != 1 ) {
1741 final Phylogeny t2 = phylogenies_1[ 0 ];
1742 if ( t2.getNumberOfExternalNodes() != 664 ) {
1745 if ( !t2.isRooted() ) {
1748 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1751 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1754 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1757 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1760 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1763 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1764 .equals( "Aquifex" ) ) {
1767 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1768 if ( parser.getErrorCount() > 0 ) {
1769 System.out.println( parser.getErrorMessages().toString() );
1772 if ( phylogenies_2.length != 1 ) {
1775 final Phylogeny t3 = phylogenies_2[ 0 ];
1776 if ( t3.getNumberOfExternalNodes() != 184 ) {
1779 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1782 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1785 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1788 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1789 if ( parser.getErrorCount() > 0 ) {
1790 System.out.println( parser.getErrorMessages().toString() );
1793 if ( phylogenies_3.length != 1 ) {
1796 final Phylogeny t4 = phylogenies_3[ 0 ];
1797 if ( t4.getNumberOfExternalNodes() != 1 ) {
1800 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1803 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1806 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1809 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1810 if ( parser.getErrorCount() > 0 ) {
1811 System.out.println( parser.getErrorMessages().toString() );
1814 if ( phylogenies_4.length != 1 ) {
1817 final Phylogeny t5 = phylogenies_4[ 0 ];
1818 if ( t5.getNumberOfExternalNodes() != 13 ) {
1821 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1824 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1827 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1831 catch ( final Exception e ) {
1832 e.printStackTrace( System.out );
1838 private static boolean testBasicTreeMethods() {
1840 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1841 final Phylogeny t1 = factory.create();
1842 if ( !t1.isEmpty() ) {
1845 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1846 if ( t2.getNumberOfExternalNodes() != 4 ) {
1849 if ( t2.getHeight() != 8.5 ) {
1852 if ( !t2.isCompletelyBinary() ) {
1855 if ( t2.isEmpty() ) {
1858 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1859 if ( t3.getNumberOfExternalNodes() != 5 ) {
1862 if ( t3.getHeight() != 11 ) {
1865 if ( t3.isCompletelyBinary() ) {
1868 final PhylogenyNode n = t3.getNode( "ABC" );
1869 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 ];
1870 if ( t4.getNumberOfExternalNodes() != 9 ) {
1873 if ( t4.getHeight() != 11 ) {
1876 if ( t4.isCompletelyBinary() ) {
1879 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)" );
1880 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1881 if ( t5.getNumberOfExternalNodes() != 8 ) {
1884 if ( t5.getHeight() != 15 ) {
1887 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)" );
1888 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1889 if ( t6.getHeight() != 15 ) {
1892 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)" );
1893 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1894 if ( t7.getHeight() != 15 ) {
1897 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)" );
1898 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1899 if ( t8.getNumberOfExternalNodes() != 10 ) {
1902 if ( t8.getHeight() != 15 ) {
1905 final char[] a9 = new char[] {};
1906 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1907 if ( t9.getHeight() != 0 ) {
1910 final char[] a10 = new char[] { 'a', ':', '6' };
1911 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1912 if ( t10.getHeight() != 6 ) {
1916 catch ( final Exception e ) {
1917 e.printStackTrace( System.out );
1923 private static boolean testConfidenceAssessor() {
1925 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1926 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1927 final Phylogeny[] ev0 = factory
1928 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1930 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1931 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1934 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1937 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1938 final Phylogeny[] ev1 = factory
1939 .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)));",
1941 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1942 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1945 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1948 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1949 final Phylogeny[] ev_b = factory
1950 .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",
1952 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1953 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1956 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1960 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1961 final Phylogeny[] ev1x = factory
1962 .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)));",
1964 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1965 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1968 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1971 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1972 final Phylogeny[] ev_bx = factory
1973 .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",
1975 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1976 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1979 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1983 final Phylogeny[] t2 = factory
1984 .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);",
1986 final Phylogeny[] ev2 = factory
1987 .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);",
1989 for( final Phylogeny target : t2 ) {
1990 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
1993 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
1994 new NHXParser() )[ 0 ];
1995 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
1996 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
1997 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2000 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2003 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2007 catch ( final Exception e ) {
2008 e.printStackTrace();
2014 private static boolean testCopyOfNodeData() {
2016 final PhylogenyNode n1 = PhylogenyNode
2017 .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]" );
2018 final PhylogenyNode n2 = n1.copyNodeData();
2019 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2023 catch ( final Exception e ) {
2024 e.printStackTrace();
2030 private static boolean testDataObjects() {
2032 final Confidence s0 = new Confidence();
2033 final Confidence s1 = new Confidence();
2034 if ( !s0.isEqual( s1 ) ) {
2037 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2038 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2039 if ( s2.isEqual( s1 ) ) {
2042 if ( !s2.isEqual( s3 ) ) {
2045 final Confidence s4 = ( Confidence ) s3.copy();
2046 if ( !s4.isEqual( s3 ) ) {
2053 final Taxonomy t1 = new Taxonomy();
2054 final Taxonomy t2 = new Taxonomy();
2055 final Taxonomy t3 = new Taxonomy();
2056 final Taxonomy t4 = new Taxonomy();
2057 final Taxonomy t5 = new Taxonomy();
2058 t1.setIdentifier( new Identifier( "ecoli" ) );
2059 t1.setTaxonomyCode( "ECOLI" );
2060 t1.setScientificName( "E. coli" );
2061 t1.setCommonName( "coli" );
2062 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2063 if ( !t1.isEqual( t0 ) ) {
2066 t2.setIdentifier( new Identifier( "ecoli" ) );
2067 t2.setTaxonomyCode( "OTHER" );
2068 t2.setScientificName( "what" );
2069 t2.setCommonName( "something" );
2070 if ( !t1.isEqual( t2 ) ) {
2073 t2.setIdentifier( new Identifier( "nemve" ) );
2074 if ( t1.isEqual( t2 ) ) {
2077 t1.setIdentifier( null );
2078 t3.setTaxonomyCode( "ECOLI" );
2079 t3.setScientificName( "what" );
2080 t3.setCommonName( "something" );
2081 if ( !t1.isEqual( t3 ) ) {
2084 t1.setIdentifier( null );
2085 t1.setTaxonomyCode( "" );
2086 t4.setScientificName( "E. ColI" );
2087 t4.setCommonName( "something" );
2088 if ( !t1.isEqual( t4 ) ) {
2091 t4.setScientificName( "B. subtilis" );
2092 t4.setCommonName( "something" );
2093 if ( t1.isEqual( t4 ) ) {
2096 t1.setIdentifier( null );
2097 t1.setTaxonomyCode( "" );
2098 t1.setScientificName( "" );
2099 t5.setCommonName( "COLI" );
2100 if ( !t1.isEqual( t5 ) ) {
2103 t5.setCommonName( "vibrio" );
2104 if ( t1.isEqual( t5 ) ) {
2109 final Identifier id0 = new Identifier( "123", "pfam" );
2110 final Identifier id1 = ( Identifier ) id0.copy();
2111 if ( !id1.isEqual( id1 ) ) {
2114 if ( !id1.isEqual( id0 ) ) {
2117 if ( !id0.isEqual( id1 ) ) {
2124 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2125 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2126 if ( !pd1.isEqual( pd1 ) ) {
2129 if ( !pd1.isEqual( pd0 ) ) {
2134 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2135 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2136 if ( !pd3.isEqual( pd3 ) ) {
2139 if ( !pd2.isEqual( pd3 ) ) {
2142 if ( !pd0.isEqual( pd3 ) ) {
2147 // DomainArchitecture
2148 // ------------------
2149 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2150 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2151 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2152 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2153 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2154 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2159 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2160 if ( ds0.getNumberOfDomains() != 4 ) {
2163 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2164 if ( !ds0.isEqual( ds0 ) ) {
2167 if ( !ds0.isEqual( ds1 ) ) {
2170 if ( ds1.getNumberOfDomains() != 4 ) {
2173 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2178 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2179 if ( ds0.isEqual( ds2 ) ) {
2185 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2186 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2187 System.out.println( ds3.toNHX() );
2190 if ( ds3.getNumberOfDomains() != 3 ) {
2195 final Event e1 = new Event( Event.EventType.fusion );
2196 if ( e1.isDuplication() ) {
2199 if ( !e1.isFusion() ) {
2202 if ( !e1.asText().toString().equals( "fusion" ) ) {
2205 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2208 final Event e11 = new Event( Event.EventType.fusion );
2209 if ( !e11.isEqual( e1 ) ) {
2212 if ( !e11.toNHX().toString().equals( "" ) ) {
2215 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2216 if ( e2.isDuplication() ) {
2219 if ( !e2.isSpeciationOrDuplication() ) {
2222 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2225 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2228 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2231 if ( e11.isEqual( e2 ) ) {
2234 final Event e2c = ( Event ) e2.copy();
2235 if ( !e2c.isEqual( e2 ) ) {
2238 Event e3 = new Event( 1, 2, 3 );
2239 if ( e3.isDuplication() ) {
2242 if ( e3.isSpeciation() ) {
2245 if ( e3.isGeneLoss() ) {
2248 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2251 final Event e3c = ( Event ) e3.copy();
2252 final Event e3cc = ( Event ) e3c.copy();
2253 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2257 if ( !e3c.isEqual( e3cc ) ) {
2260 Event e4 = new Event( 1, 2, 3 );
2261 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2264 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2267 final Event e4c = ( Event ) e4.copy();
2269 final Event e4cc = ( Event ) e4c.copy();
2270 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2273 if ( !e4c.isEqual( e4cc ) ) {
2276 final Event e5 = new Event();
2277 if ( !e5.isUnassigned() ) {
2280 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2283 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2286 final Event e6 = new Event( 1, 0, 0 );
2287 if ( !e6.asText().toString().equals( "duplication" ) ) {
2290 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2293 final Event e7 = new Event( 0, 1, 0 );
2294 if ( !e7.asText().toString().equals( "speciation" ) ) {
2297 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2300 final Event e8 = new Event( 0, 0, 1 );
2301 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2304 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2308 catch ( final Exception e ) {
2309 e.printStackTrace( System.out );
2315 private static boolean testDeletionOfExternalNodes() {
2317 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2318 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2319 final PhylogenyWriter w = new PhylogenyWriter();
2320 if ( t0.isEmpty() ) {
2323 if ( t0.getNumberOfExternalNodes() != 1 ) {
2326 t0.deleteSubtree( t0.getNode( "A" ), false );
2327 if ( t0.getNumberOfExternalNodes() != 0 ) {
2330 if ( !t0.isEmpty() ) {
2333 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2334 if ( t1.getNumberOfExternalNodes() != 2 ) {
2337 t1.deleteSubtree( t1.getNode( "A" ), false );
2338 if ( t1.getNumberOfExternalNodes() != 1 ) {
2341 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2344 t1.deleteSubtree( t1.getNode( "B" ), false );
2345 if ( t1.getNumberOfExternalNodes() != 1 ) {
2348 t1.deleteSubtree( t1.getNode( "r" ), false );
2349 if ( !t1.isEmpty() ) {
2352 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2353 if ( t2.getNumberOfExternalNodes() != 3 ) {
2356 t2.deleteSubtree( t2.getNode( "B" ), false );
2357 if ( t2.getNumberOfExternalNodes() != 2 ) {
2360 t2.toNewHampshireX();
2361 PhylogenyNode n = t2.getNode( "A" );
2362 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2365 t2.deleteSubtree( t2.getNode( "A" ), false );
2366 if ( t2.getNumberOfExternalNodes() != 2 ) {
2369 t2.deleteSubtree( t2.getNode( "C" ), true );
2370 if ( t2.getNumberOfExternalNodes() != 1 ) {
2373 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2374 if ( t3.getNumberOfExternalNodes() != 4 ) {
2377 t3.deleteSubtree( t3.getNode( "B" ), true );
2378 if ( t3.getNumberOfExternalNodes() != 3 ) {
2381 n = t3.getNode( "A" );
2382 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2385 n = n.getNextExternalNode();
2386 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2389 t3.deleteSubtree( t3.getNode( "A" ), true );
2390 if ( t3.getNumberOfExternalNodes() != 2 ) {
2393 n = t3.getNode( "C" );
2394 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2397 t3.deleteSubtree( t3.getNode( "C" ), true );
2398 if ( t3.getNumberOfExternalNodes() != 1 ) {
2401 t3.deleteSubtree( t3.getNode( "D" ), true );
2402 if ( t3.getNumberOfExternalNodes() != 0 ) {
2405 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2406 if ( t4.getNumberOfExternalNodes() != 6 ) {
2409 t4.deleteSubtree( t4.getNode( "B2" ), true );
2410 if ( t4.getNumberOfExternalNodes() != 5 ) {
2413 String s = w.toNewHampshire( t4, false, true ).toString();
2414 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2417 t4.deleteSubtree( t4.getNode( "B11" ), true );
2418 if ( t4.getNumberOfExternalNodes() != 4 ) {
2421 t4.deleteSubtree( t4.getNode( "C" ), true );
2422 if ( t4.getNumberOfExternalNodes() != 3 ) {
2425 n = t4.getNode( "A" );
2426 n = n.getNextExternalNode();
2427 if ( !n.getName().equals( "B12" ) ) {
2430 n = n.getNextExternalNode();
2431 if ( !n.getName().equals( "D" ) ) {
2434 s = w.toNewHampshire( t4, false, true ).toString();
2435 if ( !s.equals( "((A,B12),D);" ) ) {
2438 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2439 t5.deleteSubtree( t5.getNode( "A" ), true );
2440 if ( t5.getNumberOfExternalNodes() != 5 ) {
2443 s = w.toNewHampshire( t5, false, true ).toString();
2444 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2447 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2448 t6.deleteSubtree( t6.getNode( "B11" ), true );
2449 if ( t6.getNumberOfExternalNodes() != 5 ) {
2452 s = w.toNewHampshire( t6, false, false ).toString();
2453 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2456 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2457 t7.deleteSubtree( t7.getNode( "B12" ), true );
2458 if ( t7.getNumberOfExternalNodes() != 5 ) {
2461 s = w.toNewHampshire( t7, false, true ).toString();
2462 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2465 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2466 t8.deleteSubtree( t8.getNode( "B2" ), true );
2467 if ( t8.getNumberOfExternalNodes() != 5 ) {
2470 s = w.toNewHampshire( t8, false, false ).toString();
2471 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2474 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2475 t9.deleteSubtree( t9.getNode( "C" ), true );
2476 if ( t9.getNumberOfExternalNodes() != 5 ) {
2479 s = w.toNewHampshire( t9, false, true ).toString();
2480 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2483 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2484 t10.deleteSubtree( t10.getNode( "D" ), true );
2485 if ( t10.getNumberOfExternalNodes() != 5 ) {
2488 s = w.toNewHampshire( t10, false, true ).toString();
2489 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2492 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2493 t11.deleteSubtree( t11.getNode( "A" ), true );
2494 if ( t11.getNumberOfExternalNodes() != 2 ) {
2497 s = w.toNewHampshire( t11, false, true ).toString();
2498 if ( !s.equals( "(B,C);" ) ) {
2501 t11.deleteSubtree( t11.getNode( "C" ), true );
2502 if ( t11.getNumberOfExternalNodes() != 1 ) {
2505 s = w.toNewHampshire( t11, false, false ).toString();
2506 if ( !s.equals( "B;" ) ) {
2509 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2510 t12.deleteSubtree( t12.getNode( "B2" ), true );
2511 if ( t12.getNumberOfExternalNodes() != 8 ) {
2514 s = w.toNewHampshire( t12, false, true ).toString();
2515 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2518 t12.deleteSubtree( t12.getNode( "B3" ), true );
2519 if ( t12.getNumberOfExternalNodes() != 7 ) {
2522 s = w.toNewHampshire( t12, false, true ).toString();
2523 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2526 t12.deleteSubtree( t12.getNode( "C3" ), true );
2527 if ( t12.getNumberOfExternalNodes() != 6 ) {
2530 s = w.toNewHampshire( t12, false, true ).toString();
2531 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2534 t12.deleteSubtree( t12.getNode( "A1" ), true );
2535 if ( t12.getNumberOfExternalNodes() != 5 ) {
2538 s = w.toNewHampshire( t12, false, true ).toString();
2539 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2542 t12.deleteSubtree( t12.getNode( "B1" ), true );
2543 if ( t12.getNumberOfExternalNodes() != 4 ) {
2546 s = w.toNewHampshire( t12, false, true ).toString();
2547 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2550 t12.deleteSubtree( t12.getNode( "A3" ), true );
2551 if ( t12.getNumberOfExternalNodes() != 3 ) {
2554 s = w.toNewHampshire( t12, false, true ).toString();
2555 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2558 t12.deleteSubtree( t12.getNode( "A2" ), true );
2559 if ( t12.getNumberOfExternalNodes() != 2 ) {
2562 s = w.toNewHampshire( t12, false, true ).toString();
2563 if ( !s.equals( "(C1,C2);" ) ) {
2566 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2567 t13.deleteSubtree( t13.getNode( "D" ), true );
2568 if ( t13.getNumberOfExternalNodes() != 4 ) {
2571 s = w.toNewHampshire( t13, false, true ).toString();
2572 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2575 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2576 t14.deleteSubtree( t14.getNode( "E" ), true );
2577 if ( t14.getNumberOfExternalNodes() != 5 ) {
2580 s = w.toNewHampshire( t14, false, true ).toString();
2581 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2584 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2585 t15.deleteSubtree( t15.getNode( "B2" ), true );
2586 if ( t15.getNumberOfExternalNodes() != 11 ) {
2589 t15.deleteSubtree( t15.getNode( "B1" ), true );
2590 if ( t15.getNumberOfExternalNodes() != 10 ) {
2593 t15.deleteSubtree( t15.getNode( "B3" ), true );
2594 if ( t15.getNumberOfExternalNodes() != 9 ) {
2597 t15.deleteSubtree( t15.getNode( "B4" ), true );
2598 if ( t15.getNumberOfExternalNodes() != 8 ) {
2601 t15.deleteSubtree( t15.getNode( "A1" ), true );
2602 if ( t15.getNumberOfExternalNodes() != 7 ) {
2605 t15.deleteSubtree( t15.getNode( "C4" ), true );
2606 if ( t15.getNumberOfExternalNodes() != 6 ) {
2610 catch ( final Exception e ) {
2611 e.printStackTrace( System.out );
2617 private static boolean testDescriptiveStatistics() {
2619 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2620 dss1.addValue( 82 );
2621 dss1.addValue( 78 );
2622 dss1.addValue( 70 );
2623 dss1.addValue( 58 );
2624 dss1.addValue( 42 );
2625 if ( dss1.getN() != 5 ) {
2628 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2631 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2634 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2637 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2640 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2643 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2646 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2649 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2652 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2655 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2658 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2661 dss1.addValue( 123 );
2662 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2665 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2668 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2671 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2672 dss2.addValue( -1.85 );
2673 dss2.addValue( 57.5 );
2674 dss2.addValue( 92.78 );
2675 dss2.addValue( 57.78 );
2676 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2679 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2682 final double[] a = dss2.getDataAsDoubleArray();
2683 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2686 dss2.addValue( -100 );
2687 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2690 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2693 final double[] ds = new double[ 14 ];
2708 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2709 if ( bins.length != 4 ) {
2712 if ( bins[ 0 ] != 2 ) {
2715 if ( bins[ 1 ] != 3 ) {
2718 if ( bins[ 2 ] != 4 ) {
2721 if ( bins[ 3 ] != 5 ) {
2724 final double[] ds1 = new double[ 9 ];
2734 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2735 if ( bins1.length != 4 ) {
2738 if ( bins1[ 0 ] != 2 ) {
2741 if ( bins1[ 1 ] != 3 ) {
2744 if ( bins1[ 2 ] != 0 ) {
2747 if ( bins1[ 3 ] != 4 ) {
2750 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2751 if ( bins1_1.length != 3 ) {
2754 if ( bins1_1[ 0 ] != 3 ) {
2757 if ( bins1_1[ 1 ] != 2 ) {
2760 if ( bins1_1[ 2 ] != 4 ) {
2763 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2764 if ( bins1_2.length != 3 ) {
2767 if ( bins1_2[ 0 ] != 2 ) {
2770 if ( bins1_2[ 1 ] != 2 ) {
2773 if ( bins1_2[ 2 ] != 2 ) {
2776 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2790 dss3.addValue( 10 );
2791 dss3.addValue( 10 );
2792 dss3.addValue( 10 );
2793 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2794 histo.toStringBuffer( 10, '=', 40, 5 );
2795 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2797 catch ( final Exception e ) {
2798 e.printStackTrace( System.out );
2804 private static boolean testDir( final String file ) {
2806 final File f = new File( file );
2807 if ( !f.exists() ) {
2810 if ( !f.isDirectory() ) {
2813 if ( !f.canRead() ) {
2817 catch ( final Exception e ) {
2823 private static boolean testExternalNodeRelatedMethods() {
2825 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2826 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2827 PhylogenyNode n = t1.getNode( "A" );
2828 n = n.getNextExternalNode();
2829 if ( !n.getName().equals( "B" ) ) {
2832 n = n.getNextExternalNode();
2833 if ( !n.getName().equals( "C" ) ) {
2836 n = n.getNextExternalNode();
2837 if ( !n.getName().equals( "D" ) ) {
2840 n = t1.getNode( "B" );
2841 while ( !n.isLastExternalNode() ) {
2842 n = n.getNextExternalNode();
2844 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2845 n = t2.getNode( "A" );
2846 n = n.getNextExternalNode();
2847 if ( !n.getName().equals( "B" ) ) {
2850 n = n.getNextExternalNode();
2851 if ( !n.getName().equals( "C" ) ) {
2854 n = n.getNextExternalNode();
2855 if ( !n.getName().equals( "D" ) ) {
2858 n = t2.getNode( "B" );
2859 while ( !n.isLastExternalNode() ) {
2860 n = n.getNextExternalNode();
2862 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2863 n = t3.getNode( "A" );
2864 n = n.getNextExternalNode();
2865 if ( !n.getName().equals( "B" ) ) {
2868 n = n.getNextExternalNode();
2869 if ( !n.getName().equals( "C" ) ) {
2872 n = n.getNextExternalNode();
2873 if ( !n.getName().equals( "D" ) ) {
2876 n = n.getNextExternalNode();
2877 if ( !n.getName().equals( "E" ) ) {
2880 n = n.getNextExternalNode();
2881 if ( !n.getName().equals( "F" ) ) {
2884 n = n.getNextExternalNode();
2885 if ( !n.getName().equals( "G" ) ) {
2888 n = n.getNextExternalNode();
2889 if ( !n.getName().equals( "H" ) ) {
2892 n = t3.getNode( "B" );
2893 while ( !n.isLastExternalNode() ) {
2894 n = n.getNextExternalNode();
2896 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2897 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2898 final PhylogenyNode node = iter.next();
2900 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2901 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2902 final PhylogenyNode node = iter.next();
2904 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2905 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2906 if ( !iter.next().getName().equals( "A" ) ) {
2909 if ( !iter.next().getName().equals( "B" ) ) {
2912 if ( !iter.next().getName().equals( "C" ) ) {
2915 if ( !iter.next().getName().equals( "D" ) ) {
2918 if ( !iter.next().getName().equals( "E" ) ) {
2921 if ( !iter.next().getName().equals( "F" ) ) {
2924 if ( iter.hasNext() ) {
2928 catch ( final Exception e ) {
2929 e.printStackTrace( System.out );
2935 private static boolean testGeneralTable() {
2937 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2938 t0.setValue( 3, 2, "23" );
2939 t0.setValue( 10, 1, "error" );
2940 t0.setValue( 10, 1, "110" );
2941 t0.setValue( 9, 1, "19" );
2942 t0.setValue( 1, 10, "101" );
2943 t0.setValue( 10, 10, "1010" );
2944 t0.setValue( 100, 10, "10100" );
2945 t0.setValue( 0, 0, "00" );
2946 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2949 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2952 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2955 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2958 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2961 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2964 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2967 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2970 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2973 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2974 t1.setValue( "3", "2", "23" );
2975 t1.setValue( "10", "1", "error" );
2976 t1.setValue( "10", "1", "110" );
2977 t1.setValue( "9", "1", "19" );
2978 t1.setValue( "1", "10", "101" );
2979 t1.setValue( "10", "10", "1010" );
2980 t1.setValue( "100", "10", "10100" );
2981 t1.setValue( "0", "0", "00" );
2982 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2983 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2986 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2989 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2992 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2995 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2998 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3001 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3004 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3007 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3010 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3014 catch ( final Exception e ) {
3015 e.printStackTrace( System.out );
3021 private static boolean testGetDistance() {
3023 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3024 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",
3025 new NHXParser() )[ 0 ];
3026 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3029 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3032 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3035 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3038 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3041 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3044 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3047 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3050 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3053 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3056 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3059 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3062 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3065 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3068 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3071 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3074 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3077 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3080 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3083 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3086 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3089 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3092 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3095 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3098 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3101 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3104 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3107 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3110 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3113 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3116 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3119 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",
3120 new NHXParser() )[ 0 ];
3121 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3124 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3127 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3130 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3133 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3136 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3139 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3142 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3145 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3148 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3151 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3155 catch ( final Exception e ) {
3156 e.printStackTrace( System.out );
3162 private static boolean testGetLCA() {
3164 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3165 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3166 new NHXParser() )[ 0 ];
3167 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3168 if ( !A.getName().equals( "A" ) ) {
3171 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3172 if ( !gh.getName().equals( "gh" ) ) {
3175 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3176 if ( !ab.getName().equals( "ab" ) ) {
3179 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3180 if ( !ab2.getName().equals( "ab" ) ) {
3183 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3184 if ( !gh2.getName().equals( "gh" ) ) {
3187 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3188 if ( !gh3.getName().equals( "gh" ) ) {
3191 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3192 if ( !abc.getName().equals( "abc" ) ) {
3195 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3196 if ( !abc2.getName().equals( "abc" ) ) {
3199 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3200 if ( !abcd.getName().equals( "abcd" ) ) {
3203 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3204 if ( !abcd2.getName().equals( "abcd" ) ) {
3207 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3208 if ( !abcdef.getName().equals( "abcdef" ) ) {
3211 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3212 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3215 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3216 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3219 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3220 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3223 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3224 if ( !abcde.getName().equals( "abcde" ) ) {
3227 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3228 if ( !abcde2.getName().equals( "abcde" ) ) {
3231 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3232 if ( !r.getName().equals( "abcdefgh" ) ) {
3235 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3236 if ( !r2.getName().equals( "abcdefgh" ) ) {
3239 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3240 if ( !r3.getName().equals( "abcdefgh" ) ) {
3243 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3244 if ( !abcde3.getName().equals( "abcde" ) ) {
3247 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3248 if ( !abcde4.getName().equals( "abcde" ) ) {
3251 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3252 if ( !ab3.getName().equals( "ab" ) ) {
3255 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3256 if ( !ab4.getName().equals( "ab" ) ) {
3259 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3260 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3261 if ( !cd.getName().equals( "cd" ) ) {
3264 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3265 if ( !cd2.getName().equals( "cd" ) ) {
3268 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3269 if ( !cde.getName().equals( "cde" ) ) {
3272 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3273 if ( !cde2.getName().equals( "cde" ) ) {
3276 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3277 if ( !cdef.getName().equals( "cdef" ) ) {
3280 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3281 if ( !cdef2.getName().equals( "cdef" ) ) {
3284 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3285 if ( !cdef3.getName().equals( "cdef" ) ) {
3288 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3289 if ( !rt.getName().equals( "r" ) ) {
3292 final Phylogeny p3 = factory
3293 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3294 new NHXParser() )[ 0 ];
3295 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3296 if ( !bc_3.getName().equals( "bc" ) ) {
3299 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3300 if ( !ac_3.getName().equals( "abc" ) ) {
3303 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3304 if ( !ad_3.getName().equals( "abcde" ) ) {
3307 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3308 if ( !af_3.getName().equals( "abcdef" ) ) {
3311 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3312 if ( !ag_3.getName().equals( "" ) ) {
3315 if ( !ag_3.isRoot() ) {
3318 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3319 if ( !al_3.getName().equals( "" ) ) {
3322 if ( !al_3.isRoot() ) {
3325 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3326 if ( !kl_3.getName().equals( "" ) ) {
3329 if ( !kl_3.isRoot() ) {
3332 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3333 if ( !fl_3.getName().equals( "" ) ) {
3336 if ( !fl_3.isRoot() ) {
3339 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3340 if ( !gk_3.getName().equals( "ghijk" ) ) {
3343 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3344 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3345 if ( !r_4.getName().equals( "r" ) ) {
3348 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3349 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3350 if ( !r_5.getName().equals( "root" ) ) {
3353 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3354 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3355 if ( !r_6.getName().equals( "rot" ) ) {
3358 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3359 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3360 if ( !r_7.getName().equals( "rott" ) ) {
3364 catch ( final Exception e ) {
3365 e.printStackTrace( System.out );
3371 private static boolean testGetLCA2() {
3373 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3374 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3375 PhylogenyMethods.preOrderReId( p_a );
3376 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3377 p_a.getNode( "a" ) );
3378 if ( !p_a_1.getName().equals( "a" ) ) {
3381 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3382 PhylogenyMethods.preOrderReId( p_b );
3383 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3384 p_b.getNode( "a" ) );
3385 if ( !p_b_1.getName().equals( "b" ) ) {
3388 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3389 p_b.getNode( "b" ) );
3390 if ( !p_b_2.getName().equals( "b" ) ) {
3393 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3394 PhylogenyMethods.preOrderReId( p_c );
3395 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3396 p_c.getNode( "a" ) );
3397 if ( !p_c_1.getName().equals( "b" ) ) {
3400 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3401 p_c.getNode( "c" ) );
3402 if ( !p_c_2.getName().equals( "c" ) ) {
3403 System.out.println( p_c_2.getName() );
3407 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3408 p_c.getNode( "b" ) );
3409 if ( !p_c_3.getName().equals( "b" ) ) {
3412 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3413 p_c.getNode( "a" ) );
3414 if ( !p_c_4.getName().equals( "c" ) ) {
3417 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3418 new NHXParser() )[ 0 ];
3419 PhylogenyMethods.preOrderReId( p1 );
3420 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3421 p1.getNode( "A" ) );
3422 if ( !A.getName().equals( "A" ) ) {
3425 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3426 p1.getNode( "gh" ) );
3427 if ( !gh.getName().equals( "gh" ) ) {
3430 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3431 p1.getNode( "B" ) );
3432 if ( !ab.getName().equals( "ab" ) ) {
3435 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3436 p1.getNode( "A" ) );
3437 if ( !ab2.getName().equals( "ab" ) ) {
3440 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3441 p1.getNode( "G" ) );
3442 if ( !gh2.getName().equals( "gh" ) ) {
3445 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3446 p1.getNode( "H" ) );
3447 if ( !gh3.getName().equals( "gh" ) ) {
3450 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3451 p1.getNode( "A" ) );
3452 if ( !abc.getName().equals( "abc" ) ) {
3455 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3456 p1.getNode( "C" ) );
3457 if ( !abc2.getName().equals( "abc" ) ) {
3460 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3461 p1.getNode( "D" ) );
3462 if ( !abcd.getName().equals( "abcd" ) ) {
3465 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3466 p1.getNode( "A" ) );
3467 if ( !abcd2.getName().equals( "abcd" ) ) {
3470 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3471 p1.getNode( "F" ) );
3472 if ( !abcdef.getName().equals( "abcdef" ) ) {
3475 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3476 p1.getNode( "A" ) );
3477 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3480 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3481 p1.getNode( "F" ) );
3482 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3485 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3486 p1.getNode( "ab" ) );
3487 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3490 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3491 p1.getNode( "E" ) );
3492 if ( !abcde.getName().equals( "abcde" ) ) {
3495 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3496 p1.getNode( "A" ) );
3497 if ( !abcde2.getName().equals( "abcde" ) ) {
3500 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3501 p1.getNode( "abcdefgh" ) );
3502 if ( !r.getName().equals( "abcdefgh" ) ) {
3505 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3506 p1.getNode( "H" ) );
3507 if ( !r2.getName().equals( "abcdefgh" ) ) {
3510 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3511 p1.getNode( "A" ) );
3512 if ( !r3.getName().equals( "abcdefgh" ) ) {
3515 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3516 p1.getNode( "abcde" ) );
3517 if ( !abcde3.getName().equals( "abcde" ) ) {
3520 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3521 p1.getNode( "E" ) );
3522 if ( !abcde4.getName().equals( "abcde" ) ) {
3525 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3526 p1.getNode( "B" ) );
3527 if ( !ab3.getName().equals( "ab" ) ) {
3530 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3531 p1.getNode( "ab" ) );
3532 if ( !ab4.getName().equals( "ab" ) ) {
3535 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3536 PhylogenyMethods.preOrderReId( p2 );
3537 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3538 p2.getNode( "d" ) );
3539 if ( !cd.getName().equals( "cd" ) ) {
3542 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3543 p2.getNode( "c" ) );
3544 if ( !cd2.getName().equals( "cd" ) ) {
3547 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3548 p2.getNode( "e" ) );
3549 if ( !cde.getName().equals( "cde" ) ) {
3552 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3553 p2.getNode( "c" ) );
3554 if ( !cde2.getName().equals( "cde" ) ) {
3557 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3558 p2.getNode( "f" ) );
3559 if ( !cdef.getName().equals( "cdef" ) ) {
3562 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3563 p2.getNode( "f" ) );
3564 if ( !cdef2.getName().equals( "cdef" ) ) {
3567 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3568 p2.getNode( "d" ) );
3569 if ( !cdef3.getName().equals( "cdef" ) ) {
3572 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3573 p2.getNode( "a" ) );
3574 if ( !rt.getName().equals( "r" ) ) {
3577 final Phylogeny p3 = factory
3578 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3579 new NHXParser() )[ 0 ];
3580 PhylogenyMethods.preOrderReId( p3 );
3581 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3582 p3.getNode( "c" ) );
3583 if ( !bc_3.getName().equals( "bc" ) ) {
3586 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3587 p3.getNode( "c" ) );
3588 if ( !ac_3.getName().equals( "abc" ) ) {
3591 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3592 p3.getNode( "d" ) );
3593 if ( !ad_3.getName().equals( "abcde" ) ) {
3596 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3597 p3.getNode( "f" ) );
3598 if ( !af_3.getName().equals( "abcdef" ) ) {
3601 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3602 p3.getNode( "g" ) );
3603 if ( !ag_3.getName().equals( "" ) ) {
3606 if ( !ag_3.isRoot() ) {
3609 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3610 p3.getNode( "l" ) );
3611 if ( !al_3.getName().equals( "" ) ) {
3614 if ( !al_3.isRoot() ) {
3617 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3618 p3.getNode( "l" ) );
3619 if ( !kl_3.getName().equals( "" ) ) {
3622 if ( !kl_3.isRoot() ) {
3625 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3626 p3.getNode( "l" ) );
3627 if ( !fl_3.getName().equals( "" ) ) {
3630 if ( !fl_3.isRoot() ) {
3633 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3634 p3.getNode( "k" ) );
3635 if ( !gk_3.getName().equals( "ghijk" ) ) {
3638 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3639 PhylogenyMethods.preOrderReId( p4 );
3640 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3641 p4.getNode( "c" ) );
3642 if ( !r_4.getName().equals( "r" ) ) {
3645 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3646 PhylogenyMethods.preOrderReId( p5 );
3647 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3648 p5.getNode( "c" ) );
3649 if ( !r_5.getName().equals( "root" ) ) {
3652 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3653 PhylogenyMethods.preOrderReId( p6 );
3654 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3655 p6.getNode( "a" ) );
3656 if ( !r_6.getName().equals( "rot" ) ) {
3659 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3660 PhylogenyMethods.preOrderReId( p7 );
3661 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3662 p7.getNode( "e" ) );
3663 if ( !r_7.getName().equals( "rott" ) ) {
3666 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3667 p7.getNode( "a" ) );
3668 if ( !r_71.getName().equals( "rott" ) ) {
3671 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3672 p7.getNode( "rott" ) );
3673 if ( !r_72.getName().equals( "rott" ) ) {
3676 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3677 p7.getNode( "a" ) );
3678 if ( !r_73.getName().equals( "rott" ) ) {
3681 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3682 p7.getNode( "rott" ) );
3683 if ( !r_74.getName().equals( "rott" ) ) {
3686 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3687 p7.getNode( "e" ) );
3688 if ( !r_75.getName().equals( "e" ) ) {
3692 catch ( final Exception e ) {
3693 e.printStackTrace( System.out );
3699 private static boolean testHmmscanOutputParser() {
3700 final String test_dir = Test.PATH_TO_TEST_DATA;
3702 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3703 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3705 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3706 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3707 final List<Protein> proteins = parser2.parse();
3708 if ( parser2.getProteinsEncountered() != 4 ) {
3711 if ( proteins.size() != 4 ) {
3714 if ( parser2.getDomainsEncountered() != 69 ) {
3717 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3720 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3723 final Protein p1 = proteins.get( 0 );
3724 if ( p1.getNumberOfProteinDomains() != 15 ) {
3727 if ( p1.getLength() != 850 ) {
3730 final Protein p2 = proteins.get( 1 );
3731 if ( p2.getNumberOfProteinDomains() != 51 ) {
3734 if ( p2.getLength() != 1291 ) {
3737 final Protein p3 = proteins.get( 2 );
3738 if ( p3.getNumberOfProteinDomains() != 2 ) {
3741 final Protein p4 = proteins.get( 3 );
3742 if ( p4.getNumberOfProteinDomains() != 1 ) {
3745 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3748 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3751 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3754 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3757 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3760 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3763 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3766 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3769 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3773 catch ( final Exception e ) {
3774 e.printStackTrace( System.out );
3780 private static boolean testLastExternalNodeMethods() {
3782 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3783 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3784 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3785 final PhylogenyNode n1 = t0.getNode( "A" );
3786 if ( n1.isLastExternalNode() ) {
3789 final PhylogenyNode n2 = t0.getNode( "B" );
3790 if ( n2.isLastExternalNode() ) {
3793 final PhylogenyNode n3 = t0.getNode( "C" );
3794 if ( n3.isLastExternalNode() ) {
3797 final PhylogenyNode n4 = t0.getNode( "D" );
3798 if ( !n4.isLastExternalNode() ) {
3802 catch ( final Exception e ) {
3803 e.printStackTrace( System.out );
3809 private static boolean testLevelOrderIterator() {
3811 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3812 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3813 PhylogenyNodeIterator it0;
3814 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3817 for( it0.reset(); it0.hasNext(); ) {
3820 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3821 if ( !it.next().getName().equals( "r" ) ) {
3824 if ( !it.next().getName().equals( "ab" ) ) {
3827 if ( !it.next().getName().equals( "cd" ) ) {
3830 if ( !it.next().getName().equals( "A" ) ) {
3833 if ( !it.next().getName().equals( "B" ) ) {
3836 if ( !it.next().getName().equals( "C" ) ) {
3839 if ( !it.next().getName().equals( "D" ) ) {
3842 if ( it.hasNext() ) {
3845 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",
3846 new NHXParser() )[ 0 ];
3847 PhylogenyNodeIterator it2;
3848 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3851 for( it2.reset(); it2.hasNext(); ) {
3854 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3855 if ( !it3.next().getName().equals( "r" ) ) {
3858 if ( !it3.next().getName().equals( "abc" ) ) {
3861 if ( !it3.next().getName().equals( "defg" ) ) {
3864 if ( !it3.next().getName().equals( "A" ) ) {
3867 if ( !it3.next().getName().equals( "B" ) ) {
3870 if ( !it3.next().getName().equals( "C" ) ) {
3873 if ( !it3.next().getName().equals( "D" ) ) {
3876 if ( !it3.next().getName().equals( "E" ) ) {
3879 if ( !it3.next().getName().equals( "F" ) ) {
3882 if ( !it3.next().getName().equals( "G" ) ) {
3885 if ( !it3.next().getName().equals( "1" ) ) {
3888 if ( !it3.next().getName().equals( "2" ) ) {
3891 if ( !it3.next().getName().equals( "3" ) ) {
3894 if ( !it3.next().getName().equals( "4" ) ) {
3897 if ( !it3.next().getName().equals( "5" ) ) {
3900 if ( !it3.next().getName().equals( "6" ) ) {
3903 if ( !it3.next().getName().equals( "f1" ) ) {
3906 if ( !it3.next().getName().equals( "f2" ) ) {
3909 if ( !it3.next().getName().equals( "f3" ) ) {
3912 if ( !it3.next().getName().equals( "a" ) ) {
3915 if ( !it3.next().getName().equals( "b" ) ) {
3918 if ( !it3.next().getName().equals( "f21" ) ) {
3921 if ( !it3.next().getName().equals( "X" ) ) {
3924 if ( !it3.next().getName().equals( "Y" ) ) {
3927 if ( !it3.next().getName().equals( "Z" ) ) {
3930 if ( it3.hasNext() ) {
3933 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3934 PhylogenyNodeIterator it4;
3935 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3938 for( it4.reset(); it4.hasNext(); ) {
3941 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3942 if ( !it5.next().getName().equals( "r" ) ) {
3945 if ( !it5.next().getName().equals( "A" ) ) {
3948 if ( !it5.next().getName().equals( "B" ) ) {
3951 if ( !it5.next().getName().equals( "C" ) ) {
3954 if ( !it5.next().getName().equals( "D" ) ) {
3957 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3958 PhylogenyNodeIterator it6;
3959 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3962 for( it6.reset(); it6.hasNext(); ) {
3965 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3966 if ( !it7.next().getName().equals( "A" ) ) {
3969 if ( it.hasNext() ) {
3973 catch ( final Exception e ) {
3974 e.printStackTrace( System.out );
3980 private static boolean testNodeRemoval() {
3982 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3983 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3984 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
3985 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
3988 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
3989 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
3990 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
3993 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
3994 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
3995 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
3999 catch ( final Exception e ) {
4000 e.printStackTrace( System.out );
4006 private static boolean testMidpointrooting() {
4008 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4009 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4010 PhylogenyMethods.midpointRoot( t0 );
4011 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4014 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4017 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4021 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",
4022 new NHXParser() )[ 0 ];
4023 if ( !t1.isRooted() ) {
4026 PhylogenyMethods.midpointRoot( t1 );
4027 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4030 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4033 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4036 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4039 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4042 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4045 t1.reRoot( t1.getNode( "A" ) );
4046 PhylogenyMethods.midpointRoot( t1 );
4047 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4050 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4053 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4056 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4059 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4063 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4067 catch ( final Exception e ) {
4068 e.printStackTrace( System.out );
4074 private static boolean testNexusCharactersParsing() {
4076 final NexusCharactersParser parser = new NexusCharactersParser();
4077 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4079 String[] labels = parser.getCharStateLabels();
4080 if ( labels.length != 7 ) {
4083 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4086 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4089 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4092 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4095 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4098 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4101 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4104 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4106 labels = parser.getCharStateLabels();
4107 if ( labels.length != 7 ) {
4110 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4113 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4116 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4119 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4122 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4125 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4128 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4132 catch ( final Exception e ) {
4133 e.printStackTrace( System.out );
4139 private static boolean testNexusMatrixParsing() {
4141 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4142 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4144 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4145 if ( m.getNumberOfCharacters() != 9 ) {
4148 if ( m.getNumberOfIdentifiers() != 5 ) {
4151 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4154 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4157 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4160 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4163 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4166 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4169 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4172 // if ( labels.length != 7 ) {
4175 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4178 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4181 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4184 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4187 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4190 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4193 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4196 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4198 // labels = parser.getCharStateLabels();
4199 // if ( labels.length != 7 ) {
4202 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4205 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4208 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4211 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4214 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4217 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4220 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4224 catch ( final Exception e ) {
4225 e.printStackTrace( System.out );
4231 private static boolean testNexusTreeParsing() {
4233 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4234 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4235 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4236 if ( phylogenies.length != 1 ) {
4239 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4242 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4246 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4247 if ( phylogenies.length != 1 ) {
4250 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4253 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4257 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4258 if ( phylogenies.length != 1 ) {
4261 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4264 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4267 if ( phylogenies[ 0 ].isRooted() ) {
4271 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4272 if ( phylogenies.length != 18 ) {
4275 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4278 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4281 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4284 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4287 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4290 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4293 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4296 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4299 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4302 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4305 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4308 if ( phylogenies[ 8 ].isRooted() ) {
4311 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4314 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4317 if ( !phylogenies[ 9 ].isRooted() ) {
4320 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4323 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4326 if ( !phylogenies[ 10 ].isRooted() ) {
4329 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4332 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4335 if ( phylogenies[ 11 ].isRooted() ) {
4338 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4341 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4344 if ( !phylogenies[ 12 ].isRooted() ) {
4347 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4350 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4353 if ( !phylogenies[ 13 ].isRooted() ) {
4356 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4359 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4362 if ( !phylogenies[ 14 ].isRooted() ) {
4365 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4368 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4371 if ( phylogenies[ 15 ].isRooted() ) {
4374 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4377 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4380 if ( !phylogenies[ 16 ].isRooted() ) {
4383 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4386 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4389 if ( phylogenies[ 17 ].isRooted() ) {
4392 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4396 catch ( final Exception e ) {
4397 e.printStackTrace( System.out );
4403 private static boolean testNexusTreeParsingTranslating() {
4405 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4406 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4407 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4408 if ( phylogenies.length != 1 ) {
4411 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4414 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4417 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4420 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4423 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4424 .equals( "Aranaeus" ) ) {
4428 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4429 if ( phylogenies.length != 3 ) {
4432 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4435 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4438 if ( phylogenies[ 0 ].isRooted() ) {
4441 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4444 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4447 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4448 .equals( "Aranaeus" ) ) {
4451 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4454 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4457 if ( phylogenies[ 1 ].isRooted() ) {
4460 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4463 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4466 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4467 .equals( "Aranaeus" ) ) {
4470 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4473 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4476 if ( !phylogenies[ 2 ].isRooted() ) {
4479 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4482 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4485 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4486 .equals( "Aranaeus" ) ) {
4490 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4491 if ( phylogenies.length != 3 ) {
4494 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4497 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4500 if ( phylogenies[ 0 ].isRooted() ) {
4503 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4506 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4509 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4510 .equals( "Aranaeus" ) ) {
4513 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4516 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4519 if ( phylogenies[ 1 ].isRooted() ) {
4522 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4525 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4528 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4529 .equals( "Aranaeus" ) ) {
4532 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4535 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4538 if ( !phylogenies[ 2 ].isRooted() ) {
4541 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4544 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4547 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4548 .equals( "Aranaeus" ) ) {
4552 catch ( final Exception e ) {
4553 e.printStackTrace( System.out );
4559 private static boolean testNHParsing() {
4561 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4562 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4563 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4566 final NHXParser nhxp = new NHXParser();
4567 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4568 nhxp.setReplaceUnderscores( true );
4569 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4570 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4573 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4576 final Phylogeny p1b = factory
4577 .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 ",
4578 new NHXParser() )[ 0 ];
4579 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4582 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4585 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4586 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4587 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4588 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4589 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4590 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4591 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4592 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4593 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4594 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4595 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4596 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4597 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4599 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4602 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4605 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4608 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4611 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4612 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4613 final String p16_S = "((A,B),C)";
4614 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4615 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4618 final String p17_S = "(C,(A,B))";
4619 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4620 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4623 final String p18_S = "((A,B),(C,D))";
4624 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4625 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4628 final String p19_S = "(((A,B),C),D)";
4629 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4630 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4633 final String p20_S = "(A,(B,(C,D)))";
4634 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4635 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4638 final String p21_S = "(A,(B,(C,(D,E))))";
4639 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4640 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4643 final String p22_S = "((((A,B),C),D),E)";
4644 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4645 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4648 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4649 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4650 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4653 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4654 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4655 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4658 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4659 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4660 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4661 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4664 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4667 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4668 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4669 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4670 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4671 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4672 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4673 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4674 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4675 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4676 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4679 final String p26_S = "(A,B)ab";
4680 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4681 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4684 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4685 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4687 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4690 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4691 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4692 final String p28_S3 = "(A,B)ab";
4693 final String p28_S4 = "((((A,B),C),D),;E;)";
4694 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4696 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4699 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4702 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4705 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4708 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";
4709 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4710 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4713 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";
4714 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4715 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4718 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4719 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4720 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4723 final String p33_S = "A";
4724 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4725 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4728 final String p34_S = "B;";
4729 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4730 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4733 final String p35_S = "B:0.2";
4734 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4735 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4738 final String p36_S = "(A)";
4739 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4740 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4743 final String p37_S = "((A))";
4744 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4745 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4748 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4749 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4750 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4753 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4754 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4755 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4758 final String p40_S = "(A,B,C)";
4759 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4760 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4763 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4764 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4765 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4768 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4769 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4770 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4773 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)";
4774 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4775 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4778 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)))";
4779 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4780 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4783 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4784 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4785 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4788 final String p46_S = "";
4789 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4790 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4793 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4794 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4797 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4798 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4801 final Phylogeny p49 = factory
4802 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4803 new NHXParser() )[ 0 ];
4804 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4807 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4808 if ( p50.getNode( "A" ) == null ) {
4811 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4812 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4815 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4818 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4819 .equals( "((A,B)88:2.0,C);" ) ) {
4822 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4823 if ( p51.getNode( "A(A" ) == null ) {
4826 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4827 if ( p52.getNode( "A(A" ) == null ) {
4830 final Phylogeny p53 = factory
4831 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4832 new NHXParser() )[ 0 ];
4833 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4837 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4838 if ( p54.getNode( "A" ) == null ) {
4841 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4842 .equals( "((A,B)[88],C);" ) ) {
4846 catch ( final Exception e ) {
4847 e.printStackTrace( System.out );
4853 private static boolean testNHXconversion() {
4855 final PhylogenyNode n1 = new PhylogenyNode();
4856 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4857 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4858 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4859 final PhylogenyNode n5 = PhylogenyNode
4860 .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]" );
4861 final PhylogenyNode n6 = PhylogenyNode
4862 .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]" );
4863 if ( !n1.toNewHampshireX().equals( "" ) ) {
4866 if ( !n2.toNewHampshireX().equals( "" ) ) {
4869 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4872 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4875 if ( !n5.toNewHampshireX()
4876 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
4879 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
4883 catch ( final Exception e ) {
4884 e.printStackTrace( System.out );
4890 private static boolean testTaxonomyExtraction() {
4892 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
4893 NHXParser.TAXONOMY_EXTRACTION.YES );
4894 if ( n0.getNodeData().isHasTaxonomy() ) {
4897 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
4898 NHXParser.TAXONOMY_EXTRACTION.YES );
4899 if ( n1.getNodeData().isHasTaxonomy() ) {
4900 System.out.println( n1.toString() );
4903 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
4904 NHXParser.TAXONOMY_EXTRACTION.YES );
4905 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4906 System.out.println( n2.toString() );
4909 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
4910 NHXParser.TAXONOMY_EXTRACTION.YES );
4911 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4912 System.out.println( n3.toString() );
4915 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
4916 NHXParser.TAXONOMY_EXTRACTION.YES );
4917 if ( n4.getNodeData().isHasTaxonomy() ) {
4918 System.out.println( n4.toString() );
4921 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
4922 NHXParser.TAXONOMY_EXTRACTION.YES );
4923 if ( n5.getNodeData().isHasTaxonomy() ) {
4924 System.out.println( n5.toString() );
4927 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
4928 NHXParser.TAXONOMY_EXTRACTION.YES );
4929 if ( n6.getNodeData().isHasTaxonomy() ) {
4930 System.out.println( n6.toString() );
4933 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
4934 NHXParser.TAXONOMY_EXTRACTION.YES );
4935 if ( n7.getNodeData().isHasTaxonomy() ) {
4936 System.out.println( n7.toString() );
4939 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
4940 NHXParser.TAXONOMY_EXTRACTION.YES );
4941 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4942 System.out.println( n8.toString() );
4945 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
4946 NHXParser.TAXONOMY_EXTRACTION.YES );
4947 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4948 System.out.println( n9.toString() );
4951 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
4952 NHXParser.TAXONOMY_EXTRACTION.YES );
4953 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
4954 System.out.println( n10.toString() );
4958 catch ( final Exception e ) {
4959 e.printStackTrace( System.out );
4965 private static boolean testNHXNodeParsing() {
4967 final PhylogenyNode n1 = new PhylogenyNode();
4968 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4969 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4970 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4971 final PhylogenyNode n5 = PhylogenyNode
4972 .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]" );
4973 if ( !n3.getName().equals( "n3" ) ) {
4976 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4979 if ( n3.isDuplication() ) {
4982 if ( n3.isHasAssignedEvent() ) {
4985 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4988 if ( !n4.getName().equals( "n4" ) ) {
4991 if ( n4.getDistanceToParent() != 0.01 ) {
4994 if ( !n5.getName().equals( "n5" ) ) {
4997 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
5000 if ( n5.getDistanceToParent() != 0.1 ) {
5003 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
5006 if ( !n5.isDuplication() ) {
5009 if ( !n5.isHasAssignedEvent() ) {
5012 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
5015 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
5018 final PhylogenyNode n8 = PhylogenyNode
5019 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5020 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
5023 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
5026 final PhylogenyNode n9 = PhylogenyNode
5027 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5028 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
5031 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
5034 final PhylogenyNode n10 = PhylogenyNode
5035 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5036 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
5039 final PhylogenyNode n20 = PhylogenyNode
5040 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5041 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
5044 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
5047 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
5048 NHXParser.TAXONOMY_EXTRACTION.YES );
5049 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
5052 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
5055 final PhylogenyNode n20xx = PhylogenyNode
5056 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5057 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
5060 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
5063 final PhylogenyNode n20xxx = PhylogenyNode
5064 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5065 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
5068 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
5071 final PhylogenyNode n20xxxx = PhylogenyNode
5072 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5073 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
5076 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
5079 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
5080 NHXParser.TAXONOMY_EXTRACTION.YES );
5081 if ( !n21.getName().equals( "n21_PIG" ) ) {
5084 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
5087 final PhylogenyNode n21x = PhylogenyNode
5088 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5089 if ( !n21x.getName().equals( "n21_PIG" ) ) {
5092 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
5095 final PhylogenyNode n22 = PhylogenyNode
5096 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5097 if ( !n22.getName().equals( "n22/PIG" ) ) {
5100 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
5103 final PhylogenyNode n23 = PhylogenyNode
5104 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5105 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
5108 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
5111 final PhylogenyNode a = PhylogenyNode
5112 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5113 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
5116 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
5119 final PhylogenyNode b = PhylogenyNode
5120 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5121 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
5124 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
5127 final PhylogenyNode c = PhylogenyNode
5128 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
5129 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5130 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
5133 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
5136 final PhylogenyNode c1 = PhylogenyNode
5137 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
5138 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5139 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
5142 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
5145 final PhylogenyNode c2 = PhylogenyNode
5146 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
5147 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5148 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5151 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5154 final PhylogenyNode d = PhylogenyNode
5155 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5156 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5159 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5162 final PhylogenyNode e = PhylogenyNode
5163 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5164 if ( !e.getName().equals( "n10_RAT1" ) ) {
5167 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5170 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5171 NHXParser.TAXONOMY_EXTRACTION.YES );
5172 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5175 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5178 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5179 NHXParser.TAXONOMY_EXTRACTION.YES );
5180 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5183 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5186 final PhylogenyNode n11 = PhylogenyNode
5187 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5188 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5189 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5192 if ( n11.getDistanceToParent() != 0.4 ) {
5195 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5198 final PhylogenyNode n12 = PhylogenyNode
5199 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5200 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5201 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5204 if ( n12.getDistanceToParent() != 0.4 ) {
5207 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5210 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5211 NHXParser.TAXONOMY_EXTRACTION.YES );
5212 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5215 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5218 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5219 NHXParser.TAXONOMY_EXTRACTION.YES );
5220 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5223 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5226 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
5227 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
5228 if ( !tvu1.getRef().equals( "tag1" ) ) {
5231 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
5234 if ( !tvu1.getUnit().equals( "unit1" ) ) {
5237 if ( !tvu1.getValue().equals( "value1" ) ) {
5240 if ( !tvu3.getRef().equals( "tag3" ) ) {
5243 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
5246 if ( !tvu3.getUnit().equals( "unit3" ) ) {
5249 if ( !tvu3.getValue().equals( "value3" ) ) {
5252 if ( n1.getName().compareTo( "" ) != 0 ) {
5255 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5258 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5261 if ( n2.getName().compareTo( "" ) != 0 ) {
5264 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5267 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5270 final PhylogenyNode n00 = PhylogenyNode
5271 .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]" );
5272 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
5275 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5278 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5281 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
5284 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
5287 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
5290 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
5293 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
5296 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5297 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5300 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
5301 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
5304 final PhylogenyNode n13 = PhylogenyNode
5305 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5306 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5309 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5312 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5315 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5318 final PhylogenyNode n14 = PhylogenyNode
5319 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5320 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5323 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5326 final PhylogenyNode n15 = PhylogenyNode
5327 .createInstanceFromNhxString( "something_wicked[123]",
5328 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5329 if ( !n15.getName().equals( "something_wicked" ) ) {
5332 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5335 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5338 final PhylogenyNode n16 = PhylogenyNode
5339 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5340 if ( !n16.getName().equals( "something_wicked2" ) ) {
5343 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5346 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5349 final PhylogenyNode n17 = PhylogenyNode
5350 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5351 if ( !n17.getName().equals( "something_wicked3" ) ) {
5354 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5357 final PhylogenyNode n18 = PhylogenyNode
5358 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5359 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5362 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5365 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5368 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
5369 NHXParser.TAXONOMY_EXTRACTION.YES );
5370 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
5373 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5376 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
5377 NHXParser.TAXONOMY_EXTRACTION.YES );
5378 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
5381 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5384 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
5385 NHXParser.TAXONOMY_EXTRACTION.YES );
5386 if ( n31.getNodeData().isHasTaxonomy() ) {
5389 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5390 NHXParser.TAXONOMY_EXTRACTION.YES );
5391 if ( n32.getNodeData().isHasTaxonomy() ) {
5395 catch ( final Exception e ) {
5396 e.printStackTrace( System.out );
5402 private static boolean testNHXParsing() {
5404 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5405 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5406 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5409 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]";
5410 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5411 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5414 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]";
5415 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5416 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5419 final Phylogeny[] p3 = factory
5420 .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]",
5422 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5425 final Phylogeny[] p4 = factory
5426 .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(]",
5428 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5431 final Phylogeny[] p5 = factory
5432 .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(((]",
5434 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5437 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)";
5438 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)";
5439 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5440 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5443 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)))";
5444 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)))";
5445 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5446 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5449 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]) ))[,,, ])))))))";
5450 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5451 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5452 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5455 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5456 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5459 final Phylogeny p10 = factory
5460 .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]",
5461 new NHXParser() )[ 0 ];
5462 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5466 catch ( final Exception e ) {
5467 e.printStackTrace( System.out );
5473 private static boolean testNHXParsingQuotes() {
5475 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5476 final NHXParser p = new NHXParser();
5477 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5478 if ( phylogenies_0.length != 5 ) {
5481 final Phylogeny phy = phylogenies_0[ 4 ];
5482 if ( phy.getNumberOfExternalNodes() != 7 ) {
5485 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5488 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5491 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5492 .getScientificName().equals( "hsapiens" ) ) {
5495 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5498 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5501 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5504 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5507 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5510 final NHXParser p1p = new NHXParser();
5511 p1p.setIgnoreQuotes( true );
5512 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5513 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5516 final NHXParser p2p = new NHXParser();
5517 p1p.setIgnoreQuotes( false );
5518 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5519 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5522 final NHXParser p3p = new NHXParser();
5523 p3p.setIgnoreQuotes( false );
5524 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5525 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5528 final NHXParser p4p = new NHXParser();
5529 p4p.setIgnoreQuotes( false );
5530 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5531 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5534 final Phylogeny p10 = factory
5535 .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]",
5536 new NHXParser() )[ 0 ];
5537 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5538 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5541 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5542 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5546 final Phylogeny p12 = factory
5547 .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]",
5548 new NHXParser() )[ 0 ];
5549 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
5550 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5553 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5554 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5557 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;";
5558 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5561 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5562 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5566 catch ( final Exception e ) {
5567 e.printStackTrace( System.out );
5573 private static boolean testNHXParsingMB() {
5575 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5576 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5577 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5578 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5579 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5580 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5581 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5582 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5583 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5584 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5585 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5588 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5591 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5592 0.1100000000000000e+00 ) ) {
5595 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5598 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5601 final Phylogeny p2 = factory
5602 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5603 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5604 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5605 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5606 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5607 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5608 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5609 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5610 + "7.369400000000000e-02}])",
5611 new NHXParser() )[ 0 ];
5612 if ( p2.getNode( "1" ) == null ) {
5615 if ( p2.getNode( "2" ) == null ) {
5619 catch ( final Exception e ) {
5620 e.printStackTrace( System.out );
5627 private static boolean testPhylogenyBranch() {
5629 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5630 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5631 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5632 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5633 if ( !a1b1.equals( a1b1 ) ) {
5636 if ( !a1b1.equals( b1a1 ) ) {
5639 if ( !b1a1.equals( a1b1 ) ) {
5642 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5643 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5644 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5645 if ( a1_b1.equals( b1_a1 ) ) {
5648 if ( a1_b1.equals( a1_b1_ ) ) {
5651 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5652 if ( !a1_b1.equals( b1_a1_ ) ) {
5655 if ( a1_b1_.equals( b1_a1_ ) ) {
5658 if ( !a1_b1_.equals( b1_a1 ) ) {
5662 catch ( final Exception e ) {
5663 e.printStackTrace( System.out );
5669 private static boolean testPhyloXMLparsingOfDistributionElement() {
5671 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5672 PhyloXmlParser xml_parser = null;
5674 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5676 catch ( final Exception e ) {
5677 // Do nothing -- means were not running from jar.
5679 if ( xml_parser == null ) {
5680 xml_parser = new PhyloXmlParser();
5681 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5682 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5685 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5688 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5690 if ( xml_parser.getErrorCount() > 0 ) {
5691 System.out.println( xml_parser.getErrorMessages().toString() );
5694 if ( phylogenies_0.length != 1 ) {
5697 final Phylogeny t1 = phylogenies_0[ 0 ];
5698 PhylogenyNode n = null;
5699 Distribution d = null;
5700 n = t1.getNode( "root node" );
5701 if ( !n.getNodeData().isHasDistribution() ) {
5704 if ( n.getNodeData().getDistributions().size() != 1 ) {
5707 d = n.getNodeData().getDistribution();
5708 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5711 if ( d.getPoints().size() != 1 ) {
5714 if ( d.getPolygons() != null ) {
5717 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5720 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5723 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5726 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5729 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5732 n = t1.getNode( "node a" );
5733 if ( !n.getNodeData().isHasDistribution() ) {
5736 if ( n.getNodeData().getDistributions().size() != 2 ) {
5739 d = n.getNodeData().getDistribution( 1 );
5740 if ( !d.getDesc().equals( "San Diego" ) ) {
5743 if ( d.getPoints().size() != 1 ) {
5746 if ( d.getPolygons() != null ) {
5749 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5752 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5755 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5758 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5761 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5764 n = t1.getNode( "node bb" );
5765 if ( !n.getNodeData().isHasDistribution() ) {
5768 if ( n.getNodeData().getDistributions().size() != 1 ) {
5771 d = n.getNodeData().getDistribution( 0 );
5772 if ( d.getPoints().size() != 3 ) {
5775 if ( d.getPolygons().size() != 2 ) {
5778 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5781 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5784 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5787 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5790 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5793 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5796 Polygon p = d.getPolygons().get( 0 );
5797 if ( p.getPoints().size() != 3 ) {
5800 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5803 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5806 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5809 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5812 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5815 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5818 p = d.getPolygons().get( 1 );
5819 if ( p.getPoints().size() != 3 ) {
5822 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5825 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5828 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5832 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5833 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5834 if ( rt.length != 1 ) {
5837 final Phylogeny t1_rt = rt[ 0 ];
5838 n = t1_rt.getNode( "root node" );
5839 if ( !n.getNodeData().isHasDistribution() ) {
5842 if ( n.getNodeData().getDistributions().size() != 1 ) {
5845 d = n.getNodeData().getDistribution();
5846 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5849 if ( d.getPoints().size() != 1 ) {
5852 if ( d.getPolygons() != null ) {
5855 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5858 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5861 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5864 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5867 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5870 n = t1_rt.getNode( "node a" );
5871 if ( !n.getNodeData().isHasDistribution() ) {
5874 if ( n.getNodeData().getDistributions().size() != 2 ) {
5877 d = n.getNodeData().getDistribution( 1 );
5878 if ( !d.getDesc().equals( "San Diego" ) ) {
5881 if ( d.getPoints().size() != 1 ) {
5884 if ( d.getPolygons() != null ) {
5887 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5890 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5893 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5896 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5899 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5902 n = t1_rt.getNode( "node bb" );
5903 if ( !n.getNodeData().isHasDistribution() ) {
5906 if ( n.getNodeData().getDistributions().size() != 1 ) {
5909 d = n.getNodeData().getDistribution( 0 );
5910 if ( d.getPoints().size() != 3 ) {
5913 if ( d.getPolygons().size() != 2 ) {
5916 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5919 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5922 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5925 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5928 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5931 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5934 p = d.getPolygons().get( 0 );
5935 if ( p.getPoints().size() != 3 ) {
5938 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5941 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5944 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5947 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5950 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5953 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5956 p = d.getPolygons().get( 1 );
5957 if ( p.getPoints().size() != 3 ) {
5960 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5963 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5966 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5970 catch ( final Exception e ) {
5971 e.printStackTrace( System.out );
5977 private static boolean testPostOrderIterator() {
5979 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5980 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5981 PhylogenyNodeIterator it0;
5982 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5985 for( it0.reset(); it0.hasNext(); ) {
5988 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5989 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5990 if ( !it.next().getName().equals( "A" ) ) {
5993 if ( !it.next().getName().equals( "B" ) ) {
5996 if ( !it.next().getName().equals( "ab" ) ) {
5999 if ( !it.next().getName().equals( "C" ) ) {
6002 if ( !it.next().getName().equals( "D" ) ) {
6005 if ( !it.next().getName().equals( "cd" ) ) {
6008 if ( !it.next().getName().equals( "abcd" ) ) {
6011 if ( !it.next().getName().equals( "E" ) ) {
6014 if ( !it.next().getName().equals( "F" ) ) {
6017 if ( !it.next().getName().equals( "ef" ) ) {
6020 if ( !it.next().getName().equals( "G" ) ) {
6023 if ( !it.next().getName().equals( "H" ) ) {
6026 if ( !it.next().getName().equals( "gh" ) ) {
6029 if ( !it.next().getName().equals( "efgh" ) ) {
6032 if ( !it.next().getName().equals( "r" ) ) {
6035 if ( it.hasNext() ) {
6039 catch ( final Exception e ) {
6040 e.printStackTrace( System.out );
6046 private static boolean testPreOrderIterator() {
6048 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6049 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6050 PhylogenyNodeIterator it0;
6051 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
6054 for( it0.reset(); it0.hasNext(); ) {
6057 PhylogenyNodeIterator it = t0.iteratorPreorder();
6058 if ( !it.next().getName().equals( "r" ) ) {
6061 if ( !it.next().getName().equals( "ab" ) ) {
6064 if ( !it.next().getName().equals( "A" ) ) {
6067 if ( !it.next().getName().equals( "B" ) ) {
6070 if ( !it.next().getName().equals( "cd" ) ) {
6073 if ( !it.next().getName().equals( "C" ) ) {
6076 if ( !it.next().getName().equals( "D" ) ) {
6079 if ( it.hasNext() ) {
6082 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6083 it = t1.iteratorPreorder();
6084 if ( !it.next().getName().equals( "r" ) ) {
6087 if ( !it.next().getName().equals( "abcd" ) ) {
6090 if ( !it.next().getName().equals( "ab" ) ) {
6093 if ( !it.next().getName().equals( "A" ) ) {
6096 if ( !it.next().getName().equals( "B" ) ) {
6099 if ( !it.next().getName().equals( "cd" ) ) {
6102 if ( !it.next().getName().equals( "C" ) ) {
6105 if ( !it.next().getName().equals( "D" ) ) {
6108 if ( !it.next().getName().equals( "efgh" ) ) {
6111 if ( !it.next().getName().equals( "ef" ) ) {
6114 if ( !it.next().getName().equals( "E" ) ) {
6117 if ( !it.next().getName().equals( "F" ) ) {
6120 if ( !it.next().getName().equals( "gh" ) ) {
6123 if ( !it.next().getName().equals( "G" ) ) {
6126 if ( !it.next().getName().equals( "H" ) ) {
6129 if ( it.hasNext() ) {
6133 catch ( final Exception e ) {
6134 e.printStackTrace( System.out );
6140 private static boolean testPropertiesMap() {
6142 final PropertiesMap pm = new PropertiesMap();
6143 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6144 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6145 final Property p2 = new Property( "something:else",
6147 "improbable:research",
6150 pm.addProperty( p0 );
6151 pm.addProperty( p1 );
6152 pm.addProperty( p2 );
6153 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
6156 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
6159 if ( pm.getProperties().size() != 3 ) {
6162 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
6165 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6168 if ( pm.getProperties().size() != 3 ) {
6171 pm.removeProperty( "dimensions:diameter" );
6172 if ( pm.getProperties().size() != 2 ) {
6175 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
6178 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6182 catch ( final Exception e ) {
6183 e.printStackTrace( System.out );
6189 private static boolean testReIdMethods() {
6191 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6192 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6193 final int count = PhylogenyNode.getNodeCount();
6195 if ( p.getNode( "r" ).getId() != count ) {
6198 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6201 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6204 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6207 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6210 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6213 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6216 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6219 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6222 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6225 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6228 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6231 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6234 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6237 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6241 catch ( final Exception e ) {
6242 e.printStackTrace( System.out );
6248 private static boolean testRerooting() {
6250 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6251 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",
6252 new NHXParser() )[ 0 ];
6253 if ( !t1.isRooted() ) {
6256 t1.reRoot( t1.getNode( "D" ) );
6257 t1.reRoot( t1.getNode( "CD" ) );
6258 t1.reRoot( t1.getNode( "A" ) );
6259 t1.reRoot( t1.getNode( "B" ) );
6260 t1.reRoot( t1.getNode( "AB" ) );
6261 t1.reRoot( t1.getNode( "D" ) );
6262 t1.reRoot( t1.getNode( "C" ) );
6263 t1.reRoot( t1.getNode( "CD" ) );
6264 t1.reRoot( t1.getNode( "A" ) );
6265 t1.reRoot( t1.getNode( "B" ) );
6266 t1.reRoot( t1.getNode( "AB" ) );
6267 t1.reRoot( t1.getNode( "D" ) );
6268 t1.reRoot( t1.getNode( "D" ) );
6269 t1.reRoot( t1.getNode( "C" ) );
6270 t1.reRoot( t1.getNode( "A" ) );
6271 t1.reRoot( t1.getNode( "B" ) );
6272 t1.reRoot( t1.getNode( "AB" ) );
6273 t1.reRoot( t1.getNode( "C" ) );
6274 t1.reRoot( t1.getNode( "D" ) );
6275 t1.reRoot( t1.getNode( "CD" ) );
6276 t1.reRoot( t1.getNode( "D" ) );
6277 t1.reRoot( t1.getNode( "A" ) );
6278 t1.reRoot( t1.getNode( "B" ) );
6279 t1.reRoot( t1.getNode( "AB" ) );
6280 t1.reRoot( t1.getNode( "C" ) );
6281 t1.reRoot( t1.getNode( "D" ) );
6282 t1.reRoot( t1.getNode( "CD" ) );
6283 t1.reRoot( t1.getNode( "D" ) );
6284 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6287 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6290 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6293 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6296 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6299 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6302 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",
6303 new NHXParser() )[ 0 ];
6304 t2.reRoot( t2.getNode( "A" ) );
6305 t2.reRoot( t2.getNode( "D" ) );
6306 t2.reRoot( t2.getNode( "ABC" ) );
6307 t2.reRoot( t2.getNode( "A" ) );
6308 t2.reRoot( t2.getNode( "B" ) );
6309 t2.reRoot( t2.getNode( "D" ) );
6310 t2.reRoot( t2.getNode( "C" ) );
6311 t2.reRoot( t2.getNode( "ABC" ) );
6312 t2.reRoot( t2.getNode( "A" ) );
6313 t2.reRoot( t2.getNode( "B" ) );
6314 t2.reRoot( t2.getNode( "AB" ) );
6315 t2.reRoot( t2.getNode( "AB" ) );
6316 t2.reRoot( t2.getNode( "D" ) );
6317 t2.reRoot( t2.getNode( "C" ) );
6318 t2.reRoot( t2.getNode( "B" ) );
6319 t2.reRoot( t2.getNode( "AB" ) );
6320 t2.reRoot( t2.getNode( "D" ) );
6321 t2.reRoot( t2.getNode( "D" ) );
6322 t2.reRoot( t2.getNode( "ABC" ) );
6323 t2.reRoot( t2.getNode( "A" ) );
6324 t2.reRoot( t2.getNode( "B" ) );
6325 t2.reRoot( t2.getNode( "AB" ) );
6326 t2.reRoot( t2.getNode( "D" ) );
6327 t2.reRoot( t2.getNode( "C" ) );
6328 t2.reRoot( t2.getNode( "ABC" ) );
6329 t2.reRoot( t2.getNode( "A" ) );
6330 t2.reRoot( t2.getNode( "B" ) );
6331 t2.reRoot( t2.getNode( "AB" ) );
6332 t2.reRoot( t2.getNode( "D" ) );
6333 t2.reRoot( t2.getNode( "D" ) );
6334 t2.reRoot( t2.getNode( "C" ) );
6335 t2.reRoot( t2.getNode( "A" ) );
6336 t2.reRoot( t2.getNode( "B" ) );
6337 t2.reRoot( t2.getNode( "AB" ) );
6338 t2.reRoot( t2.getNode( "C" ) );
6339 t2.reRoot( t2.getNode( "D" ) );
6340 t2.reRoot( t2.getNode( "ABC" ) );
6341 t2.reRoot( t2.getNode( "D" ) );
6342 t2.reRoot( t2.getNode( "A" ) );
6343 t2.reRoot( t2.getNode( "B" ) );
6344 t2.reRoot( t2.getNode( "AB" ) );
6345 t2.reRoot( t2.getNode( "C" ) );
6346 t2.reRoot( t2.getNode( "D" ) );
6347 t2.reRoot( t2.getNode( "ABC" ) );
6348 t2.reRoot( t2.getNode( "D" ) );
6349 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6352 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6355 t2.reRoot( t2.getNode( "ABC" ) );
6356 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6359 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6362 t2.reRoot( t2.getNode( "AB" ) );
6363 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6366 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6369 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6372 t2.reRoot( t2.getNode( "AB" ) );
6373 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6376 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6379 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6382 t2.reRoot( t2.getNode( "D" ) );
6383 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6386 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6389 t2.reRoot( t2.getNode( "ABC" ) );
6390 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6393 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6396 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6397 new NHXParser() )[ 0 ];
6398 t3.reRoot( t3.getNode( "B" ) );
6399 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6402 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6405 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6408 t3.reRoot( t3.getNode( "B" ) );
6409 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6412 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6415 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6418 t3.reRoot( t3.getRoot() );
6419 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6422 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6425 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6429 catch ( final Exception e ) {
6430 e.printStackTrace( System.out );
6436 private static boolean testSDIse() {
6438 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6439 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6440 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6441 gene1.setRooted( true );
6442 species1.setRooted( true );
6443 final SDI sdi = new SDI( gene1, species1 );
6444 if ( !gene1.getRoot().isDuplication() ) {
6447 final Phylogeny species2 = factory
6448 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6449 new NHXParser() )[ 0 ];
6450 final Phylogeny gene2 = factory
6451 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6452 new NHXParser() )[ 0 ];
6453 species2.setRooted( true );
6454 gene2.setRooted( true );
6455 final SDI sdi2 = new SDI( gene2, species2 );
6456 if ( sdi2.getDuplicationsSum() != 0 ) {
6459 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6462 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6465 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6468 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6471 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6474 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6477 final Phylogeny species3 = factory
6478 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6479 new NHXParser() )[ 0 ];
6480 final Phylogeny gene3 = factory
6481 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6482 new NHXParser() )[ 0 ];
6483 species3.setRooted( true );
6484 gene3.setRooted( true );
6485 final SDI sdi3 = new SDI( gene3, species3 );
6486 if ( sdi3.getDuplicationsSum() != 1 ) {
6489 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6492 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6495 final Phylogeny species4 = factory
6496 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6497 new NHXParser() )[ 0 ];
6498 final Phylogeny gene4 = factory
6499 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6500 new NHXParser() )[ 0 ];
6501 species4.setRooted( true );
6502 gene4.setRooted( true );
6503 final SDI sdi4 = new SDI( gene4, species4 );
6504 if ( sdi4.getDuplicationsSum() != 1 ) {
6507 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6510 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6513 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6516 if ( species4.getNumberOfExternalNodes() != 6 ) {
6519 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6522 final Phylogeny species5 = factory
6523 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6524 new NHXParser() )[ 0 ];
6525 final Phylogeny gene5 = factory
6526 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6527 new NHXParser() )[ 0 ];
6528 species5.setRooted( true );
6529 gene5.setRooted( true );
6530 final SDI sdi5 = new SDI( gene5, species5 );
6531 if ( sdi5.getDuplicationsSum() != 2 ) {
6534 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6537 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6540 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6543 if ( species5.getNumberOfExternalNodes() != 6 ) {
6546 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6549 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6550 // Conjecture for Comparing Molecular Phylogenies"
6551 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6552 final Phylogeny species6 = factory
6553 .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,"
6554 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6555 new NHXParser() )[ 0 ];
6556 final Phylogeny gene6 = factory
6557 .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,"
6558 + "((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,"
6559 + "(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;",
6560 new NHXParser() )[ 0 ];
6561 species6.setRooted( true );
6562 gene6.setRooted( true );
6563 final SDI sdi6 = new SDI( gene6, species6 );
6564 if ( sdi6.getDuplicationsSum() != 3 ) {
6567 if ( !gene6.getNode( "r" ).isDuplication() ) {
6570 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6573 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6576 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6579 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6582 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6585 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6588 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6591 sdi6.computeMappingCostL();
6592 if ( sdi6.computeMappingCostL() != 17 ) {
6595 if ( species6.getNumberOfExternalNodes() != 9 ) {
6598 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6601 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6602 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6603 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6604 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6605 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6606 species7.setRooted( true );
6607 final Phylogeny gene7_1 = Test
6608 .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])" );
6609 gene7_1.setRooted( true );
6610 final SDI sdi7 = new SDI( gene7_1, species7 );
6611 if ( sdi7.getDuplicationsSum() != 0 ) {
6614 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6617 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6620 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6623 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6626 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6629 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6632 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6635 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6638 final Phylogeny gene7_2 = Test
6639 .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])" );
6640 gene7_2.setRooted( true );
6641 final SDI sdi7_2 = new SDI( gene7_2, species7 );
6642 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6645 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6648 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6651 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6654 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6657 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6660 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6663 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6666 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6669 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6673 catch ( final Exception e ) {
6679 private static boolean testSDIunrooted() {
6681 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6682 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6683 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6684 final Iterator<PhylogenyBranch> iter = l.iterator();
6685 PhylogenyBranch br = iter.next();
6686 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6689 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6693 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6696 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6700 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6703 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6707 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6710 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6714 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6717 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6721 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6724 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6728 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6731 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6735 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6738 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6742 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6745 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6749 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6752 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6756 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6759 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6763 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6766 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6770 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6773 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6777 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6780 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6784 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6787 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6790 if ( iter.hasNext() ) {
6793 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6794 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6795 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6797 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6800 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6804 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6807 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6811 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6814 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6817 if ( iter1.hasNext() ) {
6820 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6821 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6822 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6824 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6827 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6831 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6834 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6838 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6841 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6844 if ( iter2.hasNext() ) {
6847 final Phylogeny species0 = factory
6848 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6849 new NHXParser() )[ 0 ];
6850 final Phylogeny gene1 = factory
6851 .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])",
6852 new NHXParser() )[ 0 ];
6853 species0.setRooted( true );
6854 gene1.setRooted( true );
6855 final SDIR sdi_unrooted = new SDIR();
6856 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6857 if ( sdi_unrooted.getCount() != 1 ) {
6860 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6863 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6866 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6869 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6872 final Phylogeny gene2 = factory
6873 .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])",
6874 new NHXParser() )[ 0 ];
6875 gene2.setRooted( true );
6876 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6877 if ( sdi_unrooted.getCount() != 1 ) {
6880 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6883 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6886 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6889 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6892 final Phylogeny species6 = factory
6893 .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,"
6894 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6895 new NHXParser() )[ 0 ];
6896 final Phylogeny gene6 = factory
6897 .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],"
6898 + "(((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],"
6899 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6900 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6901 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6902 new NHXParser() )[ 0 ];
6903 species6.setRooted( true );
6904 gene6.setRooted( true );
6905 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6906 if ( sdi_unrooted.getCount() != 1 ) {
6909 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6912 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6915 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6918 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6921 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6924 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6927 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6930 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6933 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6936 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6939 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6942 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6946 final Phylogeny species7 = factory
6947 .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,"
6948 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6949 new NHXParser() )[ 0 ];
6950 final Phylogeny gene7 = factory
6951 .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],"
6952 + "(((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],"
6953 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6954 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6955 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6956 new NHXParser() )[ 0 ];
6957 species7.setRooted( true );
6958 gene7.setRooted( true );
6959 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6960 if ( sdi_unrooted.getCount() != 1 ) {
6963 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6966 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6969 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6972 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6975 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6978 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6981 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6984 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6987 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6990 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6993 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6996 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7000 final Phylogeny species8 = factory
7001 .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,"
7002 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7003 new NHXParser() )[ 0 ];
7004 final Phylogeny gene8 = factory
7005 .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],"
7006 + "(((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],"
7007 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7008 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7009 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7010 new NHXParser() )[ 0 ];
7011 species8.setRooted( true );
7012 gene8.setRooted( true );
7013 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
7014 if ( sdi_unrooted.getCount() != 1 ) {
7017 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7020 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7023 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7026 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7029 if ( !p8[ 0 ].getRoot().isDuplication() ) {
7032 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7035 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7038 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
7041 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7044 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
7047 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
7050 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7055 catch ( final Exception e ) {
7056 e.printStackTrace( System.out );
7062 private static boolean testSplit() {
7064 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7065 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7066 //Archaeopteryx.createApplication( p0 );
7067 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7068 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7069 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7070 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7071 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7072 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7073 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7074 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7075 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7076 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7077 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
7078 // System.out.println( s0.toString() );
7080 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7083 if ( s0.match( query_nodes ) ) {
7086 query_nodes = new HashSet<PhylogenyNode>();
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7094 if ( !s0.match( query_nodes ) ) {
7098 query_nodes = new HashSet<PhylogenyNode>();
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7102 if ( !s0.match( query_nodes ) ) {
7106 query_nodes = new HashSet<PhylogenyNode>();
7107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7111 if ( !s0.match( query_nodes ) ) {
7115 query_nodes = new HashSet<PhylogenyNode>();
7116 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
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( "F" ) );
7127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7128 if ( !s0.match( query_nodes ) ) {
7132 query_nodes = new HashSet<PhylogenyNode>();
7133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7134 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7135 if ( !s0.match( query_nodes ) ) {
7139 query_nodes = new HashSet<PhylogenyNode>();
7140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7144 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7145 if ( !s0.match( query_nodes ) ) {
7149 query_nodes = new HashSet<PhylogenyNode>();
7150 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7151 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7152 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7153 if ( !s0.match( query_nodes ) ) {
7157 query_nodes = new HashSet<PhylogenyNode>();
7158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7159 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7160 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7161 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7162 if ( !s0.match( query_nodes ) ) {
7166 query_nodes = new HashSet<PhylogenyNode>();
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7168 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7169 if ( s0.match( query_nodes ) ) {
7173 query_nodes = new HashSet<PhylogenyNode>();
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7177 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7178 if ( s0.match( query_nodes ) ) {
7182 query_nodes = new HashSet<PhylogenyNode>();
7183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7184 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7188 if ( s0.match( query_nodes ) ) {
7192 query_nodes = new HashSet<PhylogenyNode>();
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7196 if ( s0.match( query_nodes ) ) {
7200 query_nodes = new HashSet<PhylogenyNode>();
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7203 if ( s0.match( query_nodes ) ) {
7207 query_nodes = new HashSet<PhylogenyNode>();
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7209 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7210 if ( s0.match( query_nodes ) ) {
7214 query_nodes = new HashSet<PhylogenyNode>();
7215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7217 if ( s0.match( query_nodes ) ) {
7221 query_nodes = new HashSet<PhylogenyNode>();
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7223 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7224 if ( s0.match( query_nodes ) ) {
7228 query_nodes = new HashSet<PhylogenyNode>();
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7230 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7231 if ( s0.match( query_nodes ) ) {
7235 query_nodes = new HashSet<PhylogenyNode>();
7236 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7237 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7238 if ( s0.match( query_nodes ) ) {
7242 query_nodes = new HashSet<PhylogenyNode>();
7243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7245 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7246 if ( s0.match( query_nodes ) ) {
7250 query_nodes = new HashSet<PhylogenyNode>();
7251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7254 if ( s0.match( query_nodes ) ) {
7258 query_nodes = new HashSet<PhylogenyNode>();
7259 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7260 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7261 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7262 if ( s0.match( query_nodes ) ) {
7266 query_nodes = new HashSet<PhylogenyNode>();
7267 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7268 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7269 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7271 if ( s0.match( query_nodes ) ) {
7275 // query_nodes = new HashSet<PhylogenyNode>();
7276 // query_nodes.add( new PhylogenyNode( "X" ) );
7277 // query_nodes.add( new PhylogenyNode( "Y" ) );
7278 // query_nodes.add( new PhylogenyNode( "A" ) );
7279 // query_nodes.add( new PhylogenyNode( "B" ) );
7280 // query_nodes.add( new PhylogenyNode( "C" ) );
7281 // query_nodes.add( new PhylogenyNode( "D" ) );
7282 // query_nodes.add( new PhylogenyNode( "E" ) );
7283 // query_nodes.add( new PhylogenyNode( "F" ) );
7284 // query_nodes.add( new PhylogenyNode( "G" ) );
7285 // if ( !s0.match( query_nodes ) ) {
7288 // query_nodes = new HashSet<PhylogenyNode>();
7289 // query_nodes.add( new PhylogenyNode( "X" ) );
7290 // query_nodes.add( new PhylogenyNode( "Y" ) );
7291 // query_nodes.add( new PhylogenyNode( "A" ) );
7292 // query_nodes.add( new PhylogenyNode( "B" ) );
7293 // query_nodes.add( new PhylogenyNode( "C" ) );
7294 // if ( !s0.match( query_nodes ) ) {
7298 // query_nodes = new HashSet<PhylogenyNode>();
7299 // query_nodes.add( new PhylogenyNode( "X" ) );
7300 // query_nodes.add( new PhylogenyNode( "Y" ) );
7301 // query_nodes.add( new PhylogenyNode( "D" ) );
7302 // query_nodes.add( new PhylogenyNode( "E" ) );
7303 // query_nodes.add( new PhylogenyNode( "F" ) );
7304 // query_nodes.add( new PhylogenyNode( "G" ) );
7305 // if ( !s0.match( query_nodes ) ) {
7309 // query_nodes = new HashSet<PhylogenyNode>();
7310 // query_nodes.add( new PhylogenyNode( "X" ) );
7311 // query_nodes.add( new PhylogenyNode( "Y" ) );
7312 // query_nodes.add( new PhylogenyNode( "A" ) );
7313 // query_nodes.add( new PhylogenyNode( "B" ) );
7314 // query_nodes.add( new PhylogenyNode( "C" ) );
7315 // query_nodes.add( new PhylogenyNode( "D" ) );
7316 // if ( !s0.match( query_nodes ) ) {
7320 // query_nodes = new HashSet<PhylogenyNode>();
7321 // query_nodes.add( new PhylogenyNode( "X" ) );
7322 // query_nodes.add( new PhylogenyNode( "Y" ) );
7323 // query_nodes.add( new PhylogenyNode( "E" ) );
7324 // query_nodes.add( new PhylogenyNode( "F" ) );
7325 // query_nodes.add( new PhylogenyNode( "G" ) );
7326 // if ( !s0.match( query_nodes ) ) {
7330 // query_nodes = new HashSet<PhylogenyNode>();
7331 // query_nodes.add( new PhylogenyNode( "X" ) );
7332 // query_nodes.add( new PhylogenyNode( "Y" ) );
7333 // query_nodes.add( new PhylogenyNode( "F" ) );
7334 // query_nodes.add( new PhylogenyNode( "G" ) );
7335 // if ( !s0.match( query_nodes ) ) {
7339 query_nodes = new HashSet<PhylogenyNode>();
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7342 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7343 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7344 if ( s0.match( query_nodes ) ) {
7348 query_nodes = new HashSet<PhylogenyNode>();
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7351 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7352 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7353 if ( s0.match( query_nodes ) ) {
7356 ///////////////////////////
7358 query_nodes = new HashSet<PhylogenyNode>();
7359 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7360 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7361 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7362 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7363 if ( s0.match( query_nodes ) ) {
7367 query_nodes = new HashSet<PhylogenyNode>();
7368 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7369 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7370 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7372 if ( s0.match( query_nodes ) ) {
7376 query_nodes = new HashSet<PhylogenyNode>();
7377 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7378 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7380 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7381 if ( s0.match( query_nodes ) ) {
7385 query_nodes = new HashSet<PhylogenyNode>();
7386 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7387 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7388 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7389 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7390 if ( s0.match( query_nodes ) ) {
7394 query_nodes = new HashSet<PhylogenyNode>();
7395 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7396 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7397 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7398 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7399 if ( s0.match( query_nodes ) ) {
7403 query_nodes = new HashSet<PhylogenyNode>();
7404 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7405 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7407 if ( s0.match( query_nodes ) ) {
7411 query_nodes = new HashSet<PhylogenyNode>();
7412 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7413 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7414 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7416 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7417 if ( s0.match( query_nodes ) ) {
7421 query_nodes = new HashSet<PhylogenyNode>();
7422 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7423 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7424 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7425 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7426 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7427 if ( s0.match( query_nodes ) ) {
7431 query_nodes = new HashSet<PhylogenyNode>();
7432 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7434 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7435 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7436 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7437 if ( s0.match( query_nodes ) ) {
7441 query_nodes = new HashSet<PhylogenyNode>();
7442 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7443 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7444 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7445 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7446 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7448 if ( s0.match( query_nodes ) ) {
7452 catch ( final Exception e ) {
7453 e.printStackTrace();
7459 private static boolean testSplitStrict() {
7461 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7462 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7463 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7464 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7465 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7466 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7467 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7468 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7469 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7470 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7471 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7472 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7473 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7474 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7475 if ( s0.match( query_nodes ) ) {
7478 query_nodes = new HashSet<PhylogenyNode>();
7479 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7480 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7481 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7482 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7485 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7486 if ( !s0.match( query_nodes ) ) {
7490 query_nodes = new HashSet<PhylogenyNode>();
7491 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7494 if ( !s0.match( query_nodes ) ) {
7498 query_nodes = new HashSet<PhylogenyNode>();
7499 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7500 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7501 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7502 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7503 if ( !s0.match( query_nodes ) ) {
7507 query_nodes = new HashSet<PhylogenyNode>();
7508 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7509 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7510 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7511 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7512 if ( !s0.match( query_nodes ) ) {
7516 query_nodes = new HashSet<PhylogenyNode>();
7517 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7518 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7519 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7520 if ( !s0.match( query_nodes ) ) {
7524 query_nodes = new HashSet<PhylogenyNode>();
7525 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7526 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7527 if ( !s0.match( query_nodes ) ) {
7531 query_nodes = new HashSet<PhylogenyNode>();
7532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7533 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7534 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7535 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7536 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7537 if ( !s0.match( query_nodes ) ) {
7541 query_nodes = new HashSet<PhylogenyNode>();
7542 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7543 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7544 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7545 if ( !s0.match( query_nodes ) ) {
7549 query_nodes = new HashSet<PhylogenyNode>();
7550 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7551 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7552 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7553 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7554 if ( !s0.match( query_nodes ) ) {
7558 query_nodes = new HashSet<PhylogenyNode>();
7559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7560 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7561 if ( s0.match( query_nodes ) ) {
7565 query_nodes = new HashSet<PhylogenyNode>();
7566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7569 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7570 if ( s0.match( query_nodes ) ) {
7574 query_nodes = new HashSet<PhylogenyNode>();
7575 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7580 if ( s0.match( query_nodes ) ) {
7584 query_nodes = new HashSet<PhylogenyNode>();
7585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7588 if ( s0.match( query_nodes ) ) {
7592 query_nodes = new HashSet<PhylogenyNode>();
7593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7594 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7595 if ( s0.match( query_nodes ) ) {
7599 query_nodes = new HashSet<PhylogenyNode>();
7600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7602 if ( s0.match( query_nodes ) ) {
7606 query_nodes = new HashSet<PhylogenyNode>();
7607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7609 if ( s0.match( query_nodes ) ) {
7613 query_nodes = new HashSet<PhylogenyNode>();
7614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7616 if ( s0.match( query_nodes ) ) {
7620 query_nodes = new HashSet<PhylogenyNode>();
7621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7623 if ( s0.match( query_nodes ) ) {
7627 query_nodes = new HashSet<PhylogenyNode>();
7628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7630 if ( s0.match( query_nodes ) ) {
7634 query_nodes = new HashSet<PhylogenyNode>();
7635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7638 if ( s0.match( query_nodes ) ) {
7642 query_nodes = new HashSet<PhylogenyNode>();
7643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7646 if ( s0.match( query_nodes ) ) {
7650 query_nodes = new HashSet<PhylogenyNode>();
7651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7654 if ( s0.match( query_nodes ) ) {
7658 query_nodes = new HashSet<PhylogenyNode>();
7659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7663 if ( s0.match( query_nodes ) ) {
7667 catch ( final Exception e ) {
7668 e.printStackTrace();
7674 private static boolean testSubtreeDeletion() {
7676 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7677 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7678 t1.deleteSubtree( t1.getNode( "A" ), false );
7679 if ( t1.getNumberOfExternalNodes() != 5 ) {
7682 t1.toNewHampshireX();
7683 t1.deleteSubtree( t1.getNode( "E" ), false );
7684 if ( t1.getNumberOfExternalNodes() != 4 ) {
7687 t1.toNewHampshireX();
7688 t1.deleteSubtree( t1.getNode( "F" ), false );
7689 if ( t1.getNumberOfExternalNodes() != 3 ) {
7692 t1.toNewHampshireX();
7693 t1.deleteSubtree( t1.getNode( "D" ), false );
7694 t1.toNewHampshireX();
7695 if ( t1.getNumberOfExternalNodes() != 3 ) {
7698 t1.deleteSubtree( t1.getNode( "def" ), false );
7699 t1.toNewHampshireX();
7700 if ( t1.getNumberOfExternalNodes() != 2 ) {
7703 t1.deleteSubtree( t1.getNode( "B" ), false );
7704 t1.toNewHampshireX();
7705 if ( t1.getNumberOfExternalNodes() != 1 ) {
7708 t1.deleteSubtree( t1.getNode( "C" ), false );
7709 t1.toNewHampshireX();
7710 if ( t1.getNumberOfExternalNodes() != 1 ) {
7713 t1.deleteSubtree( t1.getNode( "abc" ), false );
7714 t1.toNewHampshireX();
7715 if ( t1.getNumberOfExternalNodes() != 1 ) {
7718 t1.deleteSubtree( t1.getNode( "r" ), false );
7719 if ( t1.getNumberOfExternalNodes() != 0 ) {
7722 if ( !t1.isEmpty() ) {
7725 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7726 t2.deleteSubtree( t2.getNode( "A" ), false );
7727 t2.toNewHampshireX();
7728 if ( t2.getNumberOfExternalNodes() != 5 ) {
7731 t2.deleteSubtree( t2.getNode( "abc" ), false );
7732 t2.toNewHampshireX();
7733 if ( t2.getNumberOfExternalNodes() != 3 ) {
7736 t2.deleteSubtree( t2.getNode( "def" ), false );
7737 t2.toNewHampshireX();
7738 if ( t2.getNumberOfExternalNodes() != 1 ) {
7742 catch ( final Exception e ) {
7743 e.printStackTrace( System.out );
7749 private static boolean testSupportCount() {
7751 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7752 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7753 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7754 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7755 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7756 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7757 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7759 SupportCount.count( t0_1, phylogenies_1, true, false );
7760 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7761 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7762 + "(((((A,B),C),D),E),((F,G),X))"
7763 + "(((((A,Y),B),C),D),((F,G),E))"
7764 + "(((((A,B),C),D),E),(F,G))"
7765 + "(((((A,B),C),D),E),(F,G))"
7766 + "(((((A,B),C),D),E),(F,G))"
7767 + "(((((A,B),C),D),E),(F,G),Z)"
7768 + "(((((A,B),C),D),E),(F,G))"
7769 + "((((((A,B),C),D),E),F),G)"
7770 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7772 SupportCount.count( t0_2, phylogenies_2, true, false );
7773 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7774 while ( it.hasNext() ) {
7775 final PhylogenyNode n = it.next();
7776 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7780 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7781 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7782 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7783 SupportCount.count( t0_3, phylogenies_3, true, false );
7784 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7785 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7788 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7791 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7794 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7797 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7800 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7803 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7806 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7809 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7812 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7815 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7816 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7817 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7818 SupportCount.count( t0_4, phylogenies_4, true, false );
7819 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7820 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7823 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7826 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7829 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7832 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7835 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7838 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7841 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7844 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7847 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7850 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7851 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7852 double d = SupportCount.compare( b1, a, true, true, true );
7853 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7856 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7857 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7858 d = SupportCount.compare( b2, a, true, true, true );
7859 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7862 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7863 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7864 d = SupportCount.compare( b3, a, true, true, true );
7865 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7868 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7869 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7870 d = SupportCount.compare( b4, a, true, true, false );
7871 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7875 catch ( final Exception e ) {
7876 e.printStackTrace( System.out );
7882 private static boolean testSupportTransfer() {
7884 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7885 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)",
7886 new NHXParser() )[ 0 ];
7887 final Phylogeny p2 = factory
7888 .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 ];
7889 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7892 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7895 support_transfer.moveBranchLengthsToBootstrap( p1 );
7896 support_transfer.transferSupportValues( p1, p2 );
7897 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7900 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7903 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7906 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7909 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7912 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7915 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7918 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7922 catch ( final Exception e ) {
7923 e.printStackTrace( System.out );
7929 private static boolean testUniprotTaxonomySearch() {
7931 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7933 if ( results.size() != 1 ) {
7936 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7939 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7942 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7945 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7948 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7952 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7953 if ( results.size() != 1 ) {
7956 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7959 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7962 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7965 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7968 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7972 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7973 if ( results.size() != 1 ) {
7976 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7979 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7982 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7985 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7988 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7992 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7993 if ( results.size() != 1 ) {
7996 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7999 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8002 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8005 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8008 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8011 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
8014 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
8017 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
8018 .equals( "Nematostella vectensis" ) ) {
8019 System.out.println( results.get( 0 ).getLineage() );
8023 catch ( final IOException e ) {
8024 System.out.println();
8025 System.out.println( "the following might be due to absence internet connection:" );
8026 e.printStackTrace( System.out );
8029 catch ( final Exception e ) {
8035 private static boolean testEmblEntryRetrieval() {
8036 //The format for GenBank Accession numbers are:
8037 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
8038 //Protein: 3 letters + 5 numerals
8039 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
8040 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
8043 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
8046 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
8049 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
8052 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
8055 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
8058 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
8061 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
8064 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
8067 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
8070 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
8073 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
8076 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8082 private static boolean testUniprotEntryRetrieval() {
8083 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8086 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8089 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8092 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8095 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8098 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8101 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8104 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8107 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8110 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8113 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8116 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8119 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8123 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8124 if ( !entry.getAccession().equals( "P12345" ) ) {
8127 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8130 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8133 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8136 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8140 catch ( final IOException e ) {
8141 System.out.println();
8142 System.out.println( "the following might be due to absence internet connection:" );
8143 e.printStackTrace( System.out );
8146 catch ( final Exception e ) {
8152 private static boolean testWabiTxSearch() {
8155 result = TxSearch.searchSimple( "nematostella" );
8156 result = TxSearch.getTxId( "nematostella" );
8157 if ( !result.equals( "45350" ) ) {
8160 result = TxSearch.getTxName( "45350" );
8161 if ( !result.equals( "Nematostella" ) ) {
8164 result = TxSearch.getTxId( "nematostella vectensis" );
8165 if ( !result.equals( "45351" ) ) {
8168 result = TxSearch.getTxName( "45351" );
8169 if ( !result.equals( "Nematostella vectensis" ) ) {
8172 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8173 if ( !result.equals( "536089" ) ) {
8176 result = TxSearch.getTxName( "536089" );
8177 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8180 final List<String> queries = new ArrayList<String>();
8181 queries.add( "Campylobacter coli" );
8182 queries.add( "Escherichia coli" );
8183 queries.add( "Arabidopsis" );
8184 queries.add( "Trichoplax" );
8185 queries.add( "Samanea saman" );
8186 queries.add( "Kluyveromyces marxianus" );
8187 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8188 queries.add( "Bornavirus parrot/PDD/2008" );
8189 final List<RANKS> ranks = new ArrayList<RANKS>();
8190 ranks.add( RANKS.SUPERKINGDOM );
8191 ranks.add( RANKS.KINGDOM );
8192 ranks.add( RANKS.FAMILY );
8193 ranks.add( RANKS.GENUS );
8194 ranks.add( RANKS.TRIBE );
8195 result = TxSearch.searchLineage( queries, ranks );
8196 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8197 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8199 catch ( final Exception e ) {
8200 System.out.println();
8201 System.out.println( "the following might be due to absence internet connection:" );
8202 e.printStackTrace( System.out );
8208 private static boolean testAminoAcidSequence() {
8210 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8211 if ( aa1.getLength() != 13 ) {
8214 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8217 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8220 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8223 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8224 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8227 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8228 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8231 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8232 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8236 catch ( final Exception e ) {
8237 e.printStackTrace();
8243 private static boolean testCreateBalancedPhylogeny() {
8245 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8246 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8249 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8252 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8253 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8256 if ( p1.getNumberOfExternalNodes() != 100 ) {
8260 catch ( final Exception e ) {
8261 e.printStackTrace();
8267 private static boolean testFastaParser() {
8269 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8272 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8275 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8276 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8279 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8282 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8285 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8288 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8291 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8295 catch ( final Exception e ) {
8296 e.printStackTrace();
8302 private static boolean testGeneralMsaParser() {
8304 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8305 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8306 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8307 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8308 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8309 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8310 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8311 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8312 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8315 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8318 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8321 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8324 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8327 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8330 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8333 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8336 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8339 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8342 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8345 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8348 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8349 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8352 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8355 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8358 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8359 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8362 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8365 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8368 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8369 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8372 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8375 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8379 catch ( final Exception e ) {
8380 e.printStackTrace();
8386 private static boolean testMafft( final String path ) {
8388 final List<String> opts = new ArrayList<String>();
8389 opts.add( "--maxiterate" );
8391 opts.add( "--localpair" );
8392 opts.add( "--quiet" );
8394 final MsaInferrer mafft = Mafft.createInstance( path );
8395 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8396 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8399 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8403 catch ( final Exception e ) {
8404 e.printStackTrace( System.out );
8410 private static boolean testNextNodeWithCollapsing() {
8412 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8414 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8415 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8416 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8417 t0.getNode( "cd" ).setCollapse( true );
8418 t0.getNode( "cde" ).setCollapse( true );
8419 n = t0.getFirstExternalNode();
8420 while ( n != null ) {
8422 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8424 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8427 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8430 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8433 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8436 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8439 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8443 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8444 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8445 t1.getNode( "ab" ).setCollapse( true );
8446 t1.getNode( "cd" ).setCollapse( true );
8447 t1.getNode( "cde" ).setCollapse( true );
8448 n = t1.getNode( "ab" );
8449 ext = new ArrayList<PhylogenyNode>();
8450 while ( n != null ) {
8452 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8454 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8457 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8460 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8463 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8466 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8472 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8473 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8474 t2.getNode( "ab" ).setCollapse( true );
8475 t2.getNode( "cd" ).setCollapse( true );
8476 t2.getNode( "cde" ).setCollapse( true );
8477 t2.getNode( "c" ).setCollapse( true );
8478 t2.getNode( "d" ).setCollapse( true );
8479 t2.getNode( "e" ).setCollapse( true );
8480 t2.getNode( "gh" ).setCollapse( true );
8481 n = t2.getNode( "ab" );
8482 ext = new ArrayList<PhylogenyNode>();
8483 while ( n != null ) {
8485 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8487 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8490 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8493 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8496 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8502 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8503 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8504 t3.getNode( "ab" ).setCollapse( true );
8505 t3.getNode( "cd" ).setCollapse( true );
8506 t3.getNode( "cde" ).setCollapse( true );
8507 t3.getNode( "c" ).setCollapse( true );
8508 t3.getNode( "d" ).setCollapse( true );
8509 t3.getNode( "e" ).setCollapse( true );
8510 t3.getNode( "gh" ).setCollapse( true );
8511 t3.getNode( "fgh" ).setCollapse( true );
8512 n = t3.getNode( "ab" );
8513 ext = new ArrayList<PhylogenyNode>();
8514 while ( n != null ) {
8516 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8518 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8521 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8524 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8530 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8531 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8532 t4.getNode( "ab" ).setCollapse( true );
8533 t4.getNode( "cd" ).setCollapse( true );
8534 t4.getNode( "cde" ).setCollapse( true );
8535 t4.getNode( "c" ).setCollapse( true );
8536 t4.getNode( "d" ).setCollapse( true );
8537 t4.getNode( "e" ).setCollapse( true );
8538 t4.getNode( "gh" ).setCollapse( true );
8539 t4.getNode( "fgh" ).setCollapse( true );
8540 t4.getNode( "abcdefgh" ).setCollapse( true );
8541 n = t4.getNode( "abcdefgh" );
8542 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8547 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8548 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8550 n = t5.getFirstExternalNode();
8551 while ( n != null ) {
8553 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8555 if ( ext.size() != 8 ) {
8558 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8561 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8564 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8567 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8570 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8573 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8576 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8579 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8584 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8585 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8587 t6.getNode( "ab" ).setCollapse( true );
8588 n = t6.getNode( "ab" );
8589 while ( n != null ) {
8591 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8593 if ( ext.size() != 7 ) {
8596 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8599 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8602 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8605 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8608 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8611 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8614 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8619 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8620 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8622 t7.getNode( "cd" ).setCollapse( true );
8623 n = t7.getNode( "a" );
8624 while ( n != null ) {
8626 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8628 if ( ext.size() != 7 ) {
8631 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8634 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8637 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8640 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8643 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8646 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8649 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8654 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8655 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8657 t8.getNode( "cd" ).setCollapse( true );
8658 t8.getNode( "c" ).setCollapse( true );
8659 t8.getNode( "d" ).setCollapse( true );
8660 n = t8.getNode( "a" );
8661 while ( n != null ) {
8663 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8665 if ( ext.size() != 7 ) {
8668 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8671 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8674 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8675 System.out.println( "2 fail" );
8678 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8681 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8684 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8687 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8692 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8693 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8695 t9.getNode( "gh" ).setCollapse( true );
8696 n = t9.getNode( "a" );
8697 while ( n != null ) {
8699 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8701 if ( ext.size() != 7 ) {
8704 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8707 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8710 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8713 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8716 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8719 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8722 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8727 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8728 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8730 t10.getNode( "gh" ).setCollapse( true );
8731 t10.getNode( "g" ).setCollapse( true );
8732 t10.getNode( "h" ).setCollapse( true );
8733 n = t10.getNode( "a" );
8734 while ( n != null ) {
8736 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8738 if ( ext.size() != 7 ) {
8741 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8744 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8747 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8750 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8753 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8756 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8759 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8764 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8765 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8767 t11.getNode( "gh" ).setCollapse( true );
8768 t11.getNode( "fgh" ).setCollapse( true );
8769 n = t11.getNode( "a" );
8770 while ( n != null ) {
8772 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8774 if ( ext.size() != 6 ) {
8777 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8780 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8783 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8786 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8789 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8792 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8797 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8798 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8800 t12.getNode( "gh" ).setCollapse( true );
8801 t12.getNode( "fgh" ).setCollapse( true );
8802 t12.getNode( "g" ).setCollapse( true );
8803 t12.getNode( "h" ).setCollapse( true );
8804 t12.getNode( "f" ).setCollapse( true );
8805 n = t12.getNode( "a" );
8806 while ( n != null ) {
8808 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8810 if ( ext.size() != 6 ) {
8813 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8816 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8819 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8822 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8825 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8828 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8833 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8834 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8836 t13.getNode( "ab" ).setCollapse( true );
8837 t13.getNode( "b" ).setCollapse( true );
8838 t13.getNode( "fgh" ).setCollapse( true );
8839 t13.getNode( "gh" ).setCollapse( true );
8840 n = t13.getNode( "ab" );
8841 while ( n != null ) {
8843 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8845 if ( ext.size() != 5 ) {
8848 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8851 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8854 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8857 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8860 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8865 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8866 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8868 t14.getNode( "ab" ).setCollapse( true );
8869 t14.getNode( "a" ).setCollapse( true );
8870 t14.getNode( "fgh" ).setCollapse( true );
8871 t14.getNode( "gh" ).setCollapse( true );
8872 n = t14.getNode( "ab" );
8873 while ( n != null ) {
8875 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8877 if ( ext.size() != 5 ) {
8880 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8883 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8886 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8889 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8892 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8897 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" );
8898 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8900 t15.getNode( "ab" ).setCollapse( true );
8901 t15.getNode( "a" ).setCollapse( true );
8902 t15.getNode( "fgh" ).setCollapse( true );
8903 t15.getNode( "gh" ).setCollapse( true );
8904 n = t15.getNode( "ab" );
8905 while ( n != null ) {
8907 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8909 if ( ext.size() != 6 ) {
8912 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8915 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8918 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8921 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8924 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8927 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8932 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" );
8933 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8935 t16.getNode( "ab" ).setCollapse( true );
8936 t16.getNode( "a" ).setCollapse( true );
8937 t16.getNode( "fgh" ).setCollapse( true );
8938 t16.getNode( "gh" ).setCollapse( true );
8939 t16.getNode( "cd" ).setCollapse( true );
8940 t16.getNode( "cde" ).setCollapse( true );
8941 t16.getNode( "d" ).setCollapse( true );
8942 t16.getNode( "x" ).setCollapse( true );
8943 n = t16.getNode( "ab" );
8944 while ( n != null ) {
8946 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8948 if ( ext.size() != 4 ) {
8951 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8954 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8957 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8960 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8964 catch ( final Exception e ) {
8965 e.printStackTrace( System.out );
8971 private static boolean testMsaQualityMethod() {
8973 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8974 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8975 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8976 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8977 final List<Sequence> l = new ArrayList<Sequence>();
8982 final Msa msa = BasicMsa.createInstance( l );
8983 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8986 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8989 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8992 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8996 catch ( final Exception e ) {
8997 e.printStackTrace( System.out );
9003 private static boolean testSequenceIdParsing() {
9005 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
9006 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9007 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9009 System.out.println( "value =" + id.getValue() );
9010 System.out.println( "provider=" + id.getProvider() );
9015 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
9016 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9017 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9019 System.out.println( "value =" + id.getValue() );
9020 System.out.println( "provider=" + id.getProvider() );
9025 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
9026 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9027 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9029 System.out.println( "value =" + id.getValue() );
9030 System.out.println( "provider=" + id.getProvider() );
9035 id = SequenceIdParser.parse( "gb_AAA96518_1" );
9036 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9037 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
9039 System.out.println( "value =" + id.getValue() );
9040 System.out.println( "provider=" + id.getProvider() );
9045 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
9046 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9047 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
9049 System.out.println( "value =" + id.getValue() );
9050 System.out.println( "provider=" + id.getProvider() );
9055 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
9056 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9057 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
9059 System.out.println( "value =" + id.getValue() );
9060 System.out.println( "provider=" + id.getProvider() );
9065 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9066 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9067 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
9069 System.out.println( "value =" + id.getValue() );
9070 System.out.println( "provider=" + id.getProvider() );
9075 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9076 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9077 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9079 System.out.println( "value =" + id.getValue() );
9080 System.out.println( "provider=" + id.getProvider() );
9085 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9086 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9087 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9089 System.out.println( "value =" + id.getValue() );
9090 System.out.println( "provider=" + id.getProvider() );
9095 id = SequenceIdParser.parse( "P4A123" );
9096 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9097 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9099 System.out.println( "value =" + id.getValue() );
9100 System.out.println( "provider=" + id.getProvider() );
9105 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
9106 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9107 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9109 System.out.println( "value =" + id.getValue() );
9110 System.out.println( "provider=" + id.getProvider() );
9115 id = SequenceIdParser.parse( "XP_12345" );
9117 System.out.println( "value =" + id.getValue() );
9118 System.out.println( "provider=" + id.getProvider() );
9121 // lcl_91970_unknown_
9123 catch ( final Exception e ) {
9124 e.printStackTrace( System.out );