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.datastructures.IntMatrix;
42 import org.forester.development.DevelopmentTools;
43 import org.forester.evoinference.TestPhylogenyReconstruction;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
45 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
46 import org.forester.go.TestGo;
47 import org.forester.io.parsers.FastaParser;
48 import org.forester.io.parsers.GeneralMsaParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser;
50 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
51 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
52 import org.forester.io.parsers.nexus.NexusCharactersParser;
53 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
54 import org.forester.io.parsers.nhx.NHXParser;
55 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
56 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
57 import org.forester.io.parsers.tol.TolParser;
58 import org.forester.io.parsers.util.ParserUtils;
59 import org.forester.io.writers.PhylogenyWriter;
60 import org.forester.msa.BasicMsa;
61 import org.forester.msa.Mafft;
62 import org.forester.msa.Msa;
63 import org.forester.msa.MsaInferrer;
64 import org.forester.msa.MsaMethods;
65 import org.forester.pccx.TestPccx;
66 import org.forester.phylogeny.Phylogeny;
67 import org.forester.phylogeny.PhylogenyBranch;
68 import org.forester.phylogeny.PhylogenyMethods;
69 import org.forester.phylogeny.PhylogenyNode;
70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
71 import org.forester.phylogeny.data.BinaryCharacters;
72 import org.forester.phylogeny.data.BranchWidth;
73 import org.forester.phylogeny.data.Confidence;
74 import org.forester.phylogeny.data.Distribution;
75 import org.forester.phylogeny.data.DomainArchitecture;
76 import org.forester.phylogeny.data.Event;
77 import org.forester.phylogeny.data.Identifier;
78 import org.forester.phylogeny.data.PhylogenyData;
79 import org.forester.phylogeny.data.PhylogenyDataUtil;
80 import org.forester.phylogeny.data.Polygon;
81 import org.forester.phylogeny.data.PropertiesMap;
82 import org.forester.phylogeny.data.Property;
83 import org.forester.phylogeny.data.Property.AppliesTo;
84 import org.forester.phylogeny.data.ProteinDomain;
85 import org.forester.phylogeny.data.Taxonomy;
86 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
87 import org.forester.phylogeny.factories.PhylogenyFactory;
88 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
89 import org.forester.protein.Protein;
90 import org.forester.sdi.GSDI;
91 import org.forester.sdi.RIO;
92 import org.forester.sdi.SDI;
93 import org.forester.sdi.SDIR;
94 import org.forester.sdi.SDIse;
95 import org.forester.sdi.TestGSDI;
96 import org.forester.sequence.BasicSequence;
97 import org.forester.sequence.Sequence;
98 import org.forester.surfacing.TestSurfacing;
99 import org.forester.tools.ConfidenceAssessor;
100 import org.forester.tools.SupportCount;
101 import org.forester.tools.TreeSplitMatrix;
102 import org.forester.util.AsciiHistogram;
103 import org.forester.util.BasicDescriptiveStatistics;
104 import org.forester.util.BasicTable;
105 import org.forester.util.BasicTableParser;
106 import org.forester.util.DescriptiveStatistics;
107 import org.forester.util.ForesterConstants;
108 import org.forester.util.ForesterUtil;
109 import org.forester.util.GeneralTable;
110 import org.forester.util.SequenceIdParser;
111 import org.forester.ws.seqdb.SequenceDatabaseEntry;
112 import org.forester.ws.seqdb.SequenceDbWsTools;
113 import org.forester.ws.seqdb.UniProtTaxonomy;
114 import org.forester.ws.wabi.TxSearch;
115 import org.forester.ws.wabi.TxSearch.RANKS;
116 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
117 import org.forester.ws.wabi.TxSearch.TAX_RANK;
119 @SuppressWarnings( "unused")
120 public final class Test {
122 private final static double ZERO_DIFF = 1.0E-9;
123 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "test_data"
125 + ForesterUtil.getFileSeparator();
126 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
127 + ForesterUtil.getFileSeparator() + "resources"
128 + ForesterUtil.getFileSeparator();
129 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
130 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
133 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
134 + ForesterConstants.PHYLO_XML_VERSION + "/"
135 + ForesterConstants.PHYLO_XML_XSD;
137 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
138 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
142 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
143 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
144 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
147 public static boolean isEqual( final double a, final double b ) {
148 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
151 public static void main( final String[] args ) {
152 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
153 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
155 Locale.setDefault( Locale.US );
156 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
159 System.out.print( "[Test if directory with files for testing exists/is readable: " );
160 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
161 System.out.println( "OK.]" );
164 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
165 System.out.println( "Testing aborted." );
168 System.out.print( "[Test if resources directory exists/is readable: " );
169 if ( testDir( PATH_TO_RESOURCES ) ) {
170 System.out.println( "OK.]" );
173 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
174 System.out.println( "Testing aborted." );
177 final long start_time = new Date().getTime();
178 System.out.print( "Sequence id parsing: " );
179 if ( testSequenceIdParsing() ) {
180 System.out.println( "OK." );
184 System.out.println( "failed." );
187 System.out.print( "Hmmscan output parser: " );
188 if ( testHmmscanOutputParser() ) {
189 System.out.println( "OK." );
193 System.out.println( "failed." );
196 System.out.print( "Basic node methods: " );
197 if ( Test.testBasicNodeMethods() ) {
198 System.out.println( "OK." );
202 System.out.println( "failed." );
205 System.out.print( "Taxonomy extraction: " );
206 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
207 System.out.println( "OK." );
211 System.out.println( "failed." );
214 System.out.print( "Basic node construction and parsing of NHX (node level): " );
215 if ( Test.testNHXNodeParsing() ) {
216 System.out.println( "OK." );
220 System.out.println( "failed." );
223 System.out.print( "NH parsing: " );
224 if ( Test.testNHParsing() ) {
225 System.out.println( "OK." );
229 System.out.println( "failed." );
232 System.out.print( "Conversion to NHX (node level): " );
233 if ( Test.testNHXconversion() ) {
234 System.out.println( "OK." );
238 System.out.println( "failed." );
241 System.out.print( "NHX parsing: " );
242 if ( Test.testNHXParsing() ) {
243 System.out.println( "OK." );
247 System.out.println( "failed." );
250 System.out.print( "NHX parsing with quotes: " );
251 if ( Test.testNHXParsingQuotes() ) {
252 System.out.println( "OK." );
256 System.out.println( "failed." );
259 System.out.print( "NHX parsing (MrBayes): " );
260 if ( Test.testNHXParsingMB() ) {
261 System.out.println( "OK." );
265 System.out.println( "failed." );
268 System.out.print( "Nexus characters parsing: " );
269 if ( Test.testNexusCharactersParsing() ) {
270 System.out.println( "OK." );
274 System.out.println( "failed." );
277 System.out.print( "Nexus tree parsing: " );
278 if ( Test.testNexusTreeParsing() ) {
279 System.out.println( "OK." );
283 System.out.println( "failed." );
286 System.out.print( "Nexus tree parsing (translating): " );
287 if ( Test.testNexusTreeParsingTranslating() ) {
288 System.out.println( "OK." );
292 System.out.println( "failed." );
295 System.out.print( "Nexus matrix parsing: " );
296 if ( Test.testNexusMatrixParsing() ) {
297 System.out.println( "OK." );
301 System.out.println( "failed." );
304 System.out.print( "Basic phyloXML parsing: " );
305 if ( Test.testBasicPhyloXMLparsing() ) {
306 System.out.println( "OK." );
310 System.out.println( "failed." );
313 System.out.print( "Basic phyloXML parsing (validating against schema): " );
314 if ( testBasicPhyloXMLparsingValidating() ) {
315 System.out.println( "OK." );
319 System.out.println( "failed." );
322 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
323 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
324 System.out.println( "OK." );
328 System.out.println( "failed." );
331 System.out.print( "phyloXML Distribution Element: " );
332 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
333 System.out.println( "OK." );
337 System.out.println( "failed." );
340 System.out.print( "Tol XML parsing: " );
341 if ( Test.testBasicTolXMLparsing() ) {
342 System.out.println( "OK." );
346 System.out.println( "failed." );
349 System.out.print( "Copying of node data: " );
350 if ( Test.testCopyOfNodeData() ) {
351 System.out.println( "OK." );
355 System.out.println( "failed." );
358 System.out.print( "Basic tree methods: " );
359 if ( Test.testBasicTreeMethods() ) {
360 System.out.println( "OK." );
364 System.out.println( "failed." );
367 System.out.print( "Postorder Iterator: " );
368 if ( Test.testPostOrderIterator() ) {
369 System.out.println( "OK." );
373 System.out.println( "failed." );
376 System.out.print( "Preorder Iterator: " );
377 if ( Test.testPreOrderIterator() ) {
378 System.out.println( "OK." );
382 System.out.println( "failed." );
385 System.out.print( "Levelorder Iterator: " );
386 if ( Test.testLevelOrderIterator() ) {
387 System.out.println( "OK." );
391 System.out.println( "failed." );
394 System.out.print( "Re-id methods: " );
395 if ( Test.testReIdMethods() ) {
396 System.out.println( "OK." );
400 System.out.println( "failed." );
403 System.out.print( "Methods on last external nodes: " );
404 if ( Test.testLastExternalNodeMethods() ) {
405 System.out.println( "OK." );
409 System.out.println( "failed." );
412 System.out.print( "Methods on external nodes: " );
413 if ( Test.testExternalNodeRelatedMethods() ) {
414 System.out.println( "OK." );
418 System.out.println( "failed." );
421 System.out.print( "Deletion of external nodes: " );
422 if ( Test.testDeletionOfExternalNodes() ) {
423 System.out.println( "OK." );
427 System.out.println( "failed." );
430 System.out.print( "Subtree deletion: " );
431 if ( Test.testSubtreeDeletion() ) {
432 System.out.println( "OK." );
436 System.out.println( "failed." );
439 System.out.print( "Phylogeny branch: " );
440 if ( Test.testPhylogenyBranch() ) {
441 System.out.println( "OK." );
445 System.out.println( "failed." );
448 System.out.print( "Rerooting: " );
449 if ( Test.testRerooting() ) {
450 System.out.println( "OK." );
454 System.out.println( "failed." );
457 System.out.print( "Mipoint rooting: " );
458 if ( Test.testMidpointrooting() ) {
459 System.out.println( "OK." );
463 System.out.println( "failed." );
466 System.out.print( "Support count: " );
467 if ( Test.testSupportCount() ) {
468 System.out.println( "OK." );
472 System.out.println( "failed." );
475 System.out.print( "Support transfer: " );
476 if ( Test.testSupportTransfer() ) {
477 System.out.println( "OK." );
481 System.out.println( "failed." );
484 System.out.print( "Finding of LCA: " );
485 if ( Test.testGetLCA() ) {
486 System.out.println( "OK." );
490 System.out.println( "failed." );
493 System.out.print( "Finding of LCA 2: " );
494 if ( Test.testGetLCA2() ) {
495 System.out.println( "OK." );
499 System.out.println( "failed." );
502 System.out.print( "Calculation of distance between nodes: " );
503 if ( Test.testGetDistance() ) {
504 System.out.println( "OK." );
508 System.out.println( "failed." );
511 System.out.print( "SDIse: " );
512 if ( Test.testSDIse() ) {
513 System.out.println( "OK." );
517 System.out.println( "failed." );
520 System.out.print( "SDIunrooted: " );
521 if ( Test.testSDIunrooted() ) {
522 System.out.println( "OK." );
526 System.out.println( "failed." );
529 System.out.print( "GSDI: " );
530 if ( TestGSDI.test() ) {
531 System.out.println( "OK." );
535 System.out.println( "failed." );
538 System.out.print( "Ortholog table: " );
539 if ( Test.testOrthologTable() ) {
540 System.out.println( "OK." );
544 System.out.println( "failed." );
547 System.out.print( "Descriptive statistics: " );
548 if ( Test.testDescriptiveStatistics() ) {
549 System.out.println( "OK." );
553 System.out.println( "failed." );
556 System.out.print( "Data objects and methods: " );
557 if ( Test.testDataObjects() ) {
558 System.out.println( "OK." );
562 System.out.println( "failed." );
565 System.out.print( "Properties map: " );
566 if ( Test.testPropertiesMap() ) {
567 System.out.println( "OK." );
571 System.out.println( "failed." );
574 System.out.print( "Phylogeny reconstruction:" );
575 System.out.println();
576 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
577 System.out.println( "OK." );
581 System.out.println( "failed." );
584 System.out.print( "Analysis of domain architectures: " );
585 System.out.println();
586 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
587 System.out.println( "OK." );
591 System.out.println( "failed." );
594 System.out.print( "GO: " );
595 System.out.println();
596 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
597 System.out.println( "OK." );
601 System.out.println( "failed." );
604 System.out.print( "Modeling tools: " );
605 if ( TestPccx.test() ) {
606 System.out.println( "OK." );
610 System.out.println( "failed." );
613 System.out.print( "Split Matrix strict: " );
614 if ( Test.testSplitStrict() ) {
615 System.out.println( "OK." );
619 System.out.println( "failed." );
622 System.out.print( "Split Matrix: " );
623 if ( Test.testSplit() ) {
624 System.out.println( "OK." );
628 System.out.println( "failed." );
631 System.out.print( "Confidence Assessor: " );
632 if ( Test.testConfidenceAssessor() ) {
633 System.out.println( "OK." );
637 System.out.println( "failed." );
640 System.out.print( "Basic table: " );
641 if ( Test.testBasicTable() ) {
642 System.out.println( "OK." );
646 System.out.println( "failed." );
649 System.out.print( "General table: " );
650 if ( Test.testGeneralTable() ) {
651 System.out.println( "OK." );
655 System.out.println( "failed." );
658 System.out.print( "Amino acid sequence: " );
659 if ( Test.testAminoAcidSequence() ) {
660 System.out.println( "OK." );
664 System.out.println( "failed." );
667 System.out.print( "General MSA parser: " );
668 if ( Test.testGeneralMsaParser() ) {
669 System.out.println( "OK." );
673 System.out.println( "failed." );
676 System.out.print( "Fasta parser for msa: " );
677 if ( Test.testFastaParser() ) {
678 System.out.println( "OK." );
682 System.out.println( "failed." );
685 System.out.print( "Creation of balanced phylogeny: " );
686 if ( Test.testCreateBalancedPhylogeny() ) {
687 System.out.println( "OK." );
691 System.out.println( "failed." );
694 System.out.print( "EMBL Entry Retrieval: " );
695 if ( Test.testEmblEntryRetrieval() ) {
696 System.out.println( "OK." );
700 System.out.println( "failed." );
703 System.out.print( "Uniprot Entry Retrieval: " );
704 if ( Test.testUniprotEntryRetrieval() ) {
705 System.out.println( "OK." );
709 System.out.println( "failed." );
712 System.out.print( "Uniprot Taxonomy Search: " );
713 if ( Test.testUniprotTaxonomySearch() ) {
714 System.out.println( "OK." );
718 System.out.println( "failed." );
723 final String os = ForesterUtil.OS_NAME.toLowerCase();
724 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
725 path = "/usr/local/bin/mafft";
727 else if ( os.indexOf( "win" ) >= 0 ) {
728 path = "C:\\Program Files\\mafft-win\\mafft.bat";
731 path = "/home/czmasek/bin/mafft";
733 if ( !MsaInferrer.isInstalled( path ) ) {
736 if ( !MsaInferrer.isInstalled( path ) ) {
737 path = "/usr/local/bin/mafft";
739 if ( MsaInferrer.isInstalled( path ) ) {
740 System.out.print( "MAFFT (external program): " );
741 if ( Test.testMafft( path ) ) {
742 System.out.println( "OK." );
746 System.out.println( "failed [will not count towards failed tests]" );
750 System.out.print( "Next nodes with collapsed: " );
751 if ( Test.testNextNodeWithCollapsing() ) {
752 System.out.println( "OK." );
756 System.out.println( "failed." );
759 System.out.print( "Simple MSA quality: " );
760 if ( Test.testMsaQualityMethod() ) {
761 System.out.println( "OK." );
765 System.out.println( "failed." );
768 System.out.println();
769 final Runtime rt = java.lang.Runtime.getRuntime();
770 final long free_memory = rt.freeMemory() / 1000000;
771 final long total_memory = rt.totalMemory() / 1000000;
772 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
773 + free_memory + "MB, total memory: " + total_memory + "MB)" );
774 System.out.println();
775 System.out.println( "Successful tests: " + succeeded );
776 System.out.println( "Failed tests: " + failed );
777 System.out.println();
779 System.out.println( "OK." );
782 System.out.println( "Not OK." );
786 private static boolean testExtractTaxonomyCodeFromNodeName() {
788 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
791 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
794 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
797 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
798 .equals( "MOUSE" ) ) {
801 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
802 .equals( "MOUSE" ) ) {
805 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
806 .equals( "MOUSE" ) ) {
809 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
812 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
815 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
819 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
823 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
827 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
830 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
833 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
836 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
840 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
841 .equals( "MOUSE" ) ) {
844 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
845 .equals( "MOUSE" ) ) {
849 catch ( final Exception e ) {
850 e.printStackTrace( System.out );
856 private static boolean testBasicNodeMethods() {
858 if ( PhylogenyNode.getNodeCount() != 0 ) {
861 final PhylogenyNode n1 = new PhylogenyNode();
862 final PhylogenyNode n2 = PhylogenyNode
863 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
864 final PhylogenyNode n3 = PhylogenyNode
865 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
866 final PhylogenyNode n4 = PhylogenyNode
867 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
868 if ( n1.isHasAssignedEvent() ) {
871 if ( PhylogenyNode.getNodeCount() != 4 ) {
874 if ( n3.getIndicator() != 0 ) {
877 if ( n3.getNumberOfExternalNodes() != 1 ) {
880 if ( !n3.isExternal() ) {
883 if ( !n3.isRoot() ) {
886 if ( !n4.getName().equals( "n4" ) ) {
890 catch ( final Exception e ) {
891 e.printStackTrace( System.out );
897 private static boolean testBasicPhyloXMLparsing() {
899 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
900 final PhyloXmlParser xml_parser = new PhyloXmlParser();
901 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
903 if ( xml_parser.getErrorCount() > 0 ) {
904 System.out.println( xml_parser.getErrorMessages().toString() );
907 if ( phylogenies_0.length != 4 ) {
910 final Phylogeny t1 = phylogenies_0[ 0 ];
911 final Phylogeny t2 = phylogenies_0[ 1 ];
912 final Phylogeny t3 = phylogenies_0[ 2 ];
913 final Phylogeny t4 = phylogenies_0[ 3 ];
914 if ( t1.getNumberOfExternalNodes() != 1 ) {
917 if ( !t1.isRooted() ) {
920 if ( t1.isRerootable() ) {
923 if ( !t1.getType().equals( "gene_tree" ) ) {
926 if ( t2.getNumberOfExternalNodes() != 2 ) {
929 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
932 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
935 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
938 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
941 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
944 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
947 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
948 .startsWith( "actgtgggggt" ) ) {
951 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
952 .startsWith( "ctgtgatgcat" ) ) {
955 if ( t3.getNumberOfExternalNodes() != 4 ) {
958 if ( !t1.getName().equals( "t1" ) ) {
961 if ( !t2.getName().equals( "t2" ) ) {
964 if ( !t3.getName().equals( "t3" ) ) {
967 if ( !t4.getName().equals( "t4" ) ) {
970 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
973 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
976 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
979 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
980 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
983 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
986 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
989 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
992 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
993 .equals( "apoptosis" ) ) {
996 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
997 .equals( "GO:0006915" ) ) {
1000 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1001 .equals( "UniProtKB" ) ) {
1004 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1005 .equals( "experimental" ) ) {
1008 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1009 .equals( "function" ) ) {
1012 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1013 .getValue() != 1 ) {
1016 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1017 .getType().equals( "ml" ) ) {
1020 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1021 .equals( "apoptosis" ) ) {
1024 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1025 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1028 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1029 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1032 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1033 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1036 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1037 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1040 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1041 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1044 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1045 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1048 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1049 .equals( "GO:0005829" ) ) {
1052 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1053 .equals( "intracellular organelle" ) ) {
1056 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1059 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1060 .equals( "UniProt link" ) ) ) {
1063 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1067 catch ( final Exception e ) {
1068 e.printStackTrace( System.out );
1074 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1076 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1077 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1078 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1079 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1082 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1084 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1086 if ( xml_parser.getErrorCount() > 0 ) {
1087 System.out.println( xml_parser.getErrorMessages().toString() );
1090 if ( phylogenies_0.length != 4 ) {
1093 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1094 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1095 if ( phylogenies_t1.length != 1 ) {
1098 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1099 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1102 if ( !t1_rt.isRooted() ) {
1105 if ( t1_rt.isRerootable() ) {
1108 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1111 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1112 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1113 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1114 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1117 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1120 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1123 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1126 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1127 .startsWith( "actgtgggggt" ) ) {
1130 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1131 .startsWith( "ctgtgatgcat" ) ) {
1134 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1135 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1136 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1137 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1138 if ( phylogenies_1.length != 1 ) {
1141 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1142 if ( !t3_rt.getName().equals( "t3" ) ) {
1145 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1148 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1151 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1154 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1157 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1158 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1161 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1164 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1167 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1168 .equals( "UniProtKB" ) ) {
1171 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1172 .equals( "apoptosis" ) ) {
1175 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1176 .equals( "GO:0006915" ) ) {
1179 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1180 .equals( "UniProtKB" ) ) {
1183 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1184 .equals( "experimental" ) ) {
1187 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1188 .equals( "function" ) ) {
1191 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1192 .getValue() != 1 ) {
1195 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1196 .getType().equals( "ml" ) ) {
1199 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1200 .equals( "apoptosis" ) ) {
1203 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1204 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1207 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1208 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1211 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1212 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1215 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1216 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1219 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1220 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1223 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1224 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1228 .equals( "GO:0005829" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1232 .equals( "intracellular organelle" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1238 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1239 .equals( "UniProt link" ) ) ) {
1242 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1249 .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." ) ) ) {
1252 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1255 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1258 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1261 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1264 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1265 .equals( "ncbi" ) ) {
1268 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1271 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1272 .getName().equals( "B" ) ) {
1275 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1276 .getFrom() != 21 ) {
1279 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1282 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1283 .getLength() != 24 ) {
1286 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1287 .getConfidence() != 2144 ) {
1290 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1291 .equals( "pfam" ) ) {
1294 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1297 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1300 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1303 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1306 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1307 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1310 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1313 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1316 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1319 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1322 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1325 if ( taxbb.getSynonyms().size() != 2 ) {
1328 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1331 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1334 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1337 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1340 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1343 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1344 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1348 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1351 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1354 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1357 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1360 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1363 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1366 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1370 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1373 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1374 .equalsIgnoreCase( "435" ) ) {
1377 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1380 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1381 .equalsIgnoreCase( "443.7" ) ) {
1384 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1387 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1390 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1391 .equalsIgnoreCase( "433" ) ) {
1395 catch ( final Exception e ) {
1396 e.printStackTrace( System.out );
1402 private static boolean testBasicPhyloXMLparsingValidating() {
1404 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1405 PhyloXmlParser xml_parser = null;
1407 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1409 catch ( final Exception e ) {
1410 // Do nothing -- means were not running from jar.
1412 if ( xml_parser == null ) {
1413 xml_parser = new PhyloXmlParser();
1414 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1415 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1418 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1421 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1423 if ( xml_parser.getErrorCount() > 0 ) {
1424 System.out.println( xml_parser.getErrorMessages().toString() );
1427 if ( phylogenies_0.length != 4 ) {
1430 final Phylogeny t1 = phylogenies_0[ 0 ];
1431 final Phylogeny t2 = phylogenies_0[ 1 ];
1432 final Phylogeny t3 = phylogenies_0[ 2 ];
1433 final Phylogeny t4 = phylogenies_0[ 3 ];
1434 if ( !t1.getName().equals( "t1" ) ) {
1437 if ( !t2.getName().equals( "t2" ) ) {
1440 if ( !t3.getName().equals( "t3" ) ) {
1443 if ( !t4.getName().equals( "t4" ) ) {
1446 if ( t1.getNumberOfExternalNodes() != 1 ) {
1449 if ( t2.getNumberOfExternalNodes() != 2 ) {
1452 if ( t3.getNumberOfExternalNodes() != 4 ) {
1455 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1456 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1457 if ( xml_parser.getErrorCount() > 0 ) {
1458 System.out.println( "errors:" );
1459 System.out.println( xml_parser.getErrorMessages().toString() );
1462 if ( phylogenies_1.length != 4 ) {
1465 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1467 if ( xml_parser.getErrorCount() > 0 ) {
1468 System.out.println( "errors:" );
1469 System.out.println( xml_parser.getErrorMessages().toString() );
1472 if ( phylogenies_2.length != 1 ) {
1475 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1478 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1480 if ( xml_parser.getErrorCount() > 0 ) {
1481 System.out.println( xml_parser.getErrorMessages().toString() );
1484 if ( phylogenies_3.length != 2 ) {
1487 final Phylogeny a = phylogenies_3[ 0 ];
1488 if ( !a.getName().equals( "tree 4" ) ) {
1491 if ( a.getNumberOfExternalNodes() != 3 ) {
1494 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1497 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1500 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1502 if ( xml_parser.getErrorCount() > 0 ) {
1503 System.out.println( xml_parser.getErrorMessages().toString() );
1506 if ( phylogenies_4.length != 1 ) {
1509 final Phylogeny s = phylogenies_4[ 0 ];
1510 if ( s.getNumberOfExternalNodes() != 6 ) {
1513 s.getNode( "first" );
1515 s.getNode( "\"<a'b&c'd\">\"" );
1516 s.getNode( "'''\"" );
1517 s.getNode( "\"\"\"" );
1518 s.getNode( "dick & doof" );
1520 catch ( final Exception e ) {
1521 e.printStackTrace( System.out );
1527 private static boolean testBasicTable() {
1529 final BasicTable<String> t0 = new BasicTable<String>();
1530 if ( t0.getNumberOfColumns() != 0 ) {
1533 if ( t0.getNumberOfRows() != 0 ) {
1536 t0.setValue( 3, 2, "23" );
1537 t0.setValue( 10, 1, "error" );
1538 t0.setValue( 10, 1, "110" );
1539 t0.setValue( 9, 1, "19" );
1540 t0.setValue( 1, 10, "101" );
1541 t0.setValue( 10, 10, "1010" );
1542 t0.setValue( 100, 10, "10100" );
1543 t0.setValue( 0, 0, "00" );
1544 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1547 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1550 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1553 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1556 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1559 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1562 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1565 if ( t0.getNumberOfColumns() != 101 ) {
1568 if ( t0.getNumberOfRows() != 11 ) {
1571 if ( t0.getValueAsString( 49, 4 ) != null ) {
1574 final String l = ForesterUtil.getLineSeparator();
1575 final StringBuffer source = new StringBuffer();
1576 source.append( "" + l );
1577 source.append( "# 1 1 1 1 1 1 1 1" + l );
1578 source.append( " 00 01 02 03" + l );
1579 source.append( " 10 11 12 13 " + l );
1580 source.append( "20 21 22 23 " + l );
1581 source.append( " 30 31 32 33" + l );
1582 source.append( "40 41 42 43" + l );
1583 source.append( " # 1 1 1 1 1 " + l );
1584 source.append( "50 51 52 53 54" + l );
1585 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1586 if ( t1.getNumberOfColumns() != 5 ) {
1589 if ( t1.getNumberOfRows() != 6 ) {
1592 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1595 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1598 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1601 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1604 final StringBuffer source1 = new StringBuffer();
1605 source1.append( "" + l );
1606 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1607 source1.append( " 00; 01 ;02;03" + l );
1608 source1.append( " 10; 11; 12; 13 " + l );
1609 source1.append( "20; 21; 22; 23 " + l );
1610 source1.append( " 30; 31; 32; 33" + l );
1611 source1.append( "40;41;42;43" + l );
1612 source1.append( " # 1 1 1 1 1 " + l );
1613 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1614 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1615 if ( t2.getNumberOfColumns() != 5 ) {
1618 if ( t2.getNumberOfRows() != 6 ) {
1621 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1624 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1627 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1630 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1633 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1636 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1639 final StringBuffer source2 = new StringBuffer();
1640 source2.append( "" + l );
1641 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1642 source2.append( " 00; 01 ;02;03" + l );
1643 source2.append( " 10; 11; 12; 13 " + l );
1644 source2.append( "20; 21; 22; 23 " + l );
1645 source2.append( " " + l );
1646 source2.append( " 30; 31; 32; 33" + l );
1647 source2.append( "40;41;42;43" + l );
1648 source2.append( " comment: 1 1 1 1 1 " + l );
1649 source2.append( ";;;50 ; 52; 53;;54 " + l );
1650 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1656 if ( tl.size() != 2 ) {
1659 final BasicTable<String> t3 = tl.get( 0 );
1660 final BasicTable<String> t4 = tl.get( 1 );
1661 if ( t3.getNumberOfColumns() != 4 ) {
1664 if ( t3.getNumberOfRows() != 3 ) {
1667 if ( t4.getNumberOfColumns() != 4 ) {
1670 if ( t4.getNumberOfRows() != 3 ) {
1673 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1676 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1680 catch ( final Exception e ) {
1681 e.printStackTrace( System.out );
1687 private static boolean testBasicTolXMLparsing() {
1689 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1690 final TolParser parser = new TolParser();
1691 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1692 if ( parser.getErrorCount() > 0 ) {
1693 System.out.println( parser.getErrorMessages().toString() );
1696 if ( phylogenies_0.length != 1 ) {
1699 final Phylogeny t1 = phylogenies_0[ 0 ];
1700 if ( t1.getNumberOfExternalNodes() != 5 ) {
1703 if ( !t1.isRooted() ) {
1706 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1709 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1712 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1715 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1718 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1719 if ( parser.getErrorCount() > 0 ) {
1720 System.out.println( parser.getErrorMessages().toString() );
1723 if ( phylogenies_1.length != 1 ) {
1726 final Phylogeny t2 = phylogenies_1[ 0 ];
1727 if ( t2.getNumberOfExternalNodes() != 664 ) {
1730 if ( !t2.isRooted() ) {
1733 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1736 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1739 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1742 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1745 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1748 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1749 .equals( "Aquifex" ) ) {
1752 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1753 if ( parser.getErrorCount() > 0 ) {
1754 System.out.println( parser.getErrorMessages().toString() );
1757 if ( phylogenies_2.length != 1 ) {
1760 final Phylogeny t3 = phylogenies_2[ 0 ];
1761 if ( t3.getNumberOfExternalNodes() != 184 ) {
1764 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1767 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1770 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1773 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1774 if ( parser.getErrorCount() > 0 ) {
1775 System.out.println( parser.getErrorMessages().toString() );
1778 if ( phylogenies_3.length != 1 ) {
1781 final Phylogeny t4 = phylogenies_3[ 0 ];
1782 if ( t4.getNumberOfExternalNodes() != 1 ) {
1785 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1788 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1791 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1794 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1795 if ( parser.getErrorCount() > 0 ) {
1796 System.out.println( parser.getErrorMessages().toString() );
1799 if ( phylogenies_4.length != 1 ) {
1802 final Phylogeny t5 = phylogenies_4[ 0 ];
1803 if ( t5.getNumberOfExternalNodes() != 13 ) {
1806 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1809 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1812 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1816 catch ( final Exception e ) {
1817 e.printStackTrace( System.out );
1823 private static boolean testBasicTreeMethods() {
1825 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1826 final Phylogeny t1 = factory.create();
1827 if ( !t1.isEmpty() ) {
1830 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1831 if ( t2.getNumberOfExternalNodes() != 4 ) {
1834 if ( t2.getHeight() != 8.5 ) {
1837 if ( !t2.isCompletelyBinary() ) {
1840 if ( t2.isEmpty() ) {
1843 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1844 if ( t3.getNumberOfExternalNodes() != 5 ) {
1847 if ( t3.getHeight() != 11 ) {
1850 if ( t3.isCompletelyBinary() ) {
1853 final PhylogenyNode n = t3.getNode( "ABC" );
1854 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 ];
1855 if ( t4.getNumberOfExternalNodes() != 9 ) {
1858 if ( t4.getHeight() != 11 ) {
1861 if ( t4.isCompletelyBinary() ) {
1864 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)" );
1865 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1866 if ( t5.getNumberOfExternalNodes() != 8 ) {
1869 if ( t5.getHeight() != 15 ) {
1872 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)" );
1873 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1874 if ( t6.getHeight() != 15 ) {
1877 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)" );
1878 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1879 if ( t7.getHeight() != 15 ) {
1882 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)" );
1883 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1884 if ( t8.getNumberOfExternalNodes() != 10 ) {
1887 if ( t8.getHeight() != 15 ) {
1890 final char[] a9 = new char[] {};
1891 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1892 if ( t9.getHeight() != 0 ) {
1895 final char[] a10 = new char[] { 'a', ':', '6' };
1896 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1897 if ( t10.getHeight() != 6 ) {
1901 catch ( final Exception e ) {
1902 e.printStackTrace( System.out );
1908 private static boolean testConfidenceAssessor() {
1910 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1911 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1912 final Phylogeny[] ev0 = factory
1913 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1915 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1916 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1919 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1922 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1923 final Phylogeny[] ev1 = factory
1924 .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)));",
1926 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1927 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1930 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1933 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1934 final Phylogeny[] ev_b = factory
1935 .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",
1937 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1938 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1941 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1945 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1946 final Phylogeny[] ev1x = factory
1947 .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)));",
1949 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1950 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1953 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1956 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1957 final Phylogeny[] ev_bx = factory
1958 .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",
1960 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1961 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1964 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1968 final Phylogeny[] t2 = factory
1969 .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);",
1971 final Phylogeny[] ev2 = factory
1972 .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);",
1974 for( final Phylogeny target : t2 ) {
1975 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
1978 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
1979 new NHXParser() )[ 0 ];
1980 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
1981 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
1982 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1985 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
1988 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1992 catch ( final Exception e ) {
1993 e.printStackTrace();
1999 private static boolean testCopyOfNodeData() {
2001 final PhylogenyNode n1 = PhylogenyNode
2002 .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]" );
2003 final PhylogenyNode n2 = n1.copyNodeData();
2004 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2008 catch ( final Exception e ) {
2009 e.printStackTrace();
2015 private static boolean testDataObjects() {
2017 final Confidence s0 = new Confidence();
2018 final Confidence s1 = new Confidence();
2019 if ( !s0.isEqual( s1 ) ) {
2022 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2023 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2024 if ( s2.isEqual( s1 ) ) {
2027 if ( !s2.isEqual( s3 ) ) {
2030 final Confidence s4 = ( Confidence ) s3.copy();
2031 if ( !s4.isEqual( s3 ) ) {
2038 final Taxonomy t1 = new Taxonomy();
2039 final Taxonomy t2 = new Taxonomy();
2040 final Taxonomy t3 = new Taxonomy();
2041 final Taxonomy t4 = new Taxonomy();
2042 final Taxonomy t5 = new Taxonomy();
2043 t1.setIdentifier( new Identifier( "ecoli" ) );
2044 t1.setTaxonomyCode( "ECOLI" );
2045 t1.setScientificName( "E. coli" );
2046 t1.setCommonName( "coli" );
2047 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2048 if ( !t1.isEqual( t0 ) ) {
2051 t2.setIdentifier( new Identifier( "ecoli" ) );
2052 t2.setTaxonomyCode( "OTHER" );
2053 t2.setScientificName( "what" );
2054 t2.setCommonName( "something" );
2055 if ( !t1.isEqual( t2 ) ) {
2058 t2.setIdentifier( new Identifier( "nemve" ) );
2059 if ( t1.isEqual( t2 ) ) {
2062 t1.setIdentifier( null );
2063 t3.setTaxonomyCode( "ECOLI" );
2064 t3.setScientificName( "what" );
2065 t3.setCommonName( "something" );
2066 if ( !t1.isEqual( t3 ) ) {
2069 t1.setIdentifier( null );
2070 t1.setTaxonomyCode( "" );
2071 t4.setScientificName( "E. ColI" );
2072 t4.setCommonName( "something" );
2073 if ( !t1.isEqual( t4 ) ) {
2076 t4.setScientificName( "B. subtilis" );
2077 t4.setCommonName( "something" );
2078 if ( t1.isEqual( t4 ) ) {
2081 t1.setIdentifier( null );
2082 t1.setTaxonomyCode( "" );
2083 t1.setScientificName( "" );
2084 t5.setCommonName( "COLI" );
2085 if ( !t1.isEqual( t5 ) ) {
2088 t5.setCommonName( "vibrio" );
2089 if ( t1.isEqual( t5 ) ) {
2094 final Identifier id0 = new Identifier( "123", "pfam" );
2095 final Identifier id1 = ( Identifier ) id0.copy();
2096 if ( !id1.isEqual( id1 ) ) {
2099 if ( !id1.isEqual( id0 ) ) {
2102 if ( !id0.isEqual( id1 ) ) {
2109 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2110 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2111 if ( !pd1.isEqual( pd1 ) ) {
2114 if ( !pd1.isEqual( pd0 ) ) {
2119 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2120 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2121 if ( !pd3.isEqual( pd3 ) ) {
2124 if ( !pd2.isEqual( pd3 ) ) {
2127 if ( !pd0.isEqual( pd3 ) ) {
2132 // DomainArchitecture
2133 // ------------------
2134 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2135 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2136 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2137 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2138 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2139 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2144 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2145 if ( ds0.getNumberOfDomains() != 4 ) {
2148 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2149 if ( !ds0.isEqual( ds0 ) ) {
2152 if ( !ds0.isEqual( ds1 ) ) {
2155 if ( ds1.getNumberOfDomains() != 4 ) {
2158 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2163 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2164 if ( ds0.isEqual( ds2 ) ) {
2170 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2171 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2172 System.out.println( ds3.toNHX() );
2175 if ( ds3.getNumberOfDomains() != 3 ) {
2180 final Event e1 = new Event( Event.EventType.fusion );
2181 if ( e1.isDuplication() ) {
2184 if ( !e1.isFusion() ) {
2187 if ( !e1.asText().toString().equals( "fusion" ) ) {
2190 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2193 final Event e11 = new Event( Event.EventType.fusion );
2194 if ( !e11.isEqual( e1 ) ) {
2197 if ( !e11.toNHX().toString().equals( "" ) ) {
2200 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2201 if ( e2.isDuplication() ) {
2204 if ( !e2.isSpeciationOrDuplication() ) {
2207 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2210 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2213 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2216 if ( e11.isEqual( e2 ) ) {
2219 final Event e2c = ( Event ) e2.copy();
2220 if ( !e2c.isEqual( e2 ) ) {
2223 Event e3 = new Event( 1, 2, 3 );
2224 if ( e3.isDuplication() ) {
2227 if ( e3.isSpeciation() ) {
2230 if ( e3.isGeneLoss() ) {
2233 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2236 final Event e3c = ( Event ) e3.copy();
2237 final Event e3cc = ( Event ) e3c.copy();
2238 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2242 if ( !e3c.isEqual( e3cc ) ) {
2245 Event e4 = new Event( 1, 2, 3 );
2246 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2249 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2252 final Event e4c = ( Event ) e4.copy();
2254 final Event e4cc = ( Event ) e4c.copy();
2255 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2258 if ( !e4c.isEqual( e4cc ) ) {
2261 final Event e5 = new Event();
2262 if ( !e5.isUnassigned() ) {
2265 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2268 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2271 final Event e6 = new Event( 1, 0, 0 );
2272 if ( !e6.asText().toString().equals( "duplication" ) ) {
2275 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2278 final Event e7 = new Event( 0, 1, 0 );
2279 if ( !e7.asText().toString().equals( "speciation" ) ) {
2282 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2285 final Event e8 = new Event( 0, 0, 1 );
2286 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2289 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2293 catch ( final Exception e ) {
2294 e.printStackTrace( System.out );
2300 private static boolean testDeletionOfExternalNodes() {
2302 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2303 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2304 final PhylogenyWriter w = new PhylogenyWriter();
2305 if ( t0.isEmpty() ) {
2308 if ( t0.getNumberOfExternalNodes() != 1 ) {
2311 t0.deleteSubtree( t0.getNode( "A" ), false );
2312 if ( t0.getNumberOfExternalNodes() != 0 ) {
2315 if ( !t0.isEmpty() ) {
2318 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2319 if ( t1.getNumberOfExternalNodes() != 2 ) {
2322 t1.deleteSubtree( t1.getNode( "A" ), false );
2323 if ( t1.getNumberOfExternalNodes() != 1 ) {
2326 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2329 t1.deleteSubtree( t1.getNode( "B" ), false );
2330 if ( t1.getNumberOfExternalNodes() != 1 ) {
2333 t1.deleteSubtree( t1.getNode( "r" ), false );
2334 if ( !t1.isEmpty() ) {
2337 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2338 if ( t2.getNumberOfExternalNodes() != 3 ) {
2341 t2.deleteSubtree( t2.getNode( "B" ), false );
2342 if ( t2.getNumberOfExternalNodes() != 2 ) {
2345 t2.toNewHampshireX();
2346 PhylogenyNode n = t2.getNode( "A" );
2347 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2350 t2.deleteSubtree( t2.getNode( "A" ), false );
2351 if ( t2.getNumberOfExternalNodes() != 2 ) {
2354 t2.deleteSubtree( t2.getNode( "C" ), true );
2355 if ( t2.getNumberOfExternalNodes() != 1 ) {
2358 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2359 if ( t3.getNumberOfExternalNodes() != 4 ) {
2362 t3.deleteSubtree( t3.getNode( "B" ), true );
2363 if ( t3.getNumberOfExternalNodes() != 3 ) {
2366 n = t3.getNode( "A" );
2367 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2370 n = n.getNextExternalNode();
2371 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2374 t3.deleteSubtree( t3.getNode( "A" ), true );
2375 if ( t3.getNumberOfExternalNodes() != 2 ) {
2378 n = t3.getNode( "C" );
2379 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2382 t3.deleteSubtree( t3.getNode( "C" ), true );
2383 if ( t3.getNumberOfExternalNodes() != 1 ) {
2386 t3.deleteSubtree( t3.getNode( "D" ), true );
2387 if ( t3.getNumberOfExternalNodes() != 0 ) {
2390 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2391 if ( t4.getNumberOfExternalNodes() != 6 ) {
2394 t4.deleteSubtree( t4.getNode( "B2" ), true );
2395 if ( t4.getNumberOfExternalNodes() != 5 ) {
2398 String s = w.toNewHampshire( t4, false, true ).toString();
2399 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2402 t4.deleteSubtree( t4.getNode( "B11" ), true );
2403 if ( t4.getNumberOfExternalNodes() != 4 ) {
2406 t4.deleteSubtree( t4.getNode( "C" ), true );
2407 if ( t4.getNumberOfExternalNodes() != 3 ) {
2410 n = t4.getNode( "A" );
2411 n = n.getNextExternalNode();
2412 if ( !n.getName().equals( "B12" ) ) {
2415 n = n.getNextExternalNode();
2416 if ( !n.getName().equals( "D" ) ) {
2419 s = w.toNewHampshire( t4, false, true ).toString();
2420 if ( !s.equals( "((A,B12),D);" ) ) {
2423 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2424 t5.deleteSubtree( t5.getNode( "A" ), true );
2425 if ( t5.getNumberOfExternalNodes() != 5 ) {
2428 s = w.toNewHampshire( t5, false, true ).toString();
2429 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2432 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2433 t6.deleteSubtree( t6.getNode( "B11" ), true );
2434 if ( t6.getNumberOfExternalNodes() != 5 ) {
2437 s = w.toNewHampshire( t6, false, false ).toString();
2438 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2441 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2442 t7.deleteSubtree( t7.getNode( "B12" ), true );
2443 if ( t7.getNumberOfExternalNodes() != 5 ) {
2446 s = w.toNewHampshire( t7, false, true ).toString();
2447 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2450 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2451 t8.deleteSubtree( t8.getNode( "B2" ), true );
2452 if ( t8.getNumberOfExternalNodes() != 5 ) {
2455 s = w.toNewHampshire( t8, false, false ).toString();
2456 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2459 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2460 t9.deleteSubtree( t9.getNode( "C" ), true );
2461 if ( t9.getNumberOfExternalNodes() != 5 ) {
2464 s = w.toNewHampshire( t9, false, true ).toString();
2465 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2468 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2469 t10.deleteSubtree( t10.getNode( "D" ), true );
2470 if ( t10.getNumberOfExternalNodes() != 5 ) {
2473 s = w.toNewHampshire( t10, false, true ).toString();
2474 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2477 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2478 t11.deleteSubtree( t11.getNode( "A" ), true );
2479 if ( t11.getNumberOfExternalNodes() != 2 ) {
2482 s = w.toNewHampshire( t11, false, true ).toString();
2483 if ( !s.equals( "(B,C);" ) ) {
2486 t11.deleteSubtree( t11.getNode( "C" ), true );
2487 if ( t11.getNumberOfExternalNodes() != 1 ) {
2490 s = w.toNewHampshire( t11, false, false ).toString();
2491 if ( !s.equals( "B;" ) ) {
2494 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2495 t12.deleteSubtree( t12.getNode( "B2" ), true );
2496 if ( t12.getNumberOfExternalNodes() != 8 ) {
2499 s = w.toNewHampshire( t12, false, true ).toString();
2500 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2503 t12.deleteSubtree( t12.getNode( "B3" ), true );
2504 if ( t12.getNumberOfExternalNodes() != 7 ) {
2507 s = w.toNewHampshire( t12, false, true ).toString();
2508 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2511 t12.deleteSubtree( t12.getNode( "C3" ), true );
2512 if ( t12.getNumberOfExternalNodes() != 6 ) {
2515 s = w.toNewHampshire( t12, false, true ).toString();
2516 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2519 t12.deleteSubtree( t12.getNode( "A1" ), true );
2520 if ( t12.getNumberOfExternalNodes() != 5 ) {
2523 s = w.toNewHampshire( t12, false, true ).toString();
2524 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2527 t12.deleteSubtree( t12.getNode( "B1" ), true );
2528 if ( t12.getNumberOfExternalNodes() != 4 ) {
2531 s = w.toNewHampshire( t12, false, true ).toString();
2532 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2535 t12.deleteSubtree( t12.getNode( "A3" ), true );
2536 if ( t12.getNumberOfExternalNodes() != 3 ) {
2539 s = w.toNewHampshire( t12, false, true ).toString();
2540 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2543 t12.deleteSubtree( t12.getNode( "A2" ), true );
2544 if ( t12.getNumberOfExternalNodes() != 2 ) {
2547 s = w.toNewHampshire( t12, false, true ).toString();
2548 if ( !s.equals( "(C1,C2);" ) ) {
2551 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2552 t13.deleteSubtree( t13.getNode( "D" ), true );
2553 if ( t13.getNumberOfExternalNodes() != 4 ) {
2556 s = w.toNewHampshire( t13, false, true ).toString();
2557 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2560 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2561 t14.deleteSubtree( t14.getNode( "E" ), true );
2562 if ( t14.getNumberOfExternalNodes() != 5 ) {
2565 s = w.toNewHampshire( t14, false, true ).toString();
2566 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2569 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2570 t15.deleteSubtree( t15.getNode( "B2" ), true );
2571 if ( t15.getNumberOfExternalNodes() != 11 ) {
2574 t15.deleteSubtree( t15.getNode( "B1" ), true );
2575 if ( t15.getNumberOfExternalNodes() != 10 ) {
2578 t15.deleteSubtree( t15.getNode( "B3" ), true );
2579 if ( t15.getNumberOfExternalNodes() != 9 ) {
2582 t15.deleteSubtree( t15.getNode( "B4" ), true );
2583 if ( t15.getNumberOfExternalNodes() != 8 ) {
2586 t15.deleteSubtree( t15.getNode( "A1" ), true );
2587 if ( t15.getNumberOfExternalNodes() != 7 ) {
2590 t15.deleteSubtree( t15.getNode( "C4" ), true );
2591 if ( t15.getNumberOfExternalNodes() != 6 ) {
2595 catch ( final Exception e ) {
2596 e.printStackTrace( System.out );
2602 private static boolean testDescriptiveStatistics() {
2604 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2605 dss1.addValue( 82 );
2606 dss1.addValue( 78 );
2607 dss1.addValue( 70 );
2608 dss1.addValue( 58 );
2609 dss1.addValue( 42 );
2610 if ( dss1.getN() != 5 ) {
2613 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2616 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2619 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2622 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2625 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2628 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2631 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2634 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2637 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2640 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2643 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2646 dss1.addValue( 123 );
2647 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2650 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2653 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2656 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2657 dss2.addValue( -1.85 );
2658 dss2.addValue( 57.5 );
2659 dss2.addValue( 92.78 );
2660 dss2.addValue( 57.78 );
2661 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2664 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2667 final double[] a = dss2.getDataAsDoubleArray();
2668 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2671 dss2.addValue( -100 );
2672 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2675 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2678 final double[] ds = new double[ 14 ];
2693 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2694 if ( bins.length != 4 ) {
2697 if ( bins[ 0 ] != 2 ) {
2700 if ( bins[ 1 ] != 3 ) {
2703 if ( bins[ 2 ] != 4 ) {
2706 if ( bins[ 3 ] != 5 ) {
2709 final double[] ds1 = new double[ 9 ];
2719 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2720 if ( bins1.length != 4 ) {
2723 if ( bins1[ 0 ] != 2 ) {
2726 if ( bins1[ 1 ] != 3 ) {
2729 if ( bins1[ 2 ] != 0 ) {
2732 if ( bins1[ 3 ] != 4 ) {
2735 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2736 if ( bins1_1.length != 3 ) {
2739 if ( bins1_1[ 0 ] != 3 ) {
2742 if ( bins1_1[ 1 ] != 2 ) {
2745 if ( bins1_1[ 2 ] != 4 ) {
2748 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2749 if ( bins1_2.length != 3 ) {
2752 if ( bins1_2[ 0 ] != 2 ) {
2755 if ( bins1_2[ 1 ] != 2 ) {
2758 if ( bins1_2[ 2 ] != 2 ) {
2761 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2775 dss3.addValue( 10 );
2776 dss3.addValue( 10 );
2777 dss3.addValue( 10 );
2778 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2779 histo.toStringBuffer( 10, '=', 40, 5 );
2780 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2782 catch ( final Exception e ) {
2783 e.printStackTrace( System.out );
2789 private static boolean testDir( final String file ) {
2791 final File f = new File( file );
2792 if ( !f.exists() ) {
2795 if ( !f.isDirectory() ) {
2798 if ( !f.canRead() ) {
2802 catch ( final Exception e ) {
2808 private static boolean testExternalNodeRelatedMethods() {
2810 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2811 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2812 PhylogenyNode n = t1.getNode( "A" );
2813 n = n.getNextExternalNode();
2814 if ( !n.getName().equals( "B" ) ) {
2817 n = n.getNextExternalNode();
2818 if ( !n.getName().equals( "C" ) ) {
2821 n = n.getNextExternalNode();
2822 if ( !n.getName().equals( "D" ) ) {
2825 n = t1.getNode( "B" );
2826 while ( !n.isLastExternalNode() ) {
2827 n = n.getNextExternalNode();
2829 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2830 n = t2.getNode( "A" );
2831 n = n.getNextExternalNode();
2832 if ( !n.getName().equals( "B" ) ) {
2835 n = n.getNextExternalNode();
2836 if ( !n.getName().equals( "C" ) ) {
2839 n = n.getNextExternalNode();
2840 if ( !n.getName().equals( "D" ) ) {
2843 n = t2.getNode( "B" );
2844 while ( !n.isLastExternalNode() ) {
2845 n = n.getNextExternalNode();
2847 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2848 n = t3.getNode( "A" );
2849 n = n.getNextExternalNode();
2850 if ( !n.getName().equals( "B" ) ) {
2853 n = n.getNextExternalNode();
2854 if ( !n.getName().equals( "C" ) ) {
2857 n = n.getNextExternalNode();
2858 if ( !n.getName().equals( "D" ) ) {
2861 n = n.getNextExternalNode();
2862 if ( !n.getName().equals( "E" ) ) {
2865 n = n.getNextExternalNode();
2866 if ( !n.getName().equals( "F" ) ) {
2869 n = n.getNextExternalNode();
2870 if ( !n.getName().equals( "G" ) ) {
2873 n = n.getNextExternalNode();
2874 if ( !n.getName().equals( "H" ) ) {
2877 n = t3.getNode( "B" );
2878 while ( !n.isLastExternalNode() ) {
2879 n = n.getNextExternalNode();
2881 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2882 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2883 final PhylogenyNode node = iter.next();
2885 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2886 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2887 final PhylogenyNode node = iter.next();
2890 catch ( final Exception e ) {
2891 e.printStackTrace( System.out );
2897 private static boolean testGeneralTable() {
2899 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2900 t0.setValue( 3, 2, "23" );
2901 t0.setValue( 10, 1, "error" );
2902 t0.setValue( 10, 1, "110" );
2903 t0.setValue( 9, 1, "19" );
2904 t0.setValue( 1, 10, "101" );
2905 t0.setValue( 10, 10, "1010" );
2906 t0.setValue( 100, 10, "10100" );
2907 t0.setValue( 0, 0, "00" );
2908 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2911 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2914 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2917 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2920 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2923 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2926 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2929 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2932 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2935 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2936 t1.setValue( "3", "2", "23" );
2937 t1.setValue( "10", "1", "error" );
2938 t1.setValue( "10", "1", "110" );
2939 t1.setValue( "9", "1", "19" );
2940 t1.setValue( "1", "10", "101" );
2941 t1.setValue( "10", "10", "1010" );
2942 t1.setValue( "100", "10", "10100" );
2943 t1.setValue( "0", "0", "00" );
2944 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2945 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2948 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2951 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2954 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2957 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2960 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
2963 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
2966 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
2969 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
2972 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
2976 catch ( final Exception e ) {
2977 e.printStackTrace( System.out );
2983 private static boolean testGetDistance() {
2985 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2986 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",
2987 new NHXParser() )[ 0 ];
2988 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
2989 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
2992 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
2995 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
2998 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3001 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3004 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3007 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3010 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3013 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3016 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3019 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3022 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3025 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3028 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3031 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3034 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3037 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3040 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3043 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3046 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3049 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3052 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3055 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3058 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3061 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3064 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3067 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3070 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3073 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3076 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3079 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3082 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",
3083 new NHXParser() )[ 0 ];
3084 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3087 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3090 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3093 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3096 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3099 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3102 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3105 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3108 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3111 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3114 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3118 catch ( final Exception e ) {
3119 e.printStackTrace( System.out );
3125 private static boolean testGetLCA() {
3127 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3128 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3129 new NHXParser() )[ 0 ];
3130 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3131 if ( !A.getName().equals( "A" ) ) {
3134 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3135 if ( !gh.getName().equals( "gh" ) ) {
3138 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3139 if ( !ab.getName().equals( "ab" ) ) {
3142 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3143 if ( !ab2.getName().equals( "ab" ) ) {
3146 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3147 if ( !gh2.getName().equals( "gh" ) ) {
3150 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3151 if ( !gh3.getName().equals( "gh" ) ) {
3154 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3155 if ( !abc.getName().equals( "abc" ) ) {
3158 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3159 if ( !abc2.getName().equals( "abc" ) ) {
3162 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3163 if ( !abcd.getName().equals( "abcd" ) ) {
3166 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3167 if ( !abcd2.getName().equals( "abcd" ) ) {
3170 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3171 if ( !abcdef.getName().equals( "abcdef" ) ) {
3174 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3175 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3178 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3179 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3182 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3183 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3186 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3187 if ( !abcde.getName().equals( "abcde" ) ) {
3190 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3191 if ( !abcde2.getName().equals( "abcde" ) ) {
3194 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3195 if ( !r.getName().equals( "abcdefgh" ) ) {
3198 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3199 if ( !r2.getName().equals( "abcdefgh" ) ) {
3202 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3203 if ( !r3.getName().equals( "abcdefgh" ) ) {
3206 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3207 if ( !abcde3.getName().equals( "abcde" ) ) {
3210 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3211 if ( !abcde4.getName().equals( "abcde" ) ) {
3214 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3215 if ( !ab3.getName().equals( "ab" ) ) {
3218 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3219 if ( !ab4.getName().equals( "ab" ) ) {
3222 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3223 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3224 if ( !cd.getName().equals( "cd" ) ) {
3227 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3228 if ( !cd2.getName().equals( "cd" ) ) {
3231 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3232 if ( !cde.getName().equals( "cde" ) ) {
3235 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3236 if ( !cde2.getName().equals( "cde" ) ) {
3239 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3240 if ( !cdef.getName().equals( "cdef" ) ) {
3243 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3244 if ( !cdef2.getName().equals( "cdef" ) ) {
3247 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3248 if ( !cdef3.getName().equals( "cdef" ) ) {
3251 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3252 if ( !rt.getName().equals( "r" ) ) {
3255 final Phylogeny p3 = factory
3256 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3257 new NHXParser() )[ 0 ];
3258 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3259 if ( !bc_3.getName().equals( "bc" ) ) {
3262 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3263 if ( !ac_3.getName().equals( "abc" ) ) {
3266 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3267 if ( !ad_3.getName().equals( "abcde" ) ) {
3270 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3271 if ( !af_3.getName().equals( "abcdef" ) ) {
3274 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3275 if ( !ag_3.getName().equals( "" ) ) {
3278 if ( !ag_3.isRoot() ) {
3281 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3282 if ( !al_3.getName().equals( "" ) ) {
3285 if ( !al_3.isRoot() ) {
3288 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3289 if ( !kl_3.getName().equals( "" ) ) {
3292 if ( !kl_3.isRoot() ) {
3295 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3296 if ( !fl_3.getName().equals( "" ) ) {
3299 if ( !fl_3.isRoot() ) {
3302 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3303 if ( !gk_3.getName().equals( "ghijk" ) ) {
3306 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3307 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3308 if ( !r_4.getName().equals( "r" ) ) {
3311 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3312 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3313 if ( !r_5.getName().equals( "root" ) ) {
3316 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3317 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3318 if ( !r_6.getName().equals( "rot" ) ) {
3321 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3322 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3323 if ( !r_7.getName().equals( "rott" ) ) {
3327 catch ( final Exception e ) {
3328 e.printStackTrace( System.out );
3334 private static boolean testGetLCA2() {
3336 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3337 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3338 PhylogenyMethods.preOrderReId( p_a );
3339 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3340 p_a.getNode( "a" ) );
3341 if ( !p_a_1.getName().equals( "a" ) ) {
3344 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3345 PhylogenyMethods.preOrderReId( p_b );
3346 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3347 p_b.getNode( "a" ) );
3348 if ( !p_b_1.getName().equals( "b" ) ) {
3351 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3352 p_b.getNode( "b" ) );
3353 if ( !p_b_2.getName().equals( "b" ) ) {
3356 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3357 System.out.println( p_c.toNewHampshireX() );
3358 PhylogenyMethods.preOrderReId( p_c );
3359 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3360 p_c.getNode( "a" ) );
3361 if ( !p_c_1.getName().equals( "b" ) ) {
3364 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3365 p_c.getNode( "c" ) );
3366 if ( !p_c_2.getName().equals( "c" ) ) {
3367 System.out.println( p_c_2.getName() );
3371 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3372 p_c.getNode( "b" ) );
3373 if ( !p_c_3.getName().equals( "b" ) ) {
3376 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3377 p_c.getNode( "a" ) );
3378 if ( !p_c_4.getName().equals( "c" ) ) {
3381 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3382 new NHXParser() )[ 0 ];
3383 PhylogenyMethods.preOrderReId( p1 );
3384 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3385 p1.getNode( "A" ) );
3386 if ( !A.getName().equals( "A" ) ) {
3389 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3390 p1.getNode( "gh" ) );
3391 if ( !gh.getName().equals( "gh" ) ) {
3394 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3395 p1.getNode( "B" ) );
3396 if ( !ab.getName().equals( "ab" ) ) {
3399 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3400 p1.getNode( "A" ) );
3401 if ( !ab2.getName().equals( "ab" ) ) {
3404 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3405 p1.getNode( "G" ) );
3406 if ( !gh2.getName().equals( "gh" ) ) {
3409 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3410 p1.getNode( "H" ) );
3411 if ( !gh3.getName().equals( "gh" ) ) {
3414 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3415 p1.getNode( "A" ) );
3416 if ( !abc.getName().equals( "abc" ) ) {
3419 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3420 p1.getNode( "C" ) );
3421 if ( !abc2.getName().equals( "abc" ) ) {
3424 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3425 p1.getNode( "D" ) );
3426 if ( !abcd.getName().equals( "abcd" ) ) {
3429 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3430 p1.getNode( "A" ) );
3431 if ( !abcd2.getName().equals( "abcd" ) ) {
3434 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3435 p1.getNode( "F" ) );
3436 if ( !abcdef.getName().equals( "abcdef" ) ) {
3439 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3440 p1.getNode( "A" ) );
3441 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3444 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3445 p1.getNode( "F" ) );
3446 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3449 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3450 p1.getNode( "ab" ) );
3451 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3454 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3455 p1.getNode( "E" ) );
3456 if ( !abcde.getName().equals( "abcde" ) ) {
3459 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3460 p1.getNode( "A" ) );
3461 if ( !abcde2.getName().equals( "abcde" ) ) {
3464 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3465 p1.getNode( "abcdefgh" ) );
3466 if ( !r.getName().equals( "abcdefgh" ) ) {
3469 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3470 p1.getNode( "H" ) );
3471 if ( !r2.getName().equals( "abcdefgh" ) ) {
3474 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3475 p1.getNode( "A" ) );
3476 if ( !r3.getName().equals( "abcdefgh" ) ) {
3479 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3480 p1.getNode( "abcde" ) );
3481 if ( !abcde3.getName().equals( "abcde" ) ) {
3484 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3485 p1.getNode( "E" ) );
3486 if ( !abcde4.getName().equals( "abcde" ) ) {
3489 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3490 p1.getNode( "B" ) );
3491 if ( !ab3.getName().equals( "ab" ) ) {
3494 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3495 p1.getNode( "ab" ) );
3496 if ( !ab4.getName().equals( "ab" ) ) {
3499 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3500 PhylogenyMethods.preOrderReId( p2 );
3501 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3502 p2.getNode( "d" ) );
3503 if ( !cd.getName().equals( "cd" ) ) {
3506 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3507 p2.getNode( "c" ) );
3508 if ( !cd2.getName().equals( "cd" ) ) {
3511 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3512 p2.getNode( "e" ) );
3513 if ( !cde.getName().equals( "cde" ) ) {
3516 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3517 p2.getNode( "c" ) );
3518 if ( !cde2.getName().equals( "cde" ) ) {
3521 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3522 p2.getNode( "f" ) );
3523 if ( !cdef.getName().equals( "cdef" ) ) {
3526 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3527 p2.getNode( "f" ) );
3528 if ( !cdef2.getName().equals( "cdef" ) ) {
3531 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3532 p2.getNode( "d" ) );
3533 if ( !cdef3.getName().equals( "cdef" ) ) {
3536 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3537 p2.getNode( "a" ) );
3538 if ( !rt.getName().equals( "r" ) ) {
3541 final Phylogeny p3 = factory
3542 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3543 new NHXParser() )[ 0 ];
3544 PhylogenyMethods.preOrderReId( p3 );
3545 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3546 p3.getNode( "c" ) );
3547 if ( !bc_3.getName().equals( "bc" ) ) {
3550 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3551 p3.getNode( "c" ) );
3552 if ( !ac_3.getName().equals( "abc" ) ) {
3555 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3556 p3.getNode( "d" ) );
3557 if ( !ad_3.getName().equals( "abcde" ) ) {
3560 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3561 p3.getNode( "f" ) );
3562 if ( !af_3.getName().equals( "abcdef" ) ) {
3565 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3566 p3.getNode( "g" ) );
3567 if ( !ag_3.getName().equals( "" ) ) {
3570 if ( !ag_3.isRoot() ) {
3573 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3574 p3.getNode( "l" ) );
3575 if ( !al_3.getName().equals( "" ) ) {
3578 if ( !al_3.isRoot() ) {
3581 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3582 p3.getNode( "l" ) );
3583 if ( !kl_3.getName().equals( "" ) ) {
3586 if ( !kl_3.isRoot() ) {
3589 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3590 p3.getNode( "l" ) );
3591 if ( !fl_3.getName().equals( "" ) ) {
3594 if ( !fl_3.isRoot() ) {
3597 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3598 p3.getNode( "k" ) );
3599 if ( !gk_3.getName().equals( "ghijk" ) ) {
3602 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3603 PhylogenyMethods.preOrderReId( p4 );
3604 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3605 p4.getNode( "c" ) );
3606 if ( !r_4.getName().equals( "r" ) ) {
3609 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3610 PhylogenyMethods.preOrderReId( p5 );
3611 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3612 p5.getNode( "c" ) );
3613 if ( !r_5.getName().equals( "root" ) ) {
3616 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3617 PhylogenyMethods.preOrderReId( p6 );
3618 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3619 p6.getNode( "a" ) );
3620 if ( !r_6.getName().equals( "rot" ) ) {
3623 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3624 PhylogenyMethods.preOrderReId( p7 );
3625 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3626 p7.getNode( "e" ) );
3627 if ( !r_7.getName().equals( "rott" ) ) {
3630 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3631 p7.getNode( "a" ) );
3632 if ( !r_71.getName().equals( "rott" ) ) {
3635 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3636 p7.getNode( "rott" ) );
3637 if ( !r_72.getName().equals( "rott" ) ) {
3640 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3641 p7.getNode( "a" ) );
3642 if ( !r_73.getName().equals( "rott" ) ) {
3645 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3646 p7.getNode( "rott" ) );
3647 if ( !r_74.getName().equals( "rott" ) ) {
3650 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3651 p7.getNode( "e" ) );
3652 if ( !r_75.getName().equals( "e" ) ) {
3656 catch ( final Exception e ) {
3657 e.printStackTrace( System.out );
3663 private static boolean testHmmscanOutputParser() {
3664 final String test_dir = Test.PATH_TO_TEST_DATA;
3666 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3667 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3669 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3670 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3671 final List<Protein> proteins = parser2.parse();
3672 if ( parser2.getProteinsEncountered() != 4 ) {
3675 if ( proteins.size() != 4 ) {
3678 if ( parser2.getDomainsEncountered() != 69 ) {
3681 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3684 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3687 final Protein p1 = proteins.get( 0 );
3688 if ( p1.getNumberOfProteinDomains() != 15 ) {
3691 if ( p1.getLength() != 850 ) {
3694 final Protein p2 = proteins.get( 1 );
3695 if ( p2.getNumberOfProteinDomains() != 51 ) {
3698 if ( p2.getLength() != 1291 ) {
3701 final Protein p3 = proteins.get( 2 );
3702 if ( p3.getNumberOfProteinDomains() != 2 ) {
3705 final Protein p4 = proteins.get( 3 );
3706 if ( p4.getNumberOfProteinDomains() != 1 ) {
3709 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3712 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3715 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3718 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3721 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3724 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3727 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3730 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3733 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3737 catch ( final Exception e ) {
3738 e.printStackTrace( System.out );
3744 private static boolean testLastExternalNodeMethods() {
3746 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3747 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3748 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3749 final PhylogenyNode n1 = t0.getNode( "A" );
3750 if ( n1.isLastExternalNode() ) {
3753 final PhylogenyNode n2 = t0.getNode( "B" );
3754 if ( n2.isLastExternalNode() ) {
3757 final PhylogenyNode n3 = t0.getNode( "C" );
3758 if ( n3.isLastExternalNode() ) {
3761 final PhylogenyNode n4 = t0.getNode( "D" );
3762 if ( !n4.isLastExternalNode() ) {
3766 catch ( final Exception e ) {
3767 e.printStackTrace( System.out );
3773 private static boolean testLevelOrderIterator() {
3775 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3776 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3777 PhylogenyNodeIterator it0;
3778 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3781 for( it0.reset(); it0.hasNext(); ) {
3784 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3785 if ( !it.next().getName().equals( "r" ) ) {
3788 if ( !it.next().getName().equals( "ab" ) ) {
3791 if ( !it.next().getName().equals( "cd" ) ) {
3794 if ( !it.next().getName().equals( "A" ) ) {
3797 if ( !it.next().getName().equals( "B" ) ) {
3800 if ( !it.next().getName().equals( "C" ) ) {
3803 if ( !it.next().getName().equals( "D" ) ) {
3806 if ( it.hasNext() ) {
3809 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",
3810 new NHXParser() )[ 0 ];
3811 PhylogenyNodeIterator it2;
3812 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3815 for( it2.reset(); it2.hasNext(); ) {
3818 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3819 if ( !it3.next().getName().equals( "r" ) ) {
3822 if ( !it3.next().getName().equals( "abc" ) ) {
3825 if ( !it3.next().getName().equals( "defg" ) ) {
3828 if ( !it3.next().getName().equals( "A" ) ) {
3831 if ( !it3.next().getName().equals( "B" ) ) {
3834 if ( !it3.next().getName().equals( "C" ) ) {
3837 if ( !it3.next().getName().equals( "D" ) ) {
3840 if ( !it3.next().getName().equals( "E" ) ) {
3843 if ( !it3.next().getName().equals( "F" ) ) {
3846 if ( !it3.next().getName().equals( "G" ) ) {
3849 if ( !it3.next().getName().equals( "1" ) ) {
3852 if ( !it3.next().getName().equals( "2" ) ) {
3855 if ( !it3.next().getName().equals( "3" ) ) {
3858 if ( !it3.next().getName().equals( "4" ) ) {
3861 if ( !it3.next().getName().equals( "5" ) ) {
3864 if ( !it3.next().getName().equals( "6" ) ) {
3867 if ( !it3.next().getName().equals( "f1" ) ) {
3870 if ( !it3.next().getName().equals( "f2" ) ) {
3873 if ( !it3.next().getName().equals( "f3" ) ) {
3876 if ( !it3.next().getName().equals( "a" ) ) {
3879 if ( !it3.next().getName().equals( "b" ) ) {
3882 if ( !it3.next().getName().equals( "f21" ) ) {
3885 if ( !it3.next().getName().equals( "X" ) ) {
3888 if ( !it3.next().getName().equals( "Y" ) ) {
3891 if ( !it3.next().getName().equals( "Z" ) ) {
3894 if ( it3.hasNext() ) {
3897 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3898 PhylogenyNodeIterator it4;
3899 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3902 for( it4.reset(); it4.hasNext(); ) {
3905 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3906 if ( !it5.next().getName().equals( "r" ) ) {
3909 if ( !it5.next().getName().equals( "A" ) ) {
3912 if ( !it5.next().getName().equals( "B" ) ) {
3915 if ( !it5.next().getName().equals( "C" ) ) {
3918 if ( !it5.next().getName().equals( "D" ) ) {
3921 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3922 PhylogenyNodeIterator it6;
3923 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3926 for( it6.reset(); it6.hasNext(); ) {
3929 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3930 if ( !it7.next().getName().equals( "A" ) ) {
3933 if ( it.hasNext() ) {
3937 catch ( final Exception e ) {
3938 e.printStackTrace( System.out );
3944 private static boolean testMidpointrooting() {
3946 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3947 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",
3948 new NHXParser() )[ 0 ];
3949 if ( !t1.isRooted() ) {
3952 PhylogenyMethods.midpointRoot( t1 );
3953 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3956 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3959 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3962 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3965 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3968 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3971 t1.reRoot( t1.getNode( "A" ) );
3972 PhylogenyMethods.midpointRoot( t1 );
3973 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3976 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3979 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3982 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3985 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3988 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3992 catch ( final Exception e ) {
3993 e.printStackTrace( System.out );
3999 private static boolean testNexusCharactersParsing() {
4001 final NexusCharactersParser parser = new NexusCharactersParser();
4002 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4004 String[] labels = parser.getCharStateLabels();
4005 if ( labels.length != 7 ) {
4008 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4011 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4014 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4017 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4020 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4023 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4026 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4029 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4031 labels = parser.getCharStateLabels();
4032 if ( labels.length != 7 ) {
4035 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4038 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4041 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4044 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4047 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4050 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4053 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4057 catch ( final Exception e ) {
4058 e.printStackTrace( System.out );
4064 private static boolean testNexusMatrixParsing() {
4066 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4067 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4069 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4070 if ( m.getNumberOfCharacters() != 9 ) {
4073 if ( m.getNumberOfIdentifiers() != 5 ) {
4076 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4079 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4082 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4085 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4088 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4091 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4094 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4097 // if ( labels.length != 7 ) {
4100 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4103 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4106 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4109 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4112 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4115 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4118 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4121 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4123 // labels = parser.getCharStateLabels();
4124 // if ( labels.length != 7 ) {
4127 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4130 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4133 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4136 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4139 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4142 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4145 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4149 catch ( final Exception e ) {
4150 e.printStackTrace( System.out );
4156 private static boolean testNexusTreeParsing() {
4158 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4159 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4160 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4161 if ( phylogenies.length != 1 ) {
4164 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4167 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4171 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4172 if ( phylogenies.length != 1 ) {
4175 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4178 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4182 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4183 if ( phylogenies.length != 1 ) {
4186 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4189 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4192 if ( phylogenies[ 0 ].isRooted() ) {
4196 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4197 if ( phylogenies.length != 18 ) {
4200 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4203 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4206 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4209 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4212 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4215 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4218 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4221 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4224 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4227 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4230 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4233 if ( phylogenies[ 8 ].isRooted() ) {
4236 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4239 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4242 if ( !phylogenies[ 9 ].isRooted() ) {
4245 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4248 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4251 if ( !phylogenies[ 10 ].isRooted() ) {
4254 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4257 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4260 if ( phylogenies[ 11 ].isRooted() ) {
4263 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4266 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4269 if ( !phylogenies[ 12 ].isRooted() ) {
4272 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4275 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4278 if ( !phylogenies[ 13 ].isRooted() ) {
4281 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4284 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4287 if ( !phylogenies[ 14 ].isRooted() ) {
4290 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4293 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4296 if ( phylogenies[ 15 ].isRooted() ) {
4299 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4302 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4305 if ( !phylogenies[ 16 ].isRooted() ) {
4308 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4311 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4314 if ( phylogenies[ 17 ].isRooted() ) {
4317 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4321 catch ( final Exception e ) {
4322 e.printStackTrace( System.out );
4328 private static boolean testNexusTreeParsingTranslating() {
4330 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4331 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4332 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4333 if ( phylogenies.length != 1 ) {
4336 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4339 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4342 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4345 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4348 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4349 .equals( "Aranaeus" ) ) {
4353 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4354 if ( phylogenies.length != 3 ) {
4357 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4360 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4363 if ( phylogenies[ 0 ].isRooted() ) {
4366 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4369 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4372 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4373 .equals( "Aranaeus" ) ) {
4376 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4379 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4382 if ( phylogenies[ 1 ].isRooted() ) {
4385 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4388 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4391 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4392 .equals( "Aranaeus" ) ) {
4395 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4398 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4401 if ( !phylogenies[ 2 ].isRooted() ) {
4404 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4407 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4410 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4411 .equals( "Aranaeus" ) ) {
4415 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4416 if ( phylogenies.length != 3 ) {
4419 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4422 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4425 if ( phylogenies[ 0 ].isRooted() ) {
4428 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4431 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4434 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4435 .equals( "Aranaeus" ) ) {
4438 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4441 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4444 if ( phylogenies[ 1 ].isRooted() ) {
4447 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4450 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4453 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4454 .equals( "Aranaeus" ) ) {
4457 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4460 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4463 if ( !phylogenies[ 2 ].isRooted() ) {
4466 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4469 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4472 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4473 .equals( "Aranaeus" ) ) {
4477 catch ( final Exception e ) {
4478 e.printStackTrace( System.out );
4484 private static boolean testNHParsing() {
4486 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4487 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4488 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4491 final NHXParser nhxp = new NHXParser();
4492 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4493 nhxp.setReplaceUnderscores( true );
4494 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4495 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4498 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4501 final Phylogeny p1b = factory
4502 .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 ",
4503 new NHXParser() )[ 0 ];
4504 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4507 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4510 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4511 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4512 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4513 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4514 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4515 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4516 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4517 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4518 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4519 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4520 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4521 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4522 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4524 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4527 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4530 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4533 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4536 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4537 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4538 final String p16_S = "((A,B),C)";
4539 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4540 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4543 final String p17_S = "(C,(A,B))";
4544 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4545 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4548 final String p18_S = "((A,B),(C,D))";
4549 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4550 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4553 final String p19_S = "(((A,B),C),D)";
4554 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4555 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4558 final String p20_S = "(A,(B,(C,D)))";
4559 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4560 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4563 final String p21_S = "(A,(B,(C,(D,E))))";
4564 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4565 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4568 final String p22_S = "((((A,B),C),D),E)";
4569 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4570 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4573 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4574 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4575 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4578 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4579 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4580 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4583 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4584 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4585 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4586 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4589 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4592 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4593 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4594 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4595 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4596 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4597 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4598 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4599 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4600 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4601 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4604 final String p26_S = "(A,B)ab";
4605 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4606 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4609 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4610 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4612 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4615 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4616 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4617 final String p28_S3 = "(A,B)ab";
4618 final String p28_S4 = "((((A,B),C),D),;E;)";
4619 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4621 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4624 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4627 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4630 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4633 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";
4634 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4635 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4638 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";
4639 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4640 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4643 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4644 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4645 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4648 final String p33_S = "A";
4649 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4650 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4653 final String p34_S = "B;";
4654 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4655 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4658 final String p35_S = "B:0.2";
4659 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4660 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4663 final String p36_S = "(A)";
4664 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4665 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4668 final String p37_S = "((A))";
4669 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4670 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4673 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4674 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4675 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4678 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4679 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4680 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4683 final String p40_S = "(A,B,C)";
4684 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4685 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4688 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4689 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4690 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4693 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4694 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4695 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4698 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)";
4699 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4700 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4703 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)))";
4704 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4705 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4708 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4709 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4710 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4713 final String p46_S = "";
4714 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4715 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4718 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4719 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4722 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4723 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4726 final Phylogeny p49 = factory
4727 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4728 new NHXParser() )[ 0 ];
4729 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4732 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4733 if ( p50.getNode( "A" ) == null ) {
4736 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4737 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4740 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4743 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4744 .equals( "((A,B)88:2.0,C);" ) ) {
4747 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4748 if ( p51.getNode( "A(A" ) == null ) {
4751 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4752 if ( p52.getNode( "A(A" ) == null ) {
4755 final Phylogeny p53 = factory
4756 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4757 new NHXParser() )[ 0 ];
4758 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4762 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4763 if ( p54.getNode( "A" ) == null ) {
4766 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4767 .equals( "((A,B)[88],C);" ) ) {
4771 catch ( final Exception e ) {
4772 e.printStackTrace( System.out );
4778 private static boolean testNHXconversion() {
4780 final PhylogenyNode n1 = new PhylogenyNode();
4781 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4782 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4783 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4784 final PhylogenyNode n5 = PhylogenyNode
4785 .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]" );
4786 final PhylogenyNode n6 = PhylogenyNode
4787 .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]" );
4788 if ( !n1.toNewHampshireX().equals( "" ) ) {
4791 if ( !n2.toNewHampshireX().equals( "" ) ) {
4794 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4797 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4800 if ( !n5.toNewHampshireX()
4801 .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]" ) ) {
4804 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]" ) ) {
4808 catch ( final Exception e ) {
4809 e.printStackTrace( System.out );
4815 private static boolean testNHXNodeParsing() {
4817 final PhylogenyNode n1 = new PhylogenyNode();
4818 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4819 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4820 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4821 final PhylogenyNode n5 = PhylogenyNode
4822 .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]" );
4823 if ( !n3.getName().equals( "n3" ) ) {
4826 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4829 if ( n3.isDuplication() ) {
4832 if ( n3.isHasAssignedEvent() ) {
4835 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4838 if ( !n4.getName().equals( "n4" ) ) {
4841 if ( n4.getDistanceToParent() != 0.01 ) {
4844 if ( !n5.getName().equals( "n5" ) ) {
4847 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4850 if ( n5.getDistanceToParent() != 0.1 ) {
4853 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4856 if ( !n5.isDuplication() ) {
4859 if ( !n5.isHasAssignedEvent() ) {
4862 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4865 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4868 final PhylogenyNode n8 = PhylogenyNode
4869 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4870 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4873 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4876 final PhylogenyNode n9 = PhylogenyNode
4877 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4878 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4881 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4884 final PhylogenyNode n10 = PhylogenyNode
4885 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4886 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4889 final PhylogenyNode n20 = PhylogenyNode
4890 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4891 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4894 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4897 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
4898 NHXParser.TAXONOMY_EXTRACTION.YES );
4899 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4902 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4905 final PhylogenyNode n20xx = PhylogenyNode
4906 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4907 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4910 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4913 final PhylogenyNode n20xxx = PhylogenyNode
4914 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4915 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4918 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4921 final PhylogenyNode n20xxxx = PhylogenyNode
4922 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4923 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4926 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4929 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
4930 NHXParser.TAXONOMY_EXTRACTION.YES );
4931 if ( !n21.getName().equals( "n21_PIG" ) ) {
4934 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4937 final PhylogenyNode n21x = PhylogenyNode
4938 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4939 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4942 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4945 final PhylogenyNode n22 = PhylogenyNode
4946 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4947 if ( !n22.getName().equals( "n22/PIG" ) ) {
4950 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4953 final PhylogenyNode n23 = PhylogenyNode
4954 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4955 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4958 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4961 final PhylogenyNode a = PhylogenyNode
4962 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4963 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4966 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4969 final PhylogenyNode b = PhylogenyNode
4970 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4971 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4974 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4977 final PhylogenyNode c = PhylogenyNode
4978 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4979 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4980 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4983 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4986 final PhylogenyNode c1 = PhylogenyNode
4987 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4988 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4989 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4992 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4995 final PhylogenyNode c2 = PhylogenyNode
4996 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4997 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4998 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5001 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5004 final PhylogenyNode d = PhylogenyNode
5005 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5006 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5009 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5012 final PhylogenyNode e = PhylogenyNode
5013 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5014 if ( !e.getName().equals( "n10_RAT1" ) ) {
5017 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5020 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5021 NHXParser.TAXONOMY_EXTRACTION.YES );
5022 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5025 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5028 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5029 NHXParser.TAXONOMY_EXTRACTION.YES );
5030 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5033 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5036 final PhylogenyNode n11 = PhylogenyNode
5037 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5038 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5039 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5042 if ( n11.getDistanceToParent() != 0.4 ) {
5045 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5048 final PhylogenyNode n12 = PhylogenyNode
5049 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5050 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5051 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5054 if ( n12.getDistanceToParent() != 0.4 ) {
5057 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5060 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5061 NHXParser.TAXONOMY_EXTRACTION.YES );
5062 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5065 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5068 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5069 NHXParser.TAXONOMY_EXTRACTION.YES );
5070 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5073 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5076 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
5077 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
5078 if ( !tvu1.getRef().equals( "tag1" ) ) {
5081 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
5084 if ( !tvu1.getUnit().equals( "unit1" ) ) {
5087 if ( !tvu1.getValue().equals( "value1" ) ) {
5090 if ( !tvu3.getRef().equals( "tag3" ) ) {
5093 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
5096 if ( !tvu3.getUnit().equals( "unit3" ) ) {
5099 if ( !tvu3.getValue().equals( "value3" ) ) {
5102 if ( n1.getName().compareTo( "" ) != 0 ) {
5105 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5108 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5111 if ( n2.getName().compareTo( "" ) != 0 ) {
5114 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5117 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5120 final PhylogenyNode n00 = PhylogenyNode
5121 .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]" );
5122 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
5125 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5128 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5131 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
5134 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
5137 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
5140 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
5143 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
5146 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5147 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5150 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
5151 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
5154 final PhylogenyNode n13 = PhylogenyNode
5155 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5156 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5159 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5162 final PhylogenyNode n14 = PhylogenyNode
5163 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5164 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5167 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5170 final PhylogenyNode n15 = PhylogenyNode
5171 .createInstanceFromNhxString( "something_wicked[123]",
5172 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5173 if ( !n15.getName().equals( "something_wicked" ) ) {
5176 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5179 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5182 final PhylogenyNode n16 = PhylogenyNode
5183 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5184 if ( !n16.getName().equals( "something_wicked2" ) ) {
5187 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5190 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5193 final PhylogenyNode n17 = PhylogenyNode
5194 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5195 if ( !n17.getName().equals( "something_wicked3" ) ) {
5198 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5201 final PhylogenyNode n18 = PhylogenyNode
5202 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5203 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5206 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5209 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5213 catch ( final Exception e ) {
5214 e.printStackTrace( System.out );
5220 private static boolean testNHXParsing() {
5222 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5223 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5224 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5227 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]";
5228 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5229 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5232 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]";
5233 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5234 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5237 final Phylogeny[] p3 = factory
5238 .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]",
5240 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5243 final Phylogeny[] p4 = factory
5244 .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(]",
5246 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5249 final Phylogeny[] p5 = factory
5250 .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(((]",
5252 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5255 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)";
5256 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)";
5257 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5258 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5261 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)))";
5262 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)))";
5263 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5264 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5267 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]) ))[,,, ])))))))";
5268 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5269 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5270 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5273 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5274 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5277 final Phylogeny p10 = factory
5278 .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]",
5279 new NHXParser() )[ 0 ];
5280 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5284 catch ( final Exception e ) {
5285 e.printStackTrace( System.out );
5291 private static boolean testNHXParsingQuotes() {
5293 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5294 final NHXParser p = new NHXParser();
5295 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5296 if ( phylogenies_0.length != 5 ) {
5299 final Phylogeny phy = phylogenies_0[ 4 ];
5300 if ( phy.getNumberOfExternalNodes() != 7 ) {
5303 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5306 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5309 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5310 .getScientificName().equals( "hsapiens" ) ) {
5313 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5316 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5319 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5322 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5325 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5328 final NHXParser p1p = new NHXParser();
5329 p1p.setIgnoreQuotes( true );
5330 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5331 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5334 final NHXParser p2p = new NHXParser();
5335 p1p.setIgnoreQuotes( false );
5336 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5337 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5340 final NHXParser p3p = new NHXParser();
5341 p3p.setIgnoreQuotes( false );
5342 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5343 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5346 final NHXParser p4p = new NHXParser();
5347 p4p.setIgnoreQuotes( false );
5348 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5349 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5352 final Phylogeny p10 = factory
5353 .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]",
5354 new NHXParser() )[ 0 ];
5355 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]";
5356 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5359 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5360 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5364 final Phylogeny p12 = factory
5365 .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]",
5366 new NHXParser() )[ 0 ];
5367 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]";
5368 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5371 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5372 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5375 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;";
5376 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5379 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5380 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5384 catch ( final Exception e ) {
5385 e.printStackTrace( System.out );
5391 private static boolean testNHXParsingMB() {
5393 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5394 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5395 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5396 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5397 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5398 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5399 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5400 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5401 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5402 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5403 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5406 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5409 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5410 0.1100000000000000e+00 ) ) {
5413 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5416 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5419 final Phylogeny p2 = factory
5420 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5421 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5422 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5423 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5424 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5425 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5426 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5427 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5428 + "7.369400000000000e-02}])",
5429 new NHXParser() )[ 0 ];
5430 if ( p2.getNode( "1" ) == null ) {
5433 if ( p2.getNode( "2" ) == null ) {
5437 catch ( final Exception e ) {
5438 e.printStackTrace( System.out );
5445 private static boolean testPhylogenyBranch() {
5447 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5448 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5449 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5450 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5451 if ( !a1b1.equals( a1b1 ) ) {
5454 if ( !a1b1.equals( b1a1 ) ) {
5457 if ( !b1a1.equals( a1b1 ) ) {
5460 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5461 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5462 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5463 if ( a1_b1.equals( b1_a1 ) ) {
5466 if ( a1_b1.equals( a1_b1_ ) ) {
5469 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5470 if ( !a1_b1.equals( b1_a1_ ) ) {
5473 if ( a1_b1_.equals( b1_a1_ ) ) {
5476 if ( !a1_b1_.equals( b1_a1 ) ) {
5480 catch ( final Exception e ) {
5481 e.printStackTrace( System.out );
5487 private static boolean testPhyloXMLparsingOfDistributionElement() {
5489 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5490 PhyloXmlParser xml_parser = null;
5492 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5494 catch ( final Exception e ) {
5495 // Do nothing -- means were not running from jar.
5497 if ( xml_parser == null ) {
5498 xml_parser = new PhyloXmlParser();
5499 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5500 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5503 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5506 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5508 if ( xml_parser.getErrorCount() > 0 ) {
5509 System.out.println( xml_parser.getErrorMessages().toString() );
5512 if ( phylogenies_0.length != 1 ) {
5515 final Phylogeny t1 = phylogenies_0[ 0 ];
5516 PhylogenyNode n = null;
5517 Distribution d = null;
5518 n = t1.getNode( "root node" );
5519 if ( !n.getNodeData().isHasDistribution() ) {
5522 if ( n.getNodeData().getDistributions().size() != 1 ) {
5525 d = n.getNodeData().getDistribution();
5526 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5529 if ( d.getPoints().size() != 1 ) {
5532 if ( d.getPolygons() != null ) {
5535 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5538 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5541 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5544 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5547 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5550 n = t1.getNode( "node a" );
5551 if ( !n.getNodeData().isHasDistribution() ) {
5554 if ( n.getNodeData().getDistributions().size() != 2 ) {
5557 d = n.getNodeData().getDistribution( 1 );
5558 if ( !d.getDesc().equals( "San Diego" ) ) {
5561 if ( d.getPoints().size() != 1 ) {
5564 if ( d.getPolygons() != null ) {
5567 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5570 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5573 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5576 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5579 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5582 n = t1.getNode( "node bb" );
5583 if ( !n.getNodeData().isHasDistribution() ) {
5586 if ( n.getNodeData().getDistributions().size() != 1 ) {
5589 d = n.getNodeData().getDistribution( 0 );
5590 if ( d.getPoints().size() != 3 ) {
5593 if ( d.getPolygons().size() != 2 ) {
5596 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5599 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5602 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5605 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5608 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5611 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5614 Polygon p = d.getPolygons().get( 0 );
5615 if ( p.getPoints().size() != 3 ) {
5618 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5621 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5624 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5627 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5630 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5633 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5636 p = d.getPolygons().get( 1 );
5637 if ( p.getPoints().size() != 3 ) {
5640 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5643 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5646 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5650 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5651 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5652 if ( rt.length != 1 ) {
5655 final Phylogeny t1_rt = rt[ 0 ];
5656 n = t1_rt.getNode( "root node" );
5657 if ( !n.getNodeData().isHasDistribution() ) {
5660 if ( n.getNodeData().getDistributions().size() != 1 ) {
5663 d = n.getNodeData().getDistribution();
5664 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5667 if ( d.getPoints().size() != 1 ) {
5670 if ( d.getPolygons() != null ) {
5673 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5676 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5679 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5682 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5685 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5688 n = t1_rt.getNode( "node a" );
5689 if ( !n.getNodeData().isHasDistribution() ) {
5692 if ( n.getNodeData().getDistributions().size() != 2 ) {
5695 d = n.getNodeData().getDistribution( 1 );
5696 if ( !d.getDesc().equals( "San Diego" ) ) {
5699 if ( d.getPoints().size() != 1 ) {
5702 if ( d.getPolygons() != null ) {
5705 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5708 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5711 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5714 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5717 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5720 n = t1_rt.getNode( "node bb" );
5721 if ( !n.getNodeData().isHasDistribution() ) {
5724 if ( n.getNodeData().getDistributions().size() != 1 ) {
5727 d = n.getNodeData().getDistribution( 0 );
5728 if ( d.getPoints().size() != 3 ) {
5731 if ( d.getPolygons().size() != 2 ) {
5734 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5737 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5740 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5743 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5746 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5749 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5752 p = d.getPolygons().get( 0 );
5753 if ( p.getPoints().size() != 3 ) {
5756 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5759 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5762 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5765 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5768 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5771 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5774 p = d.getPolygons().get( 1 );
5775 if ( p.getPoints().size() != 3 ) {
5778 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5781 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5784 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5788 catch ( final Exception e ) {
5789 e.printStackTrace( System.out );
5795 private static boolean testPostOrderIterator() {
5797 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5798 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5799 PhylogenyNodeIterator it0;
5800 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5803 for( it0.reset(); it0.hasNext(); ) {
5806 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5807 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5808 if ( !it.next().getName().equals( "A" ) ) {
5811 if ( !it.next().getName().equals( "B" ) ) {
5814 if ( !it.next().getName().equals( "ab" ) ) {
5817 if ( !it.next().getName().equals( "C" ) ) {
5820 if ( !it.next().getName().equals( "D" ) ) {
5823 if ( !it.next().getName().equals( "cd" ) ) {
5826 if ( !it.next().getName().equals( "abcd" ) ) {
5829 if ( !it.next().getName().equals( "E" ) ) {
5832 if ( !it.next().getName().equals( "F" ) ) {
5835 if ( !it.next().getName().equals( "ef" ) ) {
5838 if ( !it.next().getName().equals( "G" ) ) {
5841 if ( !it.next().getName().equals( "H" ) ) {
5844 if ( !it.next().getName().equals( "gh" ) ) {
5847 if ( !it.next().getName().equals( "efgh" ) ) {
5850 if ( !it.next().getName().equals( "r" ) ) {
5853 if ( it.hasNext() ) {
5857 catch ( final Exception e ) {
5858 e.printStackTrace( System.out );
5864 private static boolean testPreOrderIterator() {
5866 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5867 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5868 PhylogenyNodeIterator it0;
5869 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5872 for( it0.reset(); it0.hasNext(); ) {
5875 PhylogenyNodeIterator it = t0.iteratorPreorder();
5876 if ( !it.next().getName().equals( "r" ) ) {
5879 if ( !it.next().getName().equals( "ab" ) ) {
5882 if ( !it.next().getName().equals( "A" ) ) {
5885 if ( !it.next().getName().equals( "B" ) ) {
5888 if ( !it.next().getName().equals( "cd" ) ) {
5891 if ( !it.next().getName().equals( "C" ) ) {
5894 if ( !it.next().getName().equals( "D" ) ) {
5897 if ( it.hasNext() ) {
5900 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5901 it = t1.iteratorPreorder();
5902 if ( !it.next().getName().equals( "r" ) ) {
5905 if ( !it.next().getName().equals( "abcd" ) ) {
5908 if ( !it.next().getName().equals( "ab" ) ) {
5911 if ( !it.next().getName().equals( "A" ) ) {
5914 if ( !it.next().getName().equals( "B" ) ) {
5917 if ( !it.next().getName().equals( "cd" ) ) {
5920 if ( !it.next().getName().equals( "C" ) ) {
5923 if ( !it.next().getName().equals( "D" ) ) {
5926 if ( !it.next().getName().equals( "efgh" ) ) {
5929 if ( !it.next().getName().equals( "ef" ) ) {
5932 if ( !it.next().getName().equals( "E" ) ) {
5935 if ( !it.next().getName().equals( "F" ) ) {
5938 if ( !it.next().getName().equals( "gh" ) ) {
5941 if ( !it.next().getName().equals( "G" ) ) {
5944 if ( !it.next().getName().equals( "H" ) ) {
5947 if ( it.hasNext() ) {
5951 catch ( final Exception e ) {
5952 e.printStackTrace( System.out );
5958 private static boolean testPropertiesMap() {
5960 final PropertiesMap pm = new PropertiesMap();
5961 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5962 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5963 final Property p2 = new Property( "something:else",
5965 "improbable:research",
5968 pm.addProperty( p0 );
5969 pm.addProperty( p1 );
5970 pm.addProperty( p2 );
5971 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5974 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5977 if ( pm.getProperties().size() != 3 ) {
5980 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5983 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5986 if ( pm.getProperties().size() != 3 ) {
5989 pm.removeProperty( "dimensions:diameter" );
5990 if ( pm.getProperties().size() != 2 ) {
5993 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5996 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6000 catch ( final Exception e ) {
6001 e.printStackTrace( System.out );
6007 private static boolean testReIdMethods() {
6009 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6010 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6011 final int count = PhylogenyNode.getNodeCount();
6013 if ( p.getNode( "r" ).getId() != count ) {
6016 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6019 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6022 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6025 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6028 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6031 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6034 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6037 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6040 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6043 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6046 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6049 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6052 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6055 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6059 catch ( final Exception e ) {
6060 e.printStackTrace( System.out );
6066 private static boolean testRerooting() {
6068 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6069 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",
6070 new NHXParser() )[ 0 ];
6071 if ( !t1.isRooted() ) {
6074 t1.reRoot( t1.getNode( "D" ) );
6075 t1.reRoot( t1.getNode( "CD" ) );
6076 t1.reRoot( t1.getNode( "A" ) );
6077 t1.reRoot( t1.getNode( "B" ) );
6078 t1.reRoot( t1.getNode( "AB" ) );
6079 t1.reRoot( t1.getNode( "D" ) );
6080 t1.reRoot( t1.getNode( "C" ) );
6081 t1.reRoot( t1.getNode( "CD" ) );
6082 t1.reRoot( t1.getNode( "A" ) );
6083 t1.reRoot( t1.getNode( "B" ) );
6084 t1.reRoot( t1.getNode( "AB" ) );
6085 t1.reRoot( t1.getNode( "D" ) );
6086 t1.reRoot( t1.getNode( "D" ) );
6087 t1.reRoot( t1.getNode( "C" ) );
6088 t1.reRoot( t1.getNode( "A" ) );
6089 t1.reRoot( t1.getNode( "B" ) );
6090 t1.reRoot( t1.getNode( "AB" ) );
6091 t1.reRoot( t1.getNode( "C" ) );
6092 t1.reRoot( t1.getNode( "D" ) );
6093 t1.reRoot( t1.getNode( "CD" ) );
6094 t1.reRoot( t1.getNode( "D" ) );
6095 t1.reRoot( t1.getNode( "A" ) );
6096 t1.reRoot( t1.getNode( "B" ) );
6097 t1.reRoot( t1.getNode( "AB" ) );
6098 t1.reRoot( t1.getNode( "C" ) );
6099 t1.reRoot( t1.getNode( "D" ) );
6100 t1.reRoot( t1.getNode( "CD" ) );
6101 t1.reRoot( t1.getNode( "D" ) );
6102 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6105 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6108 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6111 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6114 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6117 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6120 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",
6121 new NHXParser() )[ 0 ];
6122 t2.reRoot( t2.getNode( "A" ) );
6123 t2.reRoot( t2.getNode( "D" ) );
6124 t2.reRoot( t2.getNode( "ABC" ) );
6125 t2.reRoot( t2.getNode( "A" ) );
6126 t2.reRoot( t2.getNode( "B" ) );
6127 t2.reRoot( t2.getNode( "D" ) );
6128 t2.reRoot( t2.getNode( "C" ) );
6129 t2.reRoot( t2.getNode( "ABC" ) );
6130 t2.reRoot( t2.getNode( "A" ) );
6131 t2.reRoot( t2.getNode( "B" ) );
6132 t2.reRoot( t2.getNode( "AB" ) );
6133 t2.reRoot( t2.getNode( "AB" ) );
6134 t2.reRoot( t2.getNode( "D" ) );
6135 t2.reRoot( t2.getNode( "C" ) );
6136 t2.reRoot( t2.getNode( "B" ) );
6137 t2.reRoot( t2.getNode( "AB" ) );
6138 t2.reRoot( t2.getNode( "D" ) );
6139 t2.reRoot( t2.getNode( "D" ) );
6140 t2.reRoot( t2.getNode( "ABC" ) );
6141 t2.reRoot( t2.getNode( "A" ) );
6142 t2.reRoot( t2.getNode( "B" ) );
6143 t2.reRoot( t2.getNode( "AB" ) );
6144 t2.reRoot( t2.getNode( "D" ) );
6145 t2.reRoot( t2.getNode( "C" ) );
6146 t2.reRoot( t2.getNode( "ABC" ) );
6147 t2.reRoot( t2.getNode( "A" ) );
6148 t2.reRoot( t2.getNode( "B" ) );
6149 t2.reRoot( t2.getNode( "AB" ) );
6150 t2.reRoot( t2.getNode( "D" ) );
6151 t2.reRoot( t2.getNode( "D" ) );
6152 t2.reRoot( t2.getNode( "C" ) );
6153 t2.reRoot( t2.getNode( "A" ) );
6154 t2.reRoot( t2.getNode( "B" ) );
6155 t2.reRoot( t2.getNode( "AB" ) );
6156 t2.reRoot( t2.getNode( "C" ) );
6157 t2.reRoot( t2.getNode( "D" ) );
6158 t2.reRoot( t2.getNode( "ABC" ) );
6159 t2.reRoot( t2.getNode( "D" ) );
6160 t2.reRoot( t2.getNode( "A" ) );
6161 t2.reRoot( t2.getNode( "B" ) );
6162 t2.reRoot( t2.getNode( "AB" ) );
6163 t2.reRoot( t2.getNode( "C" ) );
6164 t2.reRoot( t2.getNode( "D" ) );
6165 t2.reRoot( t2.getNode( "ABC" ) );
6166 t2.reRoot( t2.getNode( "D" ) );
6167 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6170 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6173 t2.reRoot( t2.getNode( "ABC" ) );
6174 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6177 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6180 t2.reRoot( t2.getNode( "AB" ) );
6181 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6184 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6187 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6190 t2.reRoot( t2.getNode( "AB" ) );
6191 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6194 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6197 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6200 t2.reRoot( t2.getNode( "D" ) );
6201 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6204 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6207 t2.reRoot( t2.getNode( "ABC" ) );
6208 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6211 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6214 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6215 new NHXParser() )[ 0 ];
6216 t3.reRoot( t3.getNode( "B" ) );
6217 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6220 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6223 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6226 t3.reRoot( t3.getNode( "B" ) );
6227 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6230 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6233 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6236 t3.reRoot( t3.getRoot() );
6237 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6240 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6243 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6247 catch ( final Exception e ) {
6248 e.printStackTrace( System.out );
6254 private static boolean testSDIse() {
6256 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6257 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6258 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6259 gene1.setRooted( true );
6260 species1.setRooted( true );
6261 final SDI sdi = new SDIse( gene1, species1 );
6262 if ( !gene1.getRoot().isDuplication() ) {
6265 final Phylogeny species2 = factory
6266 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6267 new NHXParser() )[ 0 ];
6268 final Phylogeny gene2 = factory
6269 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6270 new NHXParser() )[ 0 ];
6271 species2.setRooted( true );
6272 gene2.setRooted( true );
6273 final SDI sdi2 = new SDIse( gene2, species2 );
6274 if ( sdi2.getDuplicationsSum() != 0 ) {
6277 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6280 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6283 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6286 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6289 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6292 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6295 final Phylogeny species3 = factory
6296 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6297 new NHXParser() )[ 0 ];
6298 final Phylogeny gene3 = factory
6299 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6300 new NHXParser() )[ 0 ];
6301 species3.setRooted( true );
6302 gene3.setRooted( true );
6303 final SDI sdi3 = new SDIse( gene3, species3 );
6304 if ( sdi3.getDuplicationsSum() != 1 ) {
6307 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6310 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6313 final Phylogeny species4 = factory
6314 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6315 new NHXParser() )[ 0 ];
6316 final Phylogeny gene4 = factory
6317 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6318 new NHXParser() )[ 0 ];
6319 species4.setRooted( true );
6320 gene4.setRooted( true );
6321 final SDI sdi4 = new SDIse( gene4, species4 );
6322 if ( sdi4.getDuplicationsSum() != 1 ) {
6325 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6328 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6331 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6334 if ( species4.getNumberOfExternalNodes() != 6 ) {
6337 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6340 final Phylogeny species5 = factory
6341 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6342 new NHXParser() )[ 0 ];
6343 final Phylogeny gene5 = factory
6344 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6345 new NHXParser() )[ 0 ];
6346 species5.setRooted( true );
6347 gene5.setRooted( true );
6348 final SDI sdi5 = new SDIse( gene5, species5 );
6349 if ( sdi5.getDuplicationsSum() != 2 ) {
6352 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6355 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6358 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6361 if ( species5.getNumberOfExternalNodes() != 6 ) {
6364 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6367 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6368 // Conjecture for Comparing Molecular Phylogenies"
6369 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6370 final Phylogeny species6 = factory
6371 .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,"
6372 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6373 new NHXParser() )[ 0 ];
6374 final Phylogeny gene6 = factory
6375 .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,"
6376 + "((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,"
6377 + "(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;",
6378 new NHXParser() )[ 0 ];
6379 species6.setRooted( true );
6380 gene6.setRooted( true );
6381 final SDI sdi6 = new SDIse( gene6, species6 );
6382 if ( sdi6.getDuplicationsSum() != 3 ) {
6385 if ( !gene6.getNode( "r" ).isDuplication() ) {
6388 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6391 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6394 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6397 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6400 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6403 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6406 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6409 sdi6.computeMappingCostL();
6410 if ( sdi6.computeMappingCostL() != 17 ) {
6413 if ( species6.getNumberOfExternalNodes() != 9 ) {
6416 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6419 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6420 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6421 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6422 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6423 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6424 species7.setRooted( true );
6425 final Phylogeny gene7_1 = Test
6426 .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])" );
6427 gene7_1.setRooted( true );
6428 final SDI sdi7 = new SDIse( gene7_1, species7 );
6429 if ( sdi7.getDuplicationsSum() != 0 ) {
6432 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6435 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6438 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6441 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6444 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6447 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6450 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6453 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6456 final Phylogeny gene7_2 = Test
6457 .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])" );
6458 gene7_2.setRooted( true );
6459 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6460 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6463 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6466 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6469 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6472 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6475 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6478 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6481 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6484 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6487 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6491 catch ( final Exception e ) {
6497 private static boolean testSDIunrooted() {
6499 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6500 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6501 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6502 final Iterator<PhylogenyBranch> iter = l.iterator();
6503 PhylogenyBranch br = iter.next();
6504 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6507 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6511 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6514 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6518 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6521 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6525 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6528 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6532 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6535 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6539 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6542 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6546 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6549 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6553 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6556 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6560 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6563 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6567 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6570 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6574 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6577 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6581 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6584 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6588 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6591 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6595 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6598 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6602 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6605 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6608 if ( iter.hasNext() ) {
6611 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6612 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6613 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6615 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6618 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6622 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6625 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6629 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6632 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6635 if ( iter1.hasNext() ) {
6638 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6639 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6640 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6642 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6645 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6649 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6652 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6656 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6659 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6662 if ( iter2.hasNext() ) {
6665 final Phylogeny species0 = factory
6666 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6667 new NHXParser() )[ 0 ];
6668 final Phylogeny gene1 = factory
6669 .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])",
6670 new NHXParser() )[ 0 ];
6671 species0.setRooted( true );
6672 gene1.setRooted( true );
6673 final SDIR sdi_unrooted = new SDIR();
6674 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6675 if ( sdi_unrooted.getCount() != 1 ) {
6678 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6681 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6684 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6687 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6690 final Phylogeny gene2 = factory
6691 .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])",
6692 new NHXParser() )[ 0 ];
6693 gene2.setRooted( true );
6694 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6695 if ( sdi_unrooted.getCount() != 1 ) {
6698 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6701 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6704 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6707 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6710 final Phylogeny species6 = factory
6711 .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,"
6712 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6713 new NHXParser() )[ 0 ];
6714 final Phylogeny gene6 = factory
6715 .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],"
6716 + "(((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],"
6717 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6718 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6719 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6720 new NHXParser() )[ 0 ];
6721 species6.setRooted( true );
6722 gene6.setRooted( true );
6723 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6724 if ( sdi_unrooted.getCount() != 1 ) {
6727 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6730 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6733 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6736 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6739 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6742 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6745 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6748 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6751 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6754 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6757 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6760 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6764 final Phylogeny species7 = factory
6765 .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,"
6766 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6767 new NHXParser() )[ 0 ];
6768 final Phylogeny gene7 = factory
6769 .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],"
6770 + "(((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],"
6771 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6772 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6773 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6774 new NHXParser() )[ 0 ];
6775 species7.setRooted( true );
6776 gene7.setRooted( true );
6777 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6778 if ( sdi_unrooted.getCount() != 1 ) {
6781 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6784 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6787 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6790 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6793 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6796 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6799 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6802 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6805 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6808 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6811 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6814 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6818 final Phylogeny species8 = factory
6819 .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,"
6820 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6821 new NHXParser() )[ 0 ];
6822 final Phylogeny gene8 = factory
6823 .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],"
6824 + "(((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],"
6825 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6826 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6827 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6828 new NHXParser() )[ 0 ];
6829 species8.setRooted( true );
6830 gene8.setRooted( true );
6831 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6832 if ( sdi_unrooted.getCount() != 1 ) {
6835 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6838 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6841 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6844 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6847 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6850 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6853 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6856 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6859 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6862 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6865 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6868 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6873 catch ( final Exception e ) {
6874 e.printStackTrace( System.out );
6880 private static boolean testOrthologTable() {
6882 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6883 final Phylogeny s1 = factory.create( Test.PATH_TO_TEST_DATA + "rio_species.xml", new PhyloXmlParser() )[ 0 ];
6884 final NHXParser p = new NHXParser();
6885 p.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
6886 final Phylogeny g1[] = factory.create( new File( Test.PATH_TO_TEST_DATA
6887 + "rio_Bcl-2_e1_20_mafft_05_40_fme.mlt" ), p );
6888 for( final Phylogeny gt : g1 ) {
6889 gt.setRooted( true );
6890 final GSDI sdi = new GSDI( gt, s1, true, true, true );
6892 final IntMatrix m = RIO.calculateOrthologTable( g1 );
6893 // System.out.println( m.toString() );
6895 catch ( final Exception e ) {
6896 e.printStackTrace();
6902 private static boolean testSplit() {
6904 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6905 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6906 //Archaeopteryx.createApplication( p0 );
6907 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6908 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6909 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6910 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6911 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6912 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6913 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6914 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6915 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6916 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6917 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6918 // System.out.println( s0.toString() );
6920 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6923 if ( s0.match( query_nodes ) ) {
6926 query_nodes = new HashSet<PhylogenyNode>();
6927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6933 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6934 if ( !s0.match( query_nodes ) ) {
6938 query_nodes = new HashSet<PhylogenyNode>();
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6942 if ( !s0.match( query_nodes ) ) {
6946 query_nodes = new HashSet<PhylogenyNode>();
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6951 if ( !s0.match( query_nodes ) ) {
6955 query_nodes = new HashSet<PhylogenyNode>();
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6960 if ( !s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6968 if ( !s0.match( query_nodes ) ) {
6972 query_nodes = new HashSet<PhylogenyNode>();
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6975 if ( !s0.match( query_nodes ) ) {
6979 query_nodes = new HashSet<PhylogenyNode>();
6980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6985 if ( !s0.match( query_nodes ) ) {
6989 query_nodes = new HashSet<PhylogenyNode>();
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6993 if ( !s0.match( query_nodes ) ) {
6997 query_nodes = new HashSet<PhylogenyNode>();
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7002 if ( !s0.match( query_nodes ) ) {
7006 query_nodes = new HashSet<PhylogenyNode>();
7007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7009 if ( s0.match( query_nodes ) ) {
7013 query_nodes = new HashSet<PhylogenyNode>();
7014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7018 if ( s0.match( query_nodes ) ) {
7022 query_nodes = new HashSet<PhylogenyNode>();
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7028 if ( s0.match( query_nodes ) ) {
7032 query_nodes = new HashSet<PhylogenyNode>();
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7036 if ( s0.match( query_nodes ) ) {
7040 query_nodes = new HashSet<PhylogenyNode>();
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7043 if ( s0.match( query_nodes ) ) {
7047 query_nodes = new HashSet<PhylogenyNode>();
7048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7049 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7050 if ( s0.match( query_nodes ) ) {
7054 query_nodes = new HashSet<PhylogenyNode>();
7055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7056 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7057 if ( s0.match( query_nodes ) ) {
7061 query_nodes = new HashSet<PhylogenyNode>();
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7064 if ( s0.match( query_nodes ) ) {
7068 query_nodes = new HashSet<PhylogenyNode>();
7069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7070 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7071 if ( s0.match( query_nodes ) ) {
7075 query_nodes = new HashSet<PhylogenyNode>();
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7077 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7078 if ( s0.match( query_nodes ) ) {
7082 query_nodes = new HashSet<PhylogenyNode>();
7083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7086 if ( s0.match( query_nodes ) ) {
7090 query_nodes = new HashSet<PhylogenyNode>();
7091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7094 if ( s0.match( query_nodes ) ) {
7098 query_nodes = new HashSet<PhylogenyNode>();
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7102 if ( s0.match( query_nodes ) ) {
7106 query_nodes = new HashSet<PhylogenyNode>();
7107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7111 if ( s0.match( query_nodes ) ) {
7115 // query_nodes = new HashSet<PhylogenyNode>();
7116 // query_nodes.add( new PhylogenyNode( "X" ) );
7117 // query_nodes.add( new PhylogenyNode( "Y" ) );
7118 // query_nodes.add( new PhylogenyNode( "A" ) );
7119 // query_nodes.add( new PhylogenyNode( "B" ) );
7120 // query_nodes.add( new PhylogenyNode( "C" ) );
7121 // query_nodes.add( new PhylogenyNode( "D" ) );
7122 // query_nodes.add( new PhylogenyNode( "E" ) );
7123 // query_nodes.add( new PhylogenyNode( "F" ) );
7124 // query_nodes.add( new PhylogenyNode( "G" ) );
7125 // if ( !s0.match( query_nodes ) ) {
7128 // query_nodes = new HashSet<PhylogenyNode>();
7129 // query_nodes.add( new PhylogenyNode( "X" ) );
7130 // query_nodes.add( new PhylogenyNode( "Y" ) );
7131 // query_nodes.add( new PhylogenyNode( "A" ) );
7132 // query_nodes.add( new PhylogenyNode( "B" ) );
7133 // query_nodes.add( new PhylogenyNode( "C" ) );
7134 // if ( !s0.match( query_nodes ) ) {
7138 // query_nodes = new HashSet<PhylogenyNode>();
7139 // query_nodes.add( new PhylogenyNode( "X" ) );
7140 // query_nodes.add( new PhylogenyNode( "Y" ) );
7141 // query_nodes.add( new PhylogenyNode( "D" ) );
7142 // query_nodes.add( new PhylogenyNode( "E" ) );
7143 // query_nodes.add( new PhylogenyNode( "F" ) );
7144 // query_nodes.add( new PhylogenyNode( "G" ) );
7145 // if ( !s0.match( query_nodes ) ) {
7149 // query_nodes = new HashSet<PhylogenyNode>();
7150 // query_nodes.add( new PhylogenyNode( "X" ) );
7151 // query_nodes.add( new PhylogenyNode( "Y" ) );
7152 // query_nodes.add( new PhylogenyNode( "A" ) );
7153 // query_nodes.add( new PhylogenyNode( "B" ) );
7154 // query_nodes.add( new PhylogenyNode( "C" ) );
7155 // query_nodes.add( new PhylogenyNode( "D" ) );
7156 // if ( !s0.match( query_nodes ) ) {
7160 // query_nodes = new HashSet<PhylogenyNode>();
7161 // query_nodes.add( new PhylogenyNode( "X" ) );
7162 // query_nodes.add( new PhylogenyNode( "Y" ) );
7163 // query_nodes.add( new PhylogenyNode( "E" ) );
7164 // query_nodes.add( new PhylogenyNode( "F" ) );
7165 // query_nodes.add( new PhylogenyNode( "G" ) );
7166 // if ( !s0.match( query_nodes ) ) {
7170 // query_nodes = new HashSet<PhylogenyNode>();
7171 // query_nodes.add( new PhylogenyNode( "X" ) );
7172 // query_nodes.add( new PhylogenyNode( "Y" ) );
7173 // query_nodes.add( new PhylogenyNode( "F" ) );
7174 // query_nodes.add( new PhylogenyNode( "G" ) );
7175 // if ( !s0.match( query_nodes ) ) {
7179 query_nodes = new HashSet<PhylogenyNode>();
7180 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7184 if ( s0.match( query_nodes ) ) {
7188 query_nodes = new HashSet<PhylogenyNode>();
7189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7190 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7191 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7192 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7193 if ( s0.match( query_nodes ) ) {
7196 ///////////////////////////
7198 query_nodes = new HashSet<PhylogenyNode>();
7199 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
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( "X" ) );
7209 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7210 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7211 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7212 if ( s0.match( query_nodes ) ) {
7216 query_nodes = new HashSet<PhylogenyNode>();
7217 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7218 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7221 if ( s0.match( query_nodes ) ) {
7225 query_nodes = new HashSet<PhylogenyNode>();
7226 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7227 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7230 if ( s0.match( query_nodes ) ) {
7234 query_nodes = new HashSet<PhylogenyNode>();
7235 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7236 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7237 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7238 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7239 if ( s0.match( query_nodes ) ) {
7243 query_nodes = new HashSet<PhylogenyNode>();
7244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7245 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7246 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7247 if ( s0.match( query_nodes ) ) {
7251 query_nodes = new HashSet<PhylogenyNode>();
7252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7254 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7255 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7256 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7257 if ( s0.match( query_nodes ) ) {
7261 query_nodes = new HashSet<PhylogenyNode>();
7262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7265 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7266 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7267 if ( s0.match( query_nodes ) ) {
7271 query_nodes = new HashSet<PhylogenyNode>();
7272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7273 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7274 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7275 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7276 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7277 if ( s0.match( query_nodes ) ) {
7281 query_nodes = new HashSet<PhylogenyNode>();
7282 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7283 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7284 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7285 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7287 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7288 if ( s0.match( query_nodes ) ) {
7292 catch ( final Exception e ) {
7293 e.printStackTrace();
7299 private static boolean testSplitStrict() {
7301 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7302 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7303 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7304 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7305 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7306 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7307 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7308 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7309 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7310 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7311 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7312 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7313 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7314 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7315 if ( s0.match( query_nodes ) ) {
7318 query_nodes = new HashSet<PhylogenyNode>();
7319 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7320 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7322 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7323 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7324 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7325 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7326 if ( !s0.match( query_nodes ) ) {
7330 query_nodes = new HashSet<PhylogenyNode>();
7331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7332 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7333 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7334 if ( !s0.match( query_nodes ) ) {
7338 query_nodes = new HashSet<PhylogenyNode>();
7339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7342 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7343 if ( !s0.match( query_nodes ) ) {
7347 query_nodes = new HashSet<PhylogenyNode>();
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7351 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7352 if ( !s0.match( query_nodes ) ) {
7356 query_nodes = new HashSet<PhylogenyNode>();
7357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7359 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7360 if ( !s0.match( query_nodes ) ) {
7364 query_nodes = new HashSet<PhylogenyNode>();
7365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7366 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7367 if ( !s0.match( query_nodes ) ) {
7371 query_nodes = new HashSet<PhylogenyNode>();
7372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7375 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7376 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7377 if ( !s0.match( query_nodes ) ) {
7381 query_nodes = new HashSet<PhylogenyNode>();
7382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7383 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7384 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7385 if ( !s0.match( query_nodes ) ) {
7389 query_nodes = new HashSet<PhylogenyNode>();
7390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7391 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7393 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7394 if ( !s0.match( query_nodes ) ) {
7398 query_nodes = new HashSet<PhylogenyNode>();
7399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7400 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7401 if ( s0.match( query_nodes ) ) {
7405 query_nodes = new HashSet<PhylogenyNode>();
7406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7407 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7408 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7409 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7410 if ( s0.match( query_nodes ) ) {
7414 query_nodes = new HashSet<PhylogenyNode>();
7415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7416 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7417 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7418 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7419 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7420 if ( s0.match( query_nodes ) ) {
7424 query_nodes = new HashSet<PhylogenyNode>();
7425 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7426 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7427 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7428 if ( s0.match( query_nodes ) ) {
7432 query_nodes = new HashSet<PhylogenyNode>();
7433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7434 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7435 if ( s0.match( query_nodes ) ) {
7439 query_nodes = new HashSet<PhylogenyNode>();
7440 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7441 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7442 if ( s0.match( query_nodes ) ) {
7446 query_nodes = new HashSet<PhylogenyNode>();
7447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7448 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7449 if ( s0.match( query_nodes ) ) {
7453 query_nodes = new HashSet<PhylogenyNode>();
7454 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7455 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7456 if ( s0.match( query_nodes ) ) {
7460 query_nodes = new HashSet<PhylogenyNode>();
7461 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7462 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7463 if ( s0.match( query_nodes ) ) {
7467 query_nodes = new HashSet<PhylogenyNode>();
7468 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7469 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7470 if ( s0.match( query_nodes ) ) {
7474 query_nodes = new HashSet<PhylogenyNode>();
7475 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7476 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7477 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7478 if ( s0.match( query_nodes ) ) {
7482 query_nodes = new HashSet<PhylogenyNode>();
7483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7485 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7486 if ( s0.match( query_nodes ) ) {
7490 query_nodes = new HashSet<PhylogenyNode>();
7491 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7494 if ( s0.match( query_nodes ) ) {
7498 query_nodes = new HashSet<PhylogenyNode>();
7499 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7500 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7501 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7502 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7503 if ( s0.match( query_nodes ) ) {
7507 catch ( final Exception e ) {
7508 e.printStackTrace();
7514 private static boolean testSubtreeDeletion() {
7516 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7517 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7518 t1.deleteSubtree( t1.getNode( "A" ), false );
7519 if ( t1.getNumberOfExternalNodes() != 5 ) {
7522 t1.toNewHampshireX();
7523 t1.deleteSubtree( t1.getNode( "E" ), false );
7524 if ( t1.getNumberOfExternalNodes() != 4 ) {
7527 t1.toNewHampshireX();
7528 t1.deleteSubtree( t1.getNode( "F" ), false );
7529 if ( t1.getNumberOfExternalNodes() != 3 ) {
7532 t1.toNewHampshireX();
7533 t1.deleteSubtree( t1.getNode( "D" ), false );
7534 t1.toNewHampshireX();
7535 if ( t1.getNumberOfExternalNodes() != 3 ) {
7538 t1.deleteSubtree( t1.getNode( "def" ), false );
7539 t1.toNewHampshireX();
7540 if ( t1.getNumberOfExternalNodes() != 2 ) {
7543 t1.deleteSubtree( t1.getNode( "B" ), false );
7544 t1.toNewHampshireX();
7545 if ( t1.getNumberOfExternalNodes() != 1 ) {
7548 t1.deleteSubtree( t1.getNode( "C" ), false );
7549 t1.toNewHampshireX();
7550 if ( t1.getNumberOfExternalNodes() != 1 ) {
7553 t1.deleteSubtree( t1.getNode( "abc" ), false );
7554 t1.toNewHampshireX();
7555 if ( t1.getNumberOfExternalNodes() != 1 ) {
7558 t1.deleteSubtree( t1.getNode( "r" ), false );
7559 if ( t1.getNumberOfExternalNodes() != 0 ) {
7562 if ( !t1.isEmpty() ) {
7565 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7566 t2.deleteSubtree( t2.getNode( "A" ), false );
7567 t2.toNewHampshireX();
7568 if ( t2.getNumberOfExternalNodes() != 5 ) {
7571 t2.deleteSubtree( t2.getNode( "abc" ), false );
7572 t2.toNewHampshireX();
7573 if ( t2.getNumberOfExternalNodes() != 3 ) {
7576 t2.deleteSubtree( t2.getNode( "def" ), false );
7577 t2.toNewHampshireX();
7578 if ( t2.getNumberOfExternalNodes() != 1 ) {
7582 catch ( final Exception e ) {
7583 e.printStackTrace( System.out );
7589 private static boolean testSupportCount() {
7591 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7592 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7593 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7594 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7595 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7596 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7597 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7599 SupportCount.count( t0_1, phylogenies_1, true, false );
7600 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7601 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7602 + "(((((A,B),C),D),E),((F,G),X))"
7603 + "(((((A,Y),B),C),D),((F,G),E))"
7604 + "(((((A,B),C),D),E),(F,G))"
7605 + "(((((A,B),C),D),E),(F,G))"
7606 + "(((((A,B),C),D),E),(F,G))"
7607 + "(((((A,B),C),D),E),(F,G),Z)"
7608 + "(((((A,B),C),D),E),(F,G))"
7609 + "((((((A,B),C),D),E),F),G)"
7610 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7612 SupportCount.count( t0_2, phylogenies_2, true, false );
7613 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7614 while ( it.hasNext() ) {
7615 final PhylogenyNode n = it.next();
7616 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7620 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7621 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7622 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7623 SupportCount.count( t0_3, phylogenies_3, true, false );
7624 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7625 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7628 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7631 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7634 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7637 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7640 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7643 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7646 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7649 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7652 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7655 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7656 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7657 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7658 SupportCount.count( t0_4, phylogenies_4, true, false );
7659 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7660 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7663 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7666 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7669 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7672 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7675 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7678 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7681 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7684 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7687 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7690 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7691 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7692 double d = SupportCount.compare( b1, a, true, true, true );
7693 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7696 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7697 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7698 d = SupportCount.compare( b2, a, true, true, true );
7699 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7702 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7703 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7704 d = SupportCount.compare( b3, a, true, true, true );
7705 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7708 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7709 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7710 d = SupportCount.compare( b4, a, true, true, false );
7711 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7715 catch ( final Exception e ) {
7716 e.printStackTrace( System.out );
7722 private static boolean testSupportTransfer() {
7724 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7725 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)",
7726 new NHXParser() )[ 0 ];
7727 final Phylogeny p2 = factory
7728 .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 ];
7729 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7732 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7735 support_transfer.moveBranchLengthsToBootstrap( p1 );
7736 support_transfer.transferSupportValues( p1, p2 );
7737 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7740 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7743 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7746 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7749 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7752 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7755 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7758 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7762 catch ( final Exception e ) {
7763 e.printStackTrace( System.out );
7769 private static boolean testUniprotTaxonomySearch() {
7771 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7773 if ( results.size() != 1 ) {
7776 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7779 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7782 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7785 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7788 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7792 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7793 if ( results.size() != 1 ) {
7796 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7799 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7802 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7805 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7808 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7812 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7813 if ( results.size() != 1 ) {
7816 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7819 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7822 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7825 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7828 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7832 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7833 if ( results.size() != 1 ) {
7836 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7839 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7842 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7845 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7848 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7851 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7854 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7857 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7858 .equals( "Nematostella vectensis" ) ) {
7859 System.out.println( results.get( 0 ).getLineage() );
7863 catch ( final IOException e ) {
7864 System.out.println();
7865 System.out.println( "the following might be due to absence internet connection:" );
7866 e.printStackTrace( System.out );
7869 catch ( final Exception e ) {
7875 private static boolean testEmblEntryRetrieval() {
7876 //The format for GenBank Accession numbers are:
7877 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7878 //Protein: 3 letters + 5 numerals
7879 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7880 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7883 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7886 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7889 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7892 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7895 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7898 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7901 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7904 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7907 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7910 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7913 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7916 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7922 private static boolean testUniprotEntryRetrieval() {
7923 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7926 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7929 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7932 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7935 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7938 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7941 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7944 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7947 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7950 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7953 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7956 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7959 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7963 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7964 if ( !entry.getAccession().equals( "P12345" ) ) {
7967 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7970 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7973 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7976 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7980 catch ( final IOException e ) {
7981 System.out.println();
7982 System.out.println( "the following might be due to absence internet connection:" );
7983 e.printStackTrace( System.out );
7986 catch ( final Exception e ) {
7992 private static boolean testWabiTxSearch() {
7995 result = TxSearch.searchSimple( "nematostella" );
7996 result = TxSearch.getTxId( "nematostella" );
7997 if ( !result.equals( "45350" ) ) {
8000 result = TxSearch.getTxName( "45350" );
8001 if ( !result.equals( "Nematostella" ) ) {
8004 result = TxSearch.getTxId( "nematostella vectensis" );
8005 if ( !result.equals( "45351" ) ) {
8008 result = TxSearch.getTxName( "45351" );
8009 if ( !result.equals( "Nematostella vectensis" ) ) {
8012 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8013 if ( !result.equals( "536089" ) ) {
8016 result = TxSearch.getTxName( "536089" );
8017 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8020 final List<String> queries = new ArrayList<String>();
8021 queries.add( "Campylobacter coli" );
8022 queries.add( "Escherichia coli" );
8023 queries.add( "Arabidopsis" );
8024 queries.add( "Trichoplax" );
8025 queries.add( "Samanea saman" );
8026 queries.add( "Kluyveromyces marxianus" );
8027 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8028 queries.add( "Bornavirus parrot/PDD/2008" );
8029 final List<RANKS> ranks = new ArrayList<RANKS>();
8030 ranks.add( RANKS.SUPERKINGDOM );
8031 ranks.add( RANKS.KINGDOM );
8032 ranks.add( RANKS.FAMILY );
8033 ranks.add( RANKS.GENUS );
8034 ranks.add( RANKS.TRIBE );
8035 result = TxSearch.searchLineage( queries, ranks );
8036 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8037 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8039 catch ( final Exception e ) {
8040 System.out.println();
8041 System.out.println( "the following might be due to absence internet connection:" );
8042 e.printStackTrace( System.out );
8048 private static boolean testAminoAcidSequence() {
8050 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8051 if ( aa1.getLength() != 13 ) {
8054 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8057 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8060 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8063 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8064 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8067 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8068 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8071 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8072 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8076 catch ( final Exception e ) {
8077 e.printStackTrace();
8083 private static boolean testCreateBalancedPhylogeny() {
8085 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8086 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8089 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8092 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8093 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8096 if ( p1.getNumberOfExternalNodes() != 100 ) {
8100 catch ( final Exception e ) {
8101 e.printStackTrace();
8107 private static boolean testFastaParser() {
8109 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8112 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8115 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8116 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8119 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8122 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8125 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8128 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8131 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8135 catch ( final Exception e ) {
8136 e.printStackTrace();
8142 private static boolean testGeneralMsaParser() {
8144 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8145 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8146 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8147 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8148 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8149 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8150 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8151 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8152 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8155 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8158 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8161 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8164 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8167 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8170 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8173 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8176 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8179 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8182 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8185 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8188 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8189 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8192 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8195 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8198 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8199 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8202 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8205 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8208 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8209 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8212 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8215 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8219 catch ( final Exception e ) {
8220 e.printStackTrace();
8226 private static boolean testMafft( final String path ) {
8228 final List<String> opts = new ArrayList<String>();
8229 opts.add( "--maxiterate" );
8231 opts.add( "--localpair" );
8232 opts.add( "--quiet" );
8234 final MsaInferrer mafft = Mafft.createInstance( path );
8235 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8236 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8239 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8243 catch ( final Exception e ) {
8244 e.printStackTrace( System.out );
8250 private static boolean testNextNodeWithCollapsing() {
8252 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8254 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8255 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8256 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8257 t0.getNode( "cd" ).setCollapse( true );
8258 t0.getNode( "cde" ).setCollapse( true );
8259 n = t0.getFirstExternalNode();
8260 while ( n != null ) {
8262 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8264 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8267 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8270 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8273 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8276 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8279 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8283 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8284 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8285 t1.getNode( "ab" ).setCollapse( true );
8286 t1.getNode( "cd" ).setCollapse( true );
8287 t1.getNode( "cde" ).setCollapse( true );
8288 n = t1.getNode( "ab" );
8289 ext = new ArrayList<PhylogenyNode>();
8290 while ( n != null ) {
8292 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8294 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8297 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8300 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8303 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8306 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8312 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8313 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8314 t2.getNode( "ab" ).setCollapse( true );
8315 t2.getNode( "cd" ).setCollapse( true );
8316 t2.getNode( "cde" ).setCollapse( true );
8317 t2.getNode( "c" ).setCollapse( true );
8318 t2.getNode( "d" ).setCollapse( true );
8319 t2.getNode( "e" ).setCollapse( true );
8320 t2.getNode( "gh" ).setCollapse( true );
8321 n = t2.getNode( "ab" );
8322 ext = new ArrayList<PhylogenyNode>();
8323 while ( n != null ) {
8325 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8327 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8330 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8333 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8336 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8342 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8343 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8344 t3.getNode( "ab" ).setCollapse( true );
8345 t3.getNode( "cd" ).setCollapse( true );
8346 t3.getNode( "cde" ).setCollapse( true );
8347 t3.getNode( "c" ).setCollapse( true );
8348 t3.getNode( "d" ).setCollapse( true );
8349 t3.getNode( "e" ).setCollapse( true );
8350 t3.getNode( "gh" ).setCollapse( true );
8351 t3.getNode( "fgh" ).setCollapse( true );
8352 n = t3.getNode( "ab" );
8353 ext = new ArrayList<PhylogenyNode>();
8354 while ( n != null ) {
8356 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8358 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8361 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8364 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8370 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8371 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8372 t4.getNode( "ab" ).setCollapse( true );
8373 t4.getNode( "cd" ).setCollapse( true );
8374 t4.getNode( "cde" ).setCollapse( true );
8375 t4.getNode( "c" ).setCollapse( true );
8376 t4.getNode( "d" ).setCollapse( true );
8377 t4.getNode( "e" ).setCollapse( true );
8378 t4.getNode( "gh" ).setCollapse( true );
8379 t4.getNode( "fgh" ).setCollapse( true );
8380 t4.getNode( "abcdefgh" ).setCollapse( true );
8381 n = t4.getNode( "abcdefgh" );
8382 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8387 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8388 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8390 n = t5.getFirstExternalNode();
8391 while ( n != null ) {
8393 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8395 if ( ext.size() != 8 ) {
8398 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8401 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8404 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8407 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8410 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8413 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8416 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8419 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8424 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8425 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8427 t6.getNode( "ab" ).setCollapse( true );
8428 n = t6.getNode( "ab" );
8429 while ( n != null ) {
8431 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8433 if ( ext.size() != 7 ) {
8436 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8439 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8442 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8445 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8448 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8451 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8454 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8459 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8460 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8462 t7.getNode( "cd" ).setCollapse( true );
8463 n = t7.getNode( "a" );
8464 while ( n != null ) {
8466 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8468 if ( ext.size() != 7 ) {
8471 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8474 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8477 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8480 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8483 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8486 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8489 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8494 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8495 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8497 t8.getNode( "cd" ).setCollapse( true );
8498 t8.getNode( "c" ).setCollapse( true );
8499 t8.getNode( "d" ).setCollapse( true );
8500 n = t8.getNode( "a" );
8501 while ( n != null ) {
8503 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8505 if ( ext.size() != 7 ) {
8508 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8511 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8514 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8515 System.out.println( "2 fail" );
8518 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8521 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8524 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8527 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8532 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8533 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8535 t9.getNode( "gh" ).setCollapse( true );
8536 n = t9.getNode( "a" );
8537 while ( n != null ) {
8539 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8541 if ( ext.size() != 7 ) {
8544 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8547 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8550 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8553 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8556 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8559 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8562 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8567 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8568 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8570 t10.getNode( "gh" ).setCollapse( true );
8571 t10.getNode( "g" ).setCollapse( true );
8572 t10.getNode( "h" ).setCollapse( true );
8573 n = t10.getNode( "a" );
8574 while ( n != null ) {
8576 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8578 if ( ext.size() != 7 ) {
8581 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8584 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8587 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8590 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8593 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8596 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8599 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8604 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8605 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8607 t11.getNode( "gh" ).setCollapse( true );
8608 t11.getNode( "fgh" ).setCollapse( true );
8609 n = t11.getNode( "a" );
8610 while ( n != null ) {
8612 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8614 if ( ext.size() != 6 ) {
8617 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8620 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8623 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8626 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8629 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8632 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8637 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8638 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8640 t12.getNode( "gh" ).setCollapse( true );
8641 t12.getNode( "fgh" ).setCollapse( true );
8642 t12.getNode( "g" ).setCollapse( true );
8643 t12.getNode( "h" ).setCollapse( true );
8644 t12.getNode( "f" ).setCollapse( true );
8645 n = t12.getNode( "a" );
8646 while ( n != null ) {
8648 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8650 if ( ext.size() != 6 ) {
8653 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8656 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8659 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8662 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8665 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8668 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8673 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8674 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8676 t13.getNode( "ab" ).setCollapse( true );
8677 t13.getNode( "b" ).setCollapse( true );
8678 t13.getNode( "fgh" ).setCollapse( true );
8679 t13.getNode( "gh" ).setCollapse( true );
8680 n = t13.getNode( "ab" );
8681 while ( n != null ) {
8683 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8685 if ( ext.size() != 5 ) {
8688 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8691 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8694 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8697 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8700 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8705 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8706 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8708 t14.getNode( "ab" ).setCollapse( true );
8709 t14.getNode( "a" ).setCollapse( true );
8710 t14.getNode( "fgh" ).setCollapse( true );
8711 t14.getNode( "gh" ).setCollapse( true );
8712 n = t14.getNode( "ab" );
8713 while ( n != null ) {
8715 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8717 if ( ext.size() != 5 ) {
8720 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8723 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8726 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8729 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8732 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8737 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" );
8738 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8740 t15.getNode( "ab" ).setCollapse( true );
8741 t15.getNode( "a" ).setCollapse( true );
8742 t15.getNode( "fgh" ).setCollapse( true );
8743 t15.getNode( "gh" ).setCollapse( true );
8744 n = t15.getNode( "ab" );
8745 while ( n != null ) {
8747 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8749 if ( ext.size() != 6 ) {
8752 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8755 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8758 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8761 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8764 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8767 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8772 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" );
8773 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8775 t16.getNode( "ab" ).setCollapse( true );
8776 t16.getNode( "a" ).setCollapse( true );
8777 t16.getNode( "fgh" ).setCollapse( true );
8778 t16.getNode( "gh" ).setCollapse( true );
8779 t16.getNode( "cd" ).setCollapse( true );
8780 t16.getNode( "cde" ).setCollapse( true );
8781 t16.getNode( "d" ).setCollapse( true );
8782 t16.getNode( "x" ).setCollapse( true );
8783 n = t16.getNode( "ab" );
8784 while ( n != null ) {
8786 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8788 if ( ext.size() != 4 ) {
8791 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8794 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8797 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8800 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8804 catch ( final Exception e ) {
8805 e.printStackTrace( System.out );
8811 private static boolean testMsaQualityMethod() {
8813 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8814 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8815 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8816 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8817 final List<Sequence> l = new ArrayList<Sequence>();
8822 final Msa msa = BasicMsa.createInstance( l );
8823 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8826 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8829 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8832 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8836 catch ( final Exception e ) {
8837 e.printStackTrace( System.out );
8843 private static boolean testSequenceIdParsing() {
8845 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8846 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8847 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8849 System.out.println( "value =" + id.getValue() );
8850 System.out.println( "provider=" + id.getProvider() );
8855 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8856 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8857 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8859 System.out.println( "value =" + id.getValue() );
8860 System.out.println( "provider=" + id.getProvider() );
8865 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8866 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8867 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8869 System.out.println( "value =" + id.getValue() );
8870 System.out.println( "provider=" + id.getProvider() );
8875 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8876 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8877 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8879 System.out.println( "value =" + id.getValue() );
8880 System.out.println( "provider=" + id.getProvider() );
8885 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8886 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8887 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8889 System.out.println( "value =" + id.getValue() );
8890 System.out.println( "provider=" + id.getProvider() );
8895 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8896 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8897 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8899 System.out.println( "value =" + id.getValue() );
8900 System.out.println( "provider=" + id.getProvider() );
8905 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8906 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8907 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8909 System.out.println( "value =" + id.getValue() );
8910 System.out.println( "provider=" + id.getProvider() );
8915 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8916 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8917 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8919 System.out.println( "value =" + id.getValue() );
8920 System.out.println( "provider=" + id.getProvider() );
8925 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8926 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8927 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8929 System.out.println( "value =" + id.getValue() );
8930 System.out.println( "provider=" + id.getProvider() );
8935 id = SequenceIdParser.parse( "P4A123" );
8936 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8937 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8939 System.out.println( "value =" + id.getValue() );
8940 System.out.println( "provider=" + id.getProvider() );
8945 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
8946 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8947 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8949 System.out.println( "value =" + id.getValue() );
8950 System.out.println( "provider=" + id.getProvider() );
8955 id = SequenceIdParser.parse( "XP_12345" );
8957 System.out.println( "value =" + id.getValue() );
8958 System.out.println( "provider=" + id.getProvider() );
8961 // lcl_91970_unknown_
8963 catch ( final Exception e ) {
8964 e.printStackTrace( System.out );