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.rio.RIO;
91 import org.forester.sdi.GSDI;
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 PhylogenyMethods.preOrderReId( p_c );
3358 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3359 p_c.getNode( "a" ) );
3360 if ( !p_c_1.getName().equals( "b" ) ) {
3363 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3364 p_c.getNode( "c" ) );
3365 if ( !p_c_2.getName().equals( "c" ) ) {
3366 System.out.println( p_c_2.getName() );
3370 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3371 p_c.getNode( "b" ) );
3372 if ( !p_c_3.getName().equals( "b" ) ) {
3375 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3376 p_c.getNode( "a" ) );
3377 if ( !p_c_4.getName().equals( "c" ) ) {
3380 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3381 new NHXParser() )[ 0 ];
3382 PhylogenyMethods.preOrderReId( p1 );
3383 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3384 p1.getNode( "A" ) );
3385 if ( !A.getName().equals( "A" ) ) {
3388 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3389 p1.getNode( "gh" ) );
3390 if ( !gh.getName().equals( "gh" ) ) {
3393 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3394 p1.getNode( "B" ) );
3395 if ( !ab.getName().equals( "ab" ) ) {
3398 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3399 p1.getNode( "A" ) );
3400 if ( !ab2.getName().equals( "ab" ) ) {
3403 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3404 p1.getNode( "G" ) );
3405 if ( !gh2.getName().equals( "gh" ) ) {
3408 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3409 p1.getNode( "H" ) );
3410 if ( !gh3.getName().equals( "gh" ) ) {
3413 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3414 p1.getNode( "A" ) );
3415 if ( !abc.getName().equals( "abc" ) ) {
3418 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3419 p1.getNode( "C" ) );
3420 if ( !abc2.getName().equals( "abc" ) ) {
3423 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3424 p1.getNode( "D" ) );
3425 if ( !abcd.getName().equals( "abcd" ) ) {
3428 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3429 p1.getNode( "A" ) );
3430 if ( !abcd2.getName().equals( "abcd" ) ) {
3433 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3434 p1.getNode( "F" ) );
3435 if ( !abcdef.getName().equals( "abcdef" ) ) {
3438 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3439 p1.getNode( "A" ) );
3440 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3443 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3444 p1.getNode( "F" ) );
3445 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3448 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3449 p1.getNode( "ab" ) );
3450 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3453 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3454 p1.getNode( "E" ) );
3455 if ( !abcde.getName().equals( "abcde" ) ) {
3458 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3459 p1.getNode( "A" ) );
3460 if ( !abcde2.getName().equals( "abcde" ) ) {
3463 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3464 p1.getNode( "abcdefgh" ) );
3465 if ( !r.getName().equals( "abcdefgh" ) ) {
3468 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3469 p1.getNode( "H" ) );
3470 if ( !r2.getName().equals( "abcdefgh" ) ) {
3473 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3474 p1.getNode( "A" ) );
3475 if ( !r3.getName().equals( "abcdefgh" ) ) {
3478 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3479 p1.getNode( "abcde" ) );
3480 if ( !abcde3.getName().equals( "abcde" ) ) {
3483 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3484 p1.getNode( "E" ) );
3485 if ( !abcde4.getName().equals( "abcde" ) ) {
3488 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3489 p1.getNode( "B" ) );
3490 if ( !ab3.getName().equals( "ab" ) ) {
3493 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3494 p1.getNode( "ab" ) );
3495 if ( !ab4.getName().equals( "ab" ) ) {
3498 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3499 PhylogenyMethods.preOrderReId( p2 );
3500 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3501 p2.getNode( "d" ) );
3502 if ( !cd.getName().equals( "cd" ) ) {
3505 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3506 p2.getNode( "c" ) );
3507 if ( !cd2.getName().equals( "cd" ) ) {
3510 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3511 p2.getNode( "e" ) );
3512 if ( !cde.getName().equals( "cde" ) ) {
3515 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3516 p2.getNode( "c" ) );
3517 if ( !cde2.getName().equals( "cde" ) ) {
3520 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3521 p2.getNode( "f" ) );
3522 if ( !cdef.getName().equals( "cdef" ) ) {
3525 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3526 p2.getNode( "f" ) );
3527 if ( !cdef2.getName().equals( "cdef" ) ) {
3530 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3531 p2.getNode( "d" ) );
3532 if ( !cdef3.getName().equals( "cdef" ) ) {
3535 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3536 p2.getNode( "a" ) );
3537 if ( !rt.getName().equals( "r" ) ) {
3540 final Phylogeny p3 = factory
3541 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3542 new NHXParser() )[ 0 ];
3543 PhylogenyMethods.preOrderReId( p3 );
3544 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3545 p3.getNode( "c" ) );
3546 if ( !bc_3.getName().equals( "bc" ) ) {
3549 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3550 p3.getNode( "c" ) );
3551 if ( !ac_3.getName().equals( "abc" ) ) {
3554 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3555 p3.getNode( "d" ) );
3556 if ( !ad_3.getName().equals( "abcde" ) ) {
3559 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3560 p3.getNode( "f" ) );
3561 if ( !af_3.getName().equals( "abcdef" ) ) {
3564 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3565 p3.getNode( "g" ) );
3566 if ( !ag_3.getName().equals( "" ) ) {
3569 if ( !ag_3.isRoot() ) {
3572 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3573 p3.getNode( "l" ) );
3574 if ( !al_3.getName().equals( "" ) ) {
3577 if ( !al_3.isRoot() ) {
3580 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3581 p3.getNode( "l" ) );
3582 if ( !kl_3.getName().equals( "" ) ) {
3585 if ( !kl_3.isRoot() ) {
3588 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3589 p3.getNode( "l" ) );
3590 if ( !fl_3.getName().equals( "" ) ) {
3593 if ( !fl_3.isRoot() ) {
3596 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3597 p3.getNode( "k" ) );
3598 if ( !gk_3.getName().equals( "ghijk" ) ) {
3601 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3602 PhylogenyMethods.preOrderReId( p4 );
3603 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3604 p4.getNode( "c" ) );
3605 if ( !r_4.getName().equals( "r" ) ) {
3608 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3609 PhylogenyMethods.preOrderReId( p5 );
3610 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3611 p5.getNode( "c" ) );
3612 if ( !r_5.getName().equals( "root" ) ) {
3615 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3616 PhylogenyMethods.preOrderReId( p6 );
3617 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3618 p6.getNode( "a" ) );
3619 if ( !r_6.getName().equals( "rot" ) ) {
3622 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3623 PhylogenyMethods.preOrderReId( p7 );
3624 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3625 p7.getNode( "e" ) );
3626 if ( !r_7.getName().equals( "rott" ) ) {
3629 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3630 p7.getNode( "a" ) );
3631 if ( !r_71.getName().equals( "rott" ) ) {
3634 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3635 p7.getNode( "rott" ) );
3636 if ( !r_72.getName().equals( "rott" ) ) {
3639 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3640 p7.getNode( "a" ) );
3641 if ( !r_73.getName().equals( "rott" ) ) {
3644 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3645 p7.getNode( "rott" ) );
3646 if ( !r_74.getName().equals( "rott" ) ) {
3649 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3650 p7.getNode( "e" ) );
3651 if ( !r_75.getName().equals( "e" ) ) {
3655 catch ( final Exception e ) {
3656 e.printStackTrace( System.out );
3662 private static boolean testHmmscanOutputParser() {
3663 final String test_dir = Test.PATH_TO_TEST_DATA;
3665 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3666 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3668 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3669 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3670 final List<Protein> proteins = parser2.parse();
3671 if ( parser2.getProteinsEncountered() != 4 ) {
3674 if ( proteins.size() != 4 ) {
3677 if ( parser2.getDomainsEncountered() != 69 ) {
3680 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3683 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3686 final Protein p1 = proteins.get( 0 );
3687 if ( p1.getNumberOfProteinDomains() != 15 ) {
3690 if ( p1.getLength() != 850 ) {
3693 final Protein p2 = proteins.get( 1 );
3694 if ( p2.getNumberOfProteinDomains() != 51 ) {
3697 if ( p2.getLength() != 1291 ) {
3700 final Protein p3 = proteins.get( 2 );
3701 if ( p3.getNumberOfProteinDomains() != 2 ) {
3704 final Protein p4 = proteins.get( 3 );
3705 if ( p4.getNumberOfProteinDomains() != 1 ) {
3708 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3711 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3714 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3717 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3720 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3723 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3726 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3729 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3732 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3736 catch ( final Exception e ) {
3737 e.printStackTrace( System.out );
3743 private static boolean testLastExternalNodeMethods() {
3745 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3746 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3747 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3748 final PhylogenyNode n1 = t0.getNode( "A" );
3749 if ( n1.isLastExternalNode() ) {
3752 final PhylogenyNode n2 = t0.getNode( "B" );
3753 if ( n2.isLastExternalNode() ) {
3756 final PhylogenyNode n3 = t0.getNode( "C" );
3757 if ( n3.isLastExternalNode() ) {
3760 final PhylogenyNode n4 = t0.getNode( "D" );
3761 if ( !n4.isLastExternalNode() ) {
3765 catch ( final Exception e ) {
3766 e.printStackTrace( System.out );
3772 private static boolean testLevelOrderIterator() {
3774 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3775 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3776 PhylogenyNodeIterator it0;
3777 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3780 for( it0.reset(); it0.hasNext(); ) {
3783 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3784 if ( !it.next().getName().equals( "r" ) ) {
3787 if ( !it.next().getName().equals( "ab" ) ) {
3790 if ( !it.next().getName().equals( "cd" ) ) {
3793 if ( !it.next().getName().equals( "A" ) ) {
3796 if ( !it.next().getName().equals( "B" ) ) {
3799 if ( !it.next().getName().equals( "C" ) ) {
3802 if ( !it.next().getName().equals( "D" ) ) {
3805 if ( it.hasNext() ) {
3808 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",
3809 new NHXParser() )[ 0 ];
3810 PhylogenyNodeIterator it2;
3811 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3814 for( it2.reset(); it2.hasNext(); ) {
3817 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3818 if ( !it3.next().getName().equals( "r" ) ) {
3821 if ( !it3.next().getName().equals( "abc" ) ) {
3824 if ( !it3.next().getName().equals( "defg" ) ) {
3827 if ( !it3.next().getName().equals( "A" ) ) {
3830 if ( !it3.next().getName().equals( "B" ) ) {
3833 if ( !it3.next().getName().equals( "C" ) ) {
3836 if ( !it3.next().getName().equals( "D" ) ) {
3839 if ( !it3.next().getName().equals( "E" ) ) {
3842 if ( !it3.next().getName().equals( "F" ) ) {
3845 if ( !it3.next().getName().equals( "G" ) ) {
3848 if ( !it3.next().getName().equals( "1" ) ) {
3851 if ( !it3.next().getName().equals( "2" ) ) {
3854 if ( !it3.next().getName().equals( "3" ) ) {
3857 if ( !it3.next().getName().equals( "4" ) ) {
3860 if ( !it3.next().getName().equals( "5" ) ) {
3863 if ( !it3.next().getName().equals( "6" ) ) {
3866 if ( !it3.next().getName().equals( "f1" ) ) {
3869 if ( !it3.next().getName().equals( "f2" ) ) {
3872 if ( !it3.next().getName().equals( "f3" ) ) {
3875 if ( !it3.next().getName().equals( "a" ) ) {
3878 if ( !it3.next().getName().equals( "b" ) ) {
3881 if ( !it3.next().getName().equals( "f21" ) ) {
3884 if ( !it3.next().getName().equals( "X" ) ) {
3887 if ( !it3.next().getName().equals( "Y" ) ) {
3890 if ( !it3.next().getName().equals( "Z" ) ) {
3893 if ( it3.hasNext() ) {
3896 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3897 PhylogenyNodeIterator it4;
3898 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3901 for( it4.reset(); it4.hasNext(); ) {
3904 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3905 if ( !it5.next().getName().equals( "r" ) ) {
3908 if ( !it5.next().getName().equals( "A" ) ) {
3911 if ( !it5.next().getName().equals( "B" ) ) {
3914 if ( !it5.next().getName().equals( "C" ) ) {
3917 if ( !it5.next().getName().equals( "D" ) ) {
3920 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3921 PhylogenyNodeIterator it6;
3922 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3925 for( it6.reset(); it6.hasNext(); ) {
3928 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3929 if ( !it7.next().getName().equals( "A" ) ) {
3932 if ( it.hasNext() ) {
3936 catch ( final Exception e ) {
3937 e.printStackTrace( System.out );
3943 private static boolean testMidpointrooting() {
3945 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3946 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",
3947 new NHXParser() )[ 0 ];
3948 if ( !t1.isRooted() ) {
3951 PhylogenyMethods.midpointRoot( t1 );
3952 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3955 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3958 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3961 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3964 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3967 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3970 t1.reRoot( t1.getNode( "A" ) );
3971 PhylogenyMethods.midpointRoot( t1 );
3972 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3975 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3978 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3981 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3984 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3987 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3991 catch ( final Exception e ) {
3992 e.printStackTrace( System.out );
3998 private static boolean testNexusCharactersParsing() {
4000 final NexusCharactersParser parser = new NexusCharactersParser();
4001 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4003 String[] labels = parser.getCharStateLabels();
4004 if ( labels.length != 7 ) {
4007 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4010 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4013 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4016 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4019 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4022 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4025 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4028 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4030 labels = parser.getCharStateLabels();
4031 if ( labels.length != 7 ) {
4034 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4037 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4040 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4043 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4046 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4049 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4052 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4056 catch ( final Exception e ) {
4057 e.printStackTrace( System.out );
4063 private static boolean testNexusMatrixParsing() {
4065 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4066 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4068 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4069 if ( m.getNumberOfCharacters() != 9 ) {
4072 if ( m.getNumberOfIdentifiers() != 5 ) {
4075 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4078 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4081 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4084 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4087 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4090 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4093 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4096 // if ( labels.length != 7 ) {
4099 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4102 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4105 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4108 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4111 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4114 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4117 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4120 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4122 // labels = parser.getCharStateLabels();
4123 // if ( labels.length != 7 ) {
4126 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4129 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4132 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4135 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4138 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4141 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4144 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4148 catch ( final Exception e ) {
4149 e.printStackTrace( System.out );
4155 private static boolean testNexusTreeParsing() {
4157 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4158 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4159 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4160 if ( phylogenies.length != 1 ) {
4163 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4166 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4170 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4171 if ( phylogenies.length != 1 ) {
4174 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4177 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4181 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4182 if ( phylogenies.length != 1 ) {
4185 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4188 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4191 if ( phylogenies[ 0 ].isRooted() ) {
4195 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4196 if ( phylogenies.length != 18 ) {
4199 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4202 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4205 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4208 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4211 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4214 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4217 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4220 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4223 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4226 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4229 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4232 if ( phylogenies[ 8 ].isRooted() ) {
4235 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4238 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4241 if ( !phylogenies[ 9 ].isRooted() ) {
4244 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4247 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4250 if ( !phylogenies[ 10 ].isRooted() ) {
4253 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4256 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4259 if ( phylogenies[ 11 ].isRooted() ) {
4262 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4265 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4268 if ( !phylogenies[ 12 ].isRooted() ) {
4271 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4274 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4277 if ( !phylogenies[ 13 ].isRooted() ) {
4280 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4283 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4286 if ( !phylogenies[ 14 ].isRooted() ) {
4289 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4292 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4295 if ( phylogenies[ 15 ].isRooted() ) {
4298 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4301 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4304 if ( !phylogenies[ 16 ].isRooted() ) {
4307 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4310 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4313 if ( phylogenies[ 17 ].isRooted() ) {
4316 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4320 catch ( final Exception e ) {
4321 e.printStackTrace( System.out );
4327 private static boolean testNexusTreeParsingTranslating() {
4329 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4330 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4331 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4332 if ( phylogenies.length != 1 ) {
4335 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4338 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4341 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4344 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4347 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4348 .equals( "Aranaeus" ) ) {
4352 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4353 if ( phylogenies.length != 3 ) {
4356 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4359 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4362 if ( phylogenies[ 0 ].isRooted() ) {
4365 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4368 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4371 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4372 .equals( "Aranaeus" ) ) {
4375 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4378 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4381 if ( phylogenies[ 1 ].isRooted() ) {
4384 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4387 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4390 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4391 .equals( "Aranaeus" ) ) {
4394 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4397 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4400 if ( !phylogenies[ 2 ].isRooted() ) {
4403 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4406 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4409 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4410 .equals( "Aranaeus" ) ) {
4414 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4415 if ( phylogenies.length != 3 ) {
4418 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4421 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4424 if ( phylogenies[ 0 ].isRooted() ) {
4427 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4430 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4433 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4434 .equals( "Aranaeus" ) ) {
4437 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4440 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4443 if ( phylogenies[ 1 ].isRooted() ) {
4446 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4449 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4452 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4453 .equals( "Aranaeus" ) ) {
4456 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4459 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4462 if ( !phylogenies[ 2 ].isRooted() ) {
4465 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4468 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4471 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4472 .equals( "Aranaeus" ) ) {
4476 catch ( final Exception e ) {
4477 e.printStackTrace( System.out );
4483 private static boolean testNHParsing() {
4485 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4486 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4487 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4490 final NHXParser nhxp = new NHXParser();
4491 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4492 nhxp.setReplaceUnderscores( true );
4493 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4494 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4497 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4500 final Phylogeny p1b = factory
4501 .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 ",
4502 new NHXParser() )[ 0 ];
4503 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4506 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4509 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4510 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4511 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4512 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4513 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4514 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4515 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4516 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4517 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4518 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4519 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4520 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4521 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4523 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4526 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4529 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4532 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4535 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4536 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4537 final String p16_S = "((A,B),C)";
4538 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4539 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4542 final String p17_S = "(C,(A,B))";
4543 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4544 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4547 final String p18_S = "((A,B),(C,D))";
4548 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4549 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4552 final String p19_S = "(((A,B),C),D)";
4553 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4554 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4557 final String p20_S = "(A,(B,(C,D)))";
4558 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4559 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4562 final String p21_S = "(A,(B,(C,(D,E))))";
4563 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4564 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4567 final String p22_S = "((((A,B),C),D),E)";
4568 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4569 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4572 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4573 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4574 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4577 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4578 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4579 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4582 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4583 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4584 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4585 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4588 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4591 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4592 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4593 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4594 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4595 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4596 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4597 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4598 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4599 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4600 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4603 final String p26_S = "(A,B)ab";
4604 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4605 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4608 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4609 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4611 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4614 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4615 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4616 final String p28_S3 = "(A,B)ab";
4617 final String p28_S4 = "((((A,B),C),D),;E;)";
4618 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4620 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4623 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4626 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4629 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4632 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";
4633 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4634 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4637 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";
4638 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4639 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4642 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4643 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4644 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4647 final String p33_S = "A";
4648 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4649 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4652 final String p34_S = "B;";
4653 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4654 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4657 final String p35_S = "B:0.2";
4658 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4659 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4662 final String p36_S = "(A)";
4663 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4664 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4667 final String p37_S = "((A))";
4668 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4669 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4672 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4673 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4674 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4677 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4678 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4679 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4682 final String p40_S = "(A,B,C)";
4683 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4684 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4687 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4688 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4689 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4692 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4693 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4694 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4697 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)";
4698 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4699 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4702 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)))";
4703 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4704 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4707 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4708 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4709 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4712 final String p46_S = "";
4713 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4714 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4717 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4718 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4721 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4722 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4725 final Phylogeny p49 = factory
4726 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4727 new NHXParser() )[ 0 ];
4728 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4731 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4732 if ( p50.getNode( "A" ) == null ) {
4735 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4736 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4739 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4742 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4743 .equals( "((A,B)88:2.0,C);" ) ) {
4746 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4747 if ( p51.getNode( "A(A" ) == null ) {
4750 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4751 if ( p52.getNode( "A(A" ) == null ) {
4754 final Phylogeny p53 = factory
4755 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4756 new NHXParser() )[ 0 ];
4757 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4761 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4762 if ( p54.getNode( "A" ) == null ) {
4765 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4766 .equals( "((A,B)[88],C);" ) ) {
4770 catch ( final Exception e ) {
4771 e.printStackTrace( System.out );
4777 private static boolean testNHXconversion() {
4779 final PhylogenyNode n1 = new PhylogenyNode();
4780 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4781 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4782 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4783 final PhylogenyNode n5 = PhylogenyNode
4784 .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]" );
4785 final PhylogenyNode n6 = PhylogenyNode
4786 .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]" );
4787 if ( !n1.toNewHampshireX().equals( "" ) ) {
4790 if ( !n2.toNewHampshireX().equals( "" ) ) {
4793 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4796 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4799 if ( !n5.toNewHampshireX()
4800 .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]" ) ) {
4803 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]" ) ) {
4807 catch ( final Exception e ) {
4808 e.printStackTrace( System.out );
4814 private static boolean testNHXNodeParsing() {
4816 final PhylogenyNode n1 = new PhylogenyNode();
4817 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4818 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4819 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4820 final PhylogenyNode n5 = PhylogenyNode
4821 .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]" );
4822 if ( !n3.getName().equals( "n3" ) ) {
4825 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4828 if ( n3.isDuplication() ) {
4831 if ( n3.isHasAssignedEvent() ) {
4834 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4837 if ( !n4.getName().equals( "n4" ) ) {
4840 if ( n4.getDistanceToParent() != 0.01 ) {
4843 if ( !n5.getName().equals( "n5" ) ) {
4846 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4849 if ( n5.getDistanceToParent() != 0.1 ) {
4852 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4855 if ( !n5.isDuplication() ) {
4858 if ( !n5.isHasAssignedEvent() ) {
4861 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4864 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4867 final PhylogenyNode n8 = PhylogenyNode
4868 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4869 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4872 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4875 final PhylogenyNode n9 = PhylogenyNode
4876 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4877 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4880 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4883 final PhylogenyNode n10 = PhylogenyNode
4884 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4885 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4888 final PhylogenyNode n20 = PhylogenyNode
4889 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4890 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4893 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4896 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
4897 NHXParser.TAXONOMY_EXTRACTION.YES );
4898 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4901 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4904 final PhylogenyNode n20xx = PhylogenyNode
4905 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4906 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4909 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4912 final PhylogenyNode n20xxx = PhylogenyNode
4913 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4914 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4917 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4920 final PhylogenyNode n20xxxx = PhylogenyNode
4921 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4922 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4925 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4928 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
4929 NHXParser.TAXONOMY_EXTRACTION.YES );
4930 if ( !n21.getName().equals( "n21_PIG" ) ) {
4933 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4936 final PhylogenyNode n21x = PhylogenyNode
4937 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4938 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4941 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4944 final PhylogenyNode n22 = PhylogenyNode
4945 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4946 if ( !n22.getName().equals( "n22/PIG" ) ) {
4949 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4952 final PhylogenyNode n23 = PhylogenyNode
4953 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4954 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4957 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4960 final PhylogenyNode a = PhylogenyNode
4961 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4962 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4965 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4968 final PhylogenyNode b = PhylogenyNode
4969 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4970 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4973 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4976 final PhylogenyNode c = PhylogenyNode
4977 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4978 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4979 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4982 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4985 final PhylogenyNode c1 = PhylogenyNode
4986 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4987 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4988 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4991 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4994 final PhylogenyNode c2 = PhylogenyNode
4995 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4996 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4997 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5000 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5003 final PhylogenyNode d = PhylogenyNode
5004 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5005 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5008 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5011 final PhylogenyNode e = PhylogenyNode
5012 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5013 if ( !e.getName().equals( "n10_RAT1" ) ) {
5016 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5019 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5020 NHXParser.TAXONOMY_EXTRACTION.YES );
5021 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5024 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5027 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5028 NHXParser.TAXONOMY_EXTRACTION.YES );
5029 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5032 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5035 final PhylogenyNode n11 = PhylogenyNode
5036 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5037 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5038 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5041 if ( n11.getDistanceToParent() != 0.4 ) {
5044 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5047 final PhylogenyNode n12 = PhylogenyNode
5048 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5049 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5050 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5053 if ( n12.getDistanceToParent() != 0.4 ) {
5056 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5059 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5060 NHXParser.TAXONOMY_EXTRACTION.YES );
5061 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5064 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5067 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5068 NHXParser.TAXONOMY_EXTRACTION.YES );
5069 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5072 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5075 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
5076 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
5077 if ( !tvu1.getRef().equals( "tag1" ) ) {
5080 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
5083 if ( !tvu1.getUnit().equals( "unit1" ) ) {
5086 if ( !tvu1.getValue().equals( "value1" ) ) {
5089 if ( !tvu3.getRef().equals( "tag3" ) ) {
5092 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
5095 if ( !tvu3.getUnit().equals( "unit3" ) ) {
5098 if ( !tvu3.getValue().equals( "value3" ) ) {
5101 if ( n1.getName().compareTo( "" ) != 0 ) {
5104 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5107 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5110 if ( n2.getName().compareTo( "" ) != 0 ) {
5113 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5116 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5119 final PhylogenyNode n00 = PhylogenyNode
5120 .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]" );
5121 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
5124 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5127 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5130 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
5133 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
5136 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
5139 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
5142 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
5145 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5146 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5149 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
5150 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
5153 final PhylogenyNode n13 = PhylogenyNode
5154 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5155 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5158 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5161 final PhylogenyNode n14 = PhylogenyNode
5162 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5163 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5166 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5169 final PhylogenyNode n15 = PhylogenyNode
5170 .createInstanceFromNhxString( "something_wicked[123]",
5171 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5172 if ( !n15.getName().equals( "something_wicked" ) ) {
5175 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5178 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5181 final PhylogenyNode n16 = PhylogenyNode
5182 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5183 if ( !n16.getName().equals( "something_wicked2" ) ) {
5186 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5189 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5192 final PhylogenyNode n17 = PhylogenyNode
5193 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5194 if ( !n17.getName().equals( "something_wicked3" ) ) {
5197 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5200 final PhylogenyNode n18 = PhylogenyNode
5201 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5202 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5205 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5208 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5212 catch ( final Exception e ) {
5213 e.printStackTrace( System.out );
5219 private static boolean testNHXParsing() {
5221 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5222 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5223 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5226 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]";
5227 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5228 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5231 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]";
5232 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5233 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5236 final Phylogeny[] p3 = factory
5237 .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]",
5239 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5242 final Phylogeny[] p4 = factory
5243 .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(]",
5245 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5248 final Phylogeny[] p5 = factory
5249 .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(((]",
5251 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5254 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)";
5255 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)";
5256 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5257 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5260 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)))";
5261 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)))";
5262 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5263 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5266 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]) ))[,,, ])))))))";
5267 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5268 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5269 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5272 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5273 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5276 final Phylogeny p10 = factory
5277 .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]",
5278 new NHXParser() )[ 0 ];
5279 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5283 catch ( final Exception e ) {
5284 e.printStackTrace( System.out );
5290 private static boolean testNHXParsingQuotes() {
5292 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5293 final NHXParser p = new NHXParser();
5294 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5295 if ( phylogenies_0.length != 5 ) {
5298 final Phylogeny phy = phylogenies_0[ 4 ];
5299 if ( phy.getNumberOfExternalNodes() != 7 ) {
5302 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5305 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5308 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5309 .getScientificName().equals( "hsapiens" ) ) {
5312 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5315 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5318 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5321 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5324 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5327 final NHXParser p1p = new NHXParser();
5328 p1p.setIgnoreQuotes( true );
5329 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5330 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5333 final NHXParser p2p = new NHXParser();
5334 p1p.setIgnoreQuotes( false );
5335 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5336 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5339 final NHXParser p3p = new NHXParser();
5340 p3p.setIgnoreQuotes( false );
5341 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5342 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5345 final NHXParser p4p = new NHXParser();
5346 p4p.setIgnoreQuotes( false );
5347 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5348 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5351 final Phylogeny p10 = factory
5352 .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]",
5353 new NHXParser() )[ 0 ];
5354 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]";
5355 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5358 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5359 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5363 final Phylogeny p12 = factory
5364 .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]",
5365 new NHXParser() )[ 0 ];
5366 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]";
5367 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5370 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5371 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5374 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;";
5375 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5378 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5379 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5383 catch ( final Exception e ) {
5384 e.printStackTrace( System.out );
5390 private static boolean testNHXParsingMB() {
5392 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5393 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5394 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5395 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5396 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5397 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5398 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5399 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5400 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5401 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5402 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5405 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5408 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5409 0.1100000000000000e+00 ) ) {
5412 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5415 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5418 final Phylogeny p2 = factory
5419 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5420 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5421 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5422 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5423 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5424 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5425 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5426 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5427 + "7.369400000000000e-02}])",
5428 new NHXParser() )[ 0 ];
5429 if ( p2.getNode( "1" ) == null ) {
5432 if ( p2.getNode( "2" ) == null ) {
5436 catch ( final Exception e ) {
5437 e.printStackTrace( System.out );
5444 private static boolean testPhylogenyBranch() {
5446 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5447 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5448 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5449 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5450 if ( !a1b1.equals( a1b1 ) ) {
5453 if ( !a1b1.equals( b1a1 ) ) {
5456 if ( !b1a1.equals( a1b1 ) ) {
5459 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5460 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5461 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5462 if ( a1_b1.equals( b1_a1 ) ) {
5465 if ( a1_b1.equals( a1_b1_ ) ) {
5468 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5469 if ( !a1_b1.equals( b1_a1_ ) ) {
5472 if ( a1_b1_.equals( b1_a1_ ) ) {
5475 if ( !a1_b1_.equals( b1_a1 ) ) {
5479 catch ( final Exception e ) {
5480 e.printStackTrace( System.out );
5486 private static boolean testPhyloXMLparsingOfDistributionElement() {
5488 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5489 PhyloXmlParser xml_parser = null;
5491 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5493 catch ( final Exception e ) {
5494 // Do nothing -- means were not running from jar.
5496 if ( xml_parser == null ) {
5497 xml_parser = new PhyloXmlParser();
5498 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5499 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5502 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5505 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5507 if ( xml_parser.getErrorCount() > 0 ) {
5508 System.out.println( xml_parser.getErrorMessages().toString() );
5511 if ( phylogenies_0.length != 1 ) {
5514 final Phylogeny t1 = phylogenies_0[ 0 ];
5515 PhylogenyNode n = null;
5516 Distribution d = null;
5517 n = t1.getNode( "root node" );
5518 if ( !n.getNodeData().isHasDistribution() ) {
5521 if ( n.getNodeData().getDistributions().size() != 1 ) {
5524 d = n.getNodeData().getDistribution();
5525 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5528 if ( d.getPoints().size() != 1 ) {
5531 if ( d.getPolygons() != null ) {
5534 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5537 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5540 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5543 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5546 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5549 n = t1.getNode( "node a" );
5550 if ( !n.getNodeData().isHasDistribution() ) {
5553 if ( n.getNodeData().getDistributions().size() != 2 ) {
5556 d = n.getNodeData().getDistribution( 1 );
5557 if ( !d.getDesc().equals( "San Diego" ) ) {
5560 if ( d.getPoints().size() != 1 ) {
5563 if ( d.getPolygons() != null ) {
5566 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5569 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5572 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5575 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5578 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5581 n = t1.getNode( "node bb" );
5582 if ( !n.getNodeData().isHasDistribution() ) {
5585 if ( n.getNodeData().getDistributions().size() != 1 ) {
5588 d = n.getNodeData().getDistribution( 0 );
5589 if ( d.getPoints().size() != 3 ) {
5592 if ( d.getPolygons().size() != 2 ) {
5595 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5598 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5601 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5604 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5607 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5610 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5613 Polygon p = d.getPolygons().get( 0 );
5614 if ( p.getPoints().size() != 3 ) {
5617 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5620 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5623 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5626 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5629 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5632 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5635 p = d.getPolygons().get( 1 );
5636 if ( p.getPoints().size() != 3 ) {
5639 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5642 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5645 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5649 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5650 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5651 if ( rt.length != 1 ) {
5654 final Phylogeny t1_rt = rt[ 0 ];
5655 n = t1_rt.getNode( "root node" );
5656 if ( !n.getNodeData().isHasDistribution() ) {
5659 if ( n.getNodeData().getDistributions().size() != 1 ) {
5662 d = n.getNodeData().getDistribution();
5663 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5666 if ( d.getPoints().size() != 1 ) {
5669 if ( d.getPolygons() != null ) {
5672 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5675 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5678 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5681 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5684 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5687 n = t1_rt.getNode( "node a" );
5688 if ( !n.getNodeData().isHasDistribution() ) {
5691 if ( n.getNodeData().getDistributions().size() != 2 ) {
5694 d = n.getNodeData().getDistribution( 1 );
5695 if ( !d.getDesc().equals( "San Diego" ) ) {
5698 if ( d.getPoints().size() != 1 ) {
5701 if ( d.getPolygons() != null ) {
5704 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5707 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5710 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5713 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5716 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5719 n = t1_rt.getNode( "node bb" );
5720 if ( !n.getNodeData().isHasDistribution() ) {
5723 if ( n.getNodeData().getDistributions().size() != 1 ) {
5726 d = n.getNodeData().getDistribution( 0 );
5727 if ( d.getPoints().size() != 3 ) {
5730 if ( d.getPolygons().size() != 2 ) {
5733 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5736 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5739 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5742 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5745 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5748 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5751 p = d.getPolygons().get( 0 );
5752 if ( p.getPoints().size() != 3 ) {
5755 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5758 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5761 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5764 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5767 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5770 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5773 p = d.getPolygons().get( 1 );
5774 if ( p.getPoints().size() != 3 ) {
5777 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5780 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5783 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5787 catch ( final Exception e ) {
5788 e.printStackTrace( System.out );
5794 private static boolean testPostOrderIterator() {
5796 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5797 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5798 PhylogenyNodeIterator it0;
5799 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5802 for( it0.reset(); it0.hasNext(); ) {
5805 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5806 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5807 if ( !it.next().getName().equals( "A" ) ) {
5810 if ( !it.next().getName().equals( "B" ) ) {
5813 if ( !it.next().getName().equals( "ab" ) ) {
5816 if ( !it.next().getName().equals( "C" ) ) {
5819 if ( !it.next().getName().equals( "D" ) ) {
5822 if ( !it.next().getName().equals( "cd" ) ) {
5825 if ( !it.next().getName().equals( "abcd" ) ) {
5828 if ( !it.next().getName().equals( "E" ) ) {
5831 if ( !it.next().getName().equals( "F" ) ) {
5834 if ( !it.next().getName().equals( "ef" ) ) {
5837 if ( !it.next().getName().equals( "G" ) ) {
5840 if ( !it.next().getName().equals( "H" ) ) {
5843 if ( !it.next().getName().equals( "gh" ) ) {
5846 if ( !it.next().getName().equals( "efgh" ) ) {
5849 if ( !it.next().getName().equals( "r" ) ) {
5852 if ( it.hasNext() ) {
5856 catch ( final Exception e ) {
5857 e.printStackTrace( System.out );
5863 private static boolean testPreOrderIterator() {
5865 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5866 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5867 PhylogenyNodeIterator it0;
5868 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5871 for( it0.reset(); it0.hasNext(); ) {
5874 PhylogenyNodeIterator it = t0.iteratorPreorder();
5875 if ( !it.next().getName().equals( "r" ) ) {
5878 if ( !it.next().getName().equals( "ab" ) ) {
5881 if ( !it.next().getName().equals( "A" ) ) {
5884 if ( !it.next().getName().equals( "B" ) ) {
5887 if ( !it.next().getName().equals( "cd" ) ) {
5890 if ( !it.next().getName().equals( "C" ) ) {
5893 if ( !it.next().getName().equals( "D" ) ) {
5896 if ( it.hasNext() ) {
5899 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5900 it = t1.iteratorPreorder();
5901 if ( !it.next().getName().equals( "r" ) ) {
5904 if ( !it.next().getName().equals( "abcd" ) ) {
5907 if ( !it.next().getName().equals( "ab" ) ) {
5910 if ( !it.next().getName().equals( "A" ) ) {
5913 if ( !it.next().getName().equals( "B" ) ) {
5916 if ( !it.next().getName().equals( "cd" ) ) {
5919 if ( !it.next().getName().equals( "C" ) ) {
5922 if ( !it.next().getName().equals( "D" ) ) {
5925 if ( !it.next().getName().equals( "efgh" ) ) {
5928 if ( !it.next().getName().equals( "ef" ) ) {
5931 if ( !it.next().getName().equals( "E" ) ) {
5934 if ( !it.next().getName().equals( "F" ) ) {
5937 if ( !it.next().getName().equals( "gh" ) ) {
5940 if ( !it.next().getName().equals( "G" ) ) {
5943 if ( !it.next().getName().equals( "H" ) ) {
5946 if ( it.hasNext() ) {
5950 catch ( final Exception e ) {
5951 e.printStackTrace( System.out );
5957 private static boolean testPropertiesMap() {
5959 final PropertiesMap pm = new PropertiesMap();
5960 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5961 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5962 final Property p2 = new Property( "something:else",
5964 "improbable:research",
5967 pm.addProperty( p0 );
5968 pm.addProperty( p1 );
5969 pm.addProperty( p2 );
5970 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5973 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5976 if ( pm.getProperties().size() != 3 ) {
5979 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5982 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5985 if ( pm.getProperties().size() != 3 ) {
5988 pm.removeProperty( "dimensions:diameter" );
5989 if ( pm.getProperties().size() != 2 ) {
5992 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5995 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5999 catch ( final Exception e ) {
6000 e.printStackTrace( System.out );
6006 private static boolean testReIdMethods() {
6008 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6009 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6010 final int count = PhylogenyNode.getNodeCount();
6012 if ( p.getNode( "r" ).getId() != count ) {
6015 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6018 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6021 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6024 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6027 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6030 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6033 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6036 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6039 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6042 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6045 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6048 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6051 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6054 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6058 catch ( final Exception e ) {
6059 e.printStackTrace( System.out );
6065 private static boolean testRerooting() {
6067 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6068 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",
6069 new NHXParser() )[ 0 ];
6070 if ( !t1.isRooted() ) {
6073 t1.reRoot( t1.getNode( "D" ) );
6074 t1.reRoot( t1.getNode( "CD" ) );
6075 t1.reRoot( t1.getNode( "A" ) );
6076 t1.reRoot( t1.getNode( "B" ) );
6077 t1.reRoot( t1.getNode( "AB" ) );
6078 t1.reRoot( t1.getNode( "D" ) );
6079 t1.reRoot( t1.getNode( "C" ) );
6080 t1.reRoot( t1.getNode( "CD" ) );
6081 t1.reRoot( t1.getNode( "A" ) );
6082 t1.reRoot( t1.getNode( "B" ) );
6083 t1.reRoot( t1.getNode( "AB" ) );
6084 t1.reRoot( t1.getNode( "D" ) );
6085 t1.reRoot( t1.getNode( "D" ) );
6086 t1.reRoot( t1.getNode( "C" ) );
6087 t1.reRoot( t1.getNode( "A" ) );
6088 t1.reRoot( t1.getNode( "B" ) );
6089 t1.reRoot( t1.getNode( "AB" ) );
6090 t1.reRoot( t1.getNode( "C" ) );
6091 t1.reRoot( t1.getNode( "D" ) );
6092 t1.reRoot( t1.getNode( "CD" ) );
6093 t1.reRoot( t1.getNode( "D" ) );
6094 t1.reRoot( t1.getNode( "A" ) );
6095 t1.reRoot( t1.getNode( "B" ) );
6096 t1.reRoot( t1.getNode( "AB" ) );
6097 t1.reRoot( t1.getNode( "C" ) );
6098 t1.reRoot( t1.getNode( "D" ) );
6099 t1.reRoot( t1.getNode( "CD" ) );
6100 t1.reRoot( t1.getNode( "D" ) );
6101 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6104 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6107 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6110 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6113 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6116 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6119 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",
6120 new NHXParser() )[ 0 ];
6121 t2.reRoot( t2.getNode( "A" ) );
6122 t2.reRoot( t2.getNode( "D" ) );
6123 t2.reRoot( t2.getNode( "ABC" ) );
6124 t2.reRoot( t2.getNode( "A" ) );
6125 t2.reRoot( t2.getNode( "B" ) );
6126 t2.reRoot( t2.getNode( "D" ) );
6127 t2.reRoot( t2.getNode( "C" ) );
6128 t2.reRoot( t2.getNode( "ABC" ) );
6129 t2.reRoot( t2.getNode( "A" ) );
6130 t2.reRoot( t2.getNode( "B" ) );
6131 t2.reRoot( t2.getNode( "AB" ) );
6132 t2.reRoot( t2.getNode( "AB" ) );
6133 t2.reRoot( t2.getNode( "D" ) );
6134 t2.reRoot( t2.getNode( "C" ) );
6135 t2.reRoot( t2.getNode( "B" ) );
6136 t2.reRoot( t2.getNode( "AB" ) );
6137 t2.reRoot( t2.getNode( "D" ) );
6138 t2.reRoot( t2.getNode( "D" ) );
6139 t2.reRoot( t2.getNode( "ABC" ) );
6140 t2.reRoot( t2.getNode( "A" ) );
6141 t2.reRoot( t2.getNode( "B" ) );
6142 t2.reRoot( t2.getNode( "AB" ) );
6143 t2.reRoot( t2.getNode( "D" ) );
6144 t2.reRoot( t2.getNode( "C" ) );
6145 t2.reRoot( t2.getNode( "ABC" ) );
6146 t2.reRoot( t2.getNode( "A" ) );
6147 t2.reRoot( t2.getNode( "B" ) );
6148 t2.reRoot( t2.getNode( "AB" ) );
6149 t2.reRoot( t2.getNode( "D" ) );
6150 t2.reRoot( t2.getNode( "D" ) );
6151 t2.reRoot( t2.getNode( "C" ) );
6152 t2.reRoot( t2.getNode( "A" ) );
6153 t2.reRoot( t2.getNode( "B" ) );
6154 t2.reRoot( t2.getNode( "AB" ) );
6155 t2.reRoot( t2.getNode( "C" ) );
6156 t2.reRoot( t2.getNode( "D" ) );
6157 t2.reRoot( t2.getNode( "ABC" ) );
6158 t2.reRoot( t2.getNode( "D" ) );
6159 t2.reRoot( t2.getNode( "A" ) );
6160 t2.reRoot( t2.getNode( "B" ) );
6161 t2.reRoot( t2.getNode( "AB" ) );
6162 t2.reRoot( t2.getNode( "C" ) );
6163 t2.reRoot( t2.getNode( "D" ) );
6164 t2.reRoot( t2.getNode( "ABC" ) );
6165 t2.reRoot( t2.getNode( "D" ) );
6166 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6169 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6172 t2.reRoot( t2.getNode( "ABC" ) );
6173 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6176 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6179 t2.reRoot( t2.getNode( "AB" ) );
6180 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6183 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6186 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6189 t2.reRoot( t2.getNode( "AB" ) );
6190 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6193 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6196 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6199 t2.reRoot( t2.getNode( "D" ) );
6200 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6203 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6206 t2.reRoot( t2.getNode( "ABC" ) );
6207 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6210 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6213 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6214 new NHXParser() )[ 0 ];
6215 t3.reRoot( t3.getNode( "B" ) );
6216 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6219 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6222 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6225 t3.reRoot( t3.getNode( "B" ) );
6226 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6229 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6232 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6235 t3.reRoot( t3.getRoot() );
6236 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6239 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6242 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6246 catch ( final Exception e ) {
6247 e.printStackTrace( System.out );
6253 private static boolean testSDIse() {
6255 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6256 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6257 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6258 gene1.setRooted( true );
6259 species1.setRooted( true );
6260 final SDI sdi = new SDIse( gene1, species1 );
6261 if ( !gene1.getRoot().isDuplication() ) {
6264 final Phylogeny species2 = factory
6265 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6266 new NHXParser() )[ 0 ];
6267 final Phylogeny gene2 = factory
6268 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6269 new NHXParser() )[ 0 ];
6270 species2.setRooted( true );
6271 gene2.setRooted( true );
6272 final SDI sdi2 = new SDIse( gene2, species2 );
6273 if ( sdi2.getDuplicationsSum() != 0 ) {
6276 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6279 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6282 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6285 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6288 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6291 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6294 final Phylogeny species3 = factory
6295 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6296 new NHXParser() )[ 0 ];
6297 final Phylogeny gene3 = factory
6298 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6299 new NHXParser() )[ 0 ];
6300 species3.setRooted( true );
6301 gene3.setRooted( true );
6302 final SDI sdi3 = new SDIse( gene3, species3 );
6303 if ( sdi3.getDuplicationsSum() != 1 ) {
6306 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6309 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6312 final Phylogeny species4 = factory
6313 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6314 new NHXParser() )[ 0 ];
6315 final Phylogeny gene4 = factory
6316 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6317 new NHXParser() )[ 0 ];
6318 species4.setRooted( true );
6319 gene4.setRooted( true );
6320 final SDI sdi4 = new SDIse( gene4, species4 );
6321 if ( sdi4.getDuplicationsSum() != 1 ) {
6324 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6327 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6330 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6333 if ( species4.getNumberOfExternalNodes() != 6 ) {
6336 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6339 final Phylogeny species5 = factory
6340 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6341 new NHXParser() )[ 0 ];
6342 final Phylogeny gene5 = factory
6343 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6344 new NHXParser() )[ 0 ];
6345 species5.setRooted( true );
6346 gene5.setRooted( true );
6347 final SDI sdi5 = new SDIse( gene5, species5 );
6348 if ( sdi5.getDuplicationsSum() != 2 ) {
6351 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6354 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6357 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6360 if ( species5.getNumberOfExternalNodes() != 6 ) {
6363 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6366 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6367 // Conjecture for Comparing Molecular Phylogenies"
6368 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6369 final Phylogeny species6 = factory
6370 .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,"
6371 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6372 new NHXParser() )[ 0 ];
6373 final Phylogeny gene6 = factory
6374 .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,"
6375 + "((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,"
6376 + "(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;",
6377 new NHXParser() )[ 0 ];
6378 species6.setRooted( true );
6379 gene6.setRooted( true );
6380 final SDI sdi6 = new SDIse( gene6, species6 );
6381 if ( sdi6.getDuplicationsSum() != 3 ) {
6384 if ( !gene6.getNode( "r" ).isDuplication() ) {
6387 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6390 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6393 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6396 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6399 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6402 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6405 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6408 sdi6.computeMappingCostL();
6409 if ( sdi6.computeMappingCostL() != 17 ) {
6412 if ( species6.getNumberOfExternalNodes() != 9 ) {
6415 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6418 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6419 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6420 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6421 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6422 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6423 species7.setRooted( true );
6424 final Phylogeny gene7_1 = Test
6425 .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])" );
6426 gene7_1.setRooted( true );
6427 final SDI sdi7 = new SDIse( gene7_1, species7 );
6428 if ( sdi7.getDuplicationsSum() != 0 ) {
6431 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6434 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6437 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6440 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6443 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6446 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6449 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6452 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6455 final Phylogeny gene7_2 = Test
6456 .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])" );
6457 gene7_2.setRooted( true );
6458 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6459 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6462 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6465 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6468 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6471 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6474 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6477 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6480 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6483 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6486 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6490 catch ( final Exception e ) {
6496 private static boolean testSDIunrooted() {
6498 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6499 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6500 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6501 final Iterator<PhylogenyBranch> iter = l.iterator();
6502 PhylogenyBranch br = iter.next();
6503 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6506 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6510 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6513 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6517 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6520 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6524 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6527 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6531 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6534 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6538 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6541 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6545 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6548 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6552 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6555 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6559 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6562 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6566 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6569 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6573 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6576 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6580 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6583 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6587 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6590 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6594 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6597 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6601 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6604 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6607 if ( iter.hasNext() ) {
6610 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6611 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6612 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6614 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6617 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6621 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6624 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6628 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6631 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6634 if ( iter1.hasNext() ) {
6637 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6638 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6639 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6641 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6644 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6648 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6651 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6655 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6658 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6661 if ( iter2.hasNext() ) {
6664 final Phylogeny species0 = factory
6665 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6666 new NHXParser() )[ 0 ];
6667 final Phylogeny gene1 = factory
6668 .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])",
6669 new NHXParser() )[ 0 ];
6670 species0.setRooted( true );
6671 gene1.setRooted( true );
6672 final SDIR sdi_unrooted = new SDIR();
6673 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6674 if ( sdi_unrooted.getCount() != 1 ) {
6677 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6680 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6683 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6686 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6689 final Phylogeny gene2 = factory
6690 .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])",
6691 new NHXParser() )[ 0 ];
6692 gene2.setRooted( true );
6693 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6694 if ( sdi_unrooted.getCount() != 1 ) {
6697 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6700 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6703 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6706 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6709 final Phylogeny species6 = factory
6710 .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,"
6711 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6712 new NHXParser() )[ 0 ];
6713 final Phylogeny gene6 = factory
6714 .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],"
6715 + "(((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],"
6716 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6717 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6718 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6719 new NHXParser() )[ 0 ];
6720 species6.setRooted( true );
6721 gene6.setRooted( true );
6722 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6723 if ( sdi_unrooted.getCount() != 1 ) {
6726 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6729 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6732 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6735 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6738 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6741 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6744 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6747 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6750 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6753 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6756 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6759 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6763 final Phylogeny species7 = factory
6764 .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,"
6765 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6766 new NHXParser() )[ 0 ];
6767 final Phylogeny gene7 = factory
6768 .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],"
6769 + "(((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],"
6770 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6771 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6772 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6773 new NHXParser() )[ 0 ];
6774 species7.setRooted( true );
6775 gene7.setRooted( true );
6776 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6777 if ( sdi_unrooted.getCount() != 1 ) {
6780 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6783 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6786 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6789 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6792 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6795 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6798 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6801 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6804 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6807 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6810 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6813 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6817 final Phylogeny species8 = factory
6818 .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,"
6819 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6820 new NHXParser() )[ 0 ];
6821 final Phylogeny gene8 = factory
6822 .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],"
6823 + "(((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],"
6824 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6825 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6826 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6827 new NHXParser() )[ 0 ];
6828 species8.setRooted( true );
6829 gene8.setRooted( true );
6830 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6831 if ( sdi_unrooted.getCount() != 1 ) {
6834 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6837 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6840 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6843 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6846 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6849 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6852 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6855 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6858 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6861 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6864 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6867 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6872 catch ( final Exception e ) {
6873 e.printStackTrace( System.out );
6879 private static boolean testOrthologTable() {
6881 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6882 final Phylogeny s1 = factory.create( Test.PATH_TO_TEST_DATA + "rio_species.xml", new PhyloXmlParser() )[ 0 ];
6883 final NHXParser p = new NHXParser();
6884 p.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
6885 final Phylogeny g1[] = factory.create( new File( Test.PATH_TO_TEST_DATA
6886 + "rio_Bcl-2_e1_20_mafft_05_40_fme.mlt" ), p );
6887 for( final Phylogeny gt : g1 ) {
6888 gt.setRooted( true );
6889 final GSDI sdi = new GSDI( gt, s1, true, true, true );
6891 final IntMatrix m = RIO.calculateOrthologTable( g1, true );
6892 // System.out.println( m.toString() );
6894 catch ( final Exception e ) {
6895 e.printStackTrace();
6901 private static boolean testSplit() {
6903 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6904 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6905 //Archaeopteryx.createApplication( p0 );
6906 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6907 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6908 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6909 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6910 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6911 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6912 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6913 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6914 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6915 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6916 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6917 // System.out.println( s0.toString() );
6919 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6922 if ( s0.match( query_nodes ) ) {
6925 query_nodes = new HashSet<PhylogenyNode>();
6926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6933 if ( !s0.match( query_nodes ) ) {
6937 query_nodes = new HashSet<PhylogenyNode>();
6938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6941 if ( !s0.match( query_nodes ) ) {
6945 query_nodes = new HashSet<PhylogenyNode>();
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6950 if ( !s0.match( query_nodes ) ) {
6954 query_nodes = new HashSet<PhylogenyNode>();
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6959 if ( !s0.match( query_nodes ) ) {
6963 query_nodes = new HashSet<PhylogenyNode>();
6964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6967 if ( !s0.match( query_nodes ) ) {
6971 query_nodes = new HashSet<PhylogenyNode>();
6972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6974 if ( !s0.match( query_nodes ) ) {
6978 query_nodes = new HashSet<PhylogenyNode>();
6979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6984 if ( !s0.match( query_nodes ) ) {
6988 query_nodes = new HashSet<PhylogenyNode>();
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6992 if ( !s0.match( query_nodes ) ) {
6996 query_nodes = new HashSet<PhylogenyNode>();
6997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7001 if ( !s0.match( query_nodes ) ) {
7005 query_nodes = new HashSet<PhylogenyNode>();
7006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7008 if ( s0.match( query_nodes ) ) {
7012 query_nodes = new HashSet<PhylogenyNode>();
7013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7017 if ( s0.match( query_nodes ) ) {
7021 query_nodes = new HashSet<PhylogenyNode>();
7022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7027 if ( s0.match( query_nodes ) ) {
7031 query_nodes = new HashSet<PhylogenyNode>();
7032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7035 if ( s0.match( query_nodes ) ) {
7039 query_nodes = new HashSet<PhylogenyNode>();
7040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7042 if ( s0.match( query_nodes ) ) {
7046 query_nodes = new HashSet<PhylogenyNode>();
7047 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7049 if ( s0.match( query_nodes ) ) {
7053 query_nodes = new HashSet<PhylogenyNode>();
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7056 if ( s0.match( query_nodes ) ) {
7060 query_nodes = new HashSet<PhylogenyNode>();
7061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7063 if ( s0.match( query_nodes ) ) {
7067 query_nodes = new HashSet<PhylogenyNode>();
7068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7070 if ( s0.match( query_nodes ) ) {
7074 query_nodes = new HashSet<PhylogenyNode>();
7075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7077 if ( s0.match( query_nodes ) ) {
7081 query_nodes = new HashSet<PhylogenyNode>();
7082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7085 if ( s0.match( query_nodes ) ) {
7089 query_nodes = new HashSet<PhylogenyNode>();
7090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7093 if ( s0.match( query_nodes ) ) {
7097 query_nodes = new HashSet<PhylogenyNode>();
7098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7101 if ( s0.match( query_nodes ) ) {
7105 query_nodes = new HashSet<PhylogenyNode>();
7106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7110 if ( s0.match( query_nodes ) ) {
7114 // query_nodes = new HashSet<PhylogenyNode>();
7115 // query_nodes.add( new PhylogenyNode( "X" ) );
7116 // query_nodes.add( new PhylogenyNode( "Y" ) );
7117 // query_nodes.add( new PhylogenyNode( "A" ) );
7118 // query_nodes.add( new PhylogenyNode( "B" ) );
7119 // query_nodes.add( new PhylogenyNode( "C" ) );
7120 // query_nodes.add( new PhylogenyNode( "D" ) );
7121 // query_nodes.add( new PhylogenyNode( "E" ) );
7122 // query_nodes.add( new PhylogenyNode( "F" ) );
7123 // query_nodes.add( new PhylogenyNode( "G" ) );
7124 // if ( !s0.match( query_nodes ) ) {
7127 // query_nodes = new HashSet<PhylogenyNode>();
7128 // query_nodes.add( new PhylogenyNode( "X" ) );
7129 // query_nodes.add( new PhylogenyNode( "Y" ) );
7130 // query_nodes.add( new PhylogenyNode( "A" ) );
7131 // query_nodes.add( new PhylogenyNode( "B" ) );
7132 // query_nodes.add( new PhylogenyNode( "C" ) );
7133 // if ( !s0.match( query_nodes ) ) {
7137 // query_nodes = new HashSet<PhylogenyNode>();
7138 // query_nodes.add( new PhylogenyNode( "X" ) );
7139 // query_nodes.add( new PhylogenyNode( "Y" ) );
7140 // query_nodes.add( new PhylogenyNode( "D" ) );
7141 // query_nodes.add( new PhylogenyNode( "E" ) );
7142 // query_nodes.add( new PhylogenyNode( "F" ) );
7143 // query_nodes.add( new PhylogenyNode( "G" ) );
7144 // if ( !s0.match( query_nodes ) ) {
7148 // query_nodes = new HashSet<PhylogenyNode>();
7149 // query_nodes.add( new PhylogenyNode( "X" ) );
7150 // query_nodes.add( new PhylogenyNode( "Y" ) );
7151 // query_nodes.add( new PhylogenyNode( "A" ) );
7152 // query_nodes.add( new PhylogenyNode( "B" ) );
7153 // query_nodes.add( new PhylogenyNode( "C" ) );
7154 // query_nodes.add( new PhylogenyNode( "D" ) );
7155 // if ( !s0.match( query_nodes ) ) {
7159 // query_nodes = new HashSet<PhylogenyNode>();
7160 // query_nodes.add( new PhylogenyNode( "X" ) );
7161 // query_nodes.add( new PhylogenyNode( "Y" ) );
7162 // query_nodes.add( new PhylogenyNode( "E" ) );
7163 // query_nodes.add( new PhylogenyNode( "F" ) );
7164 // query_nodes.add( new PhylogenyNode( "G" ) );
7165 // if ( !s0.match( query_nodes ) ) {
7169 // query_nodes = new HashSet<PhylogenyNode>();
7170 // query_nodes.add( new PhylogenyNode( "X" ) );
7171 // query_nodes.add( new PhylogenyNode( "Y" ) );
7172 // query_nodes.add( new PhylogenyNode( "F" ) );
7173 // query_nodes.add( new PhylogenyNode( "G" ) );
7174 // if ( !s0.match( query_nodes ) ) {
7178 query_nodes = new HashSet<PhylogenyNode>();
7179 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7180 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7183 if ( s0.match( query_nodes ) ) {
7187 query_nodes = new HashSet<PhylogenyNode>();
7188 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7190 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7191 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7192 if ( s0.match( query_nodes ) ) {
7195 ///////////////////////////
7197 query_nodes = new HashSet<PhylogenyNode>();
7198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7199 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7202 if ( s0.match( query_nodes ) ) {
7206 query_nodes = new HashSet<PhylogenyNode>();
7207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7209 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7210 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7211 if ( s0.match( query_nodes ) ) {
7215 query_nodes = new HashSet<PhylogenyNode>();
7216 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7217 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7218 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7220 if ( s0.match( query_nodes ) ) {
7224 query_nodes = new HashSet<PhylogenyNode>();
7225 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7226 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7227 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7229 if ( s0.match( query_nodes ) ) {
7233 query_nodes = new HashSet<PhylogenyNode>();
7234 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7235 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7236 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7237 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7238 if ( s0.match( query_nodes ) ) {
7242 query_nodes = new HashSet<PhylogenyNode>();
7243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7245 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7246 if ( s0.match( query_nodes ) ) {
7250 query_nodes = new HashSet<PhylogenyNode>();
7251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7254 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7255 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7256 if ( s0.match( query_nodes ) ) {
7260 query_nodes = new HashSet<PhylogenyNode>();
7261 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7265 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7266 if ( s0.match( query_nodes ) ) {
7270 query_nodes = new HashSet<PhylogenyNode>();
7271 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7273 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7274 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7275 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7276 if ( s0.match( query_nodes ) ) {
7280 query_nodes = new HashSet<PhylogenyNode>();
7281 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7282 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7283 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7284 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7285 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7287 if ( s0.match( query_nodes ) ) {
7291 catch ( final Exception e ) {
7292 e.printStackTrace();
7298 private static boolean testSplitStrict() {
7300 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7301 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7302 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7303 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7304 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7305 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7306 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7307 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7308 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7309 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7310 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7311 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7312 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7313 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7314 if ( s0.match( query_nodes ) ) {
7317 query_nodes = new HashSet<PhylogenyNode>();
7318 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7319 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7320 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7322 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7323 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7324 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7325 if ( !s0.match( query_nodes ) ) {
7329 query_nodes = new HashSet<PhylogenyNode>();
7330 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7332 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7333 if ( !s0.match( query_nodes ) ) {
7337 query_nodes = new HashSet<PhylogenyNode>();
7338 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7342 if ( !s0.match( query_nodes ) ) {
7346 query_nodes = new HashSet<PhylogenyNode>();
7347 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7351 if ( !s0.match( query_nodes ) ) {
7355 query_nodes = new HashSet<PhylogenyNode>();
7356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7359 if ( !s0.match( query_nodes ) ) {
7363 query_nodes = new HashSet<PhylogenyNode>();
7364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7366 if ( !s0.match( query_nodes ) ) {
7370 query_nodes = new HashSet<PhylogenyNode>();
7371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7375 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7376 if ( !s0.match( query_nodes ) ) {
7380 query_nodes = new HashSet<PhylogenyNode>();
7381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7383 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7384 if ( !s0.match( query_nodes ) ) {
7388 query_nodes = new HashSet<PhylogenyNode>();
7389 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7391 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7393 if ( !s0.match( query_nodes ) ) {
7397 query_nodes = new HashSet<PhylogenyNode>();
7398 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7400 if ( s0.match( query_nodes ) ) {
7404 query_nodes = new HashSet<PhylogenyNode>();
7405 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7407 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7408 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7409 if ( s0.match( query_nodes ) ) {
7413 query_nodes = new HashSet<PhylogenyNode>();
7414 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7416 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7417 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7418 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7419 if ( s0.match( query_nodes ) ) {
7423 query_nodes = new HashSet<PhylogenyNode>();
7424 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7425 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7426 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7427 if ( s0.match( query_nodes ) ) {
7431 query_nodes = new HashSet<PhylogenyNode>();
7432 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7434 if ( s0.match( query_nodes ) ) {
7438 query_nodes = new HashSet<PhylogenyNode>();
7439 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7440 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7441 if ( s0.match( query_nodes ) ) {
7445 query_nodes = new HashSet<PhylogenyNode>();
7446 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7448 if ( s0.match( query_nodes ) ) {
7452 query_nodes = new HashSet<PhylogenyNode>();
7453 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7454 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7455 if ( s0.match( query_nodes ) ) {
7459 query_nodes = new HashSet<PhylogenyNode>();
7460 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7461 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7462 if ( s0.match( query_nodes ) ) {
7466 query_nodes = new HashSet<PhylogenyNode>();
7467 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7468 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7469 if ( s0.match( query_nodes ) ) {
7473 query_nodes = new HashSet<PhylogenyNode>();
7474 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7475 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7476 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7477 if ( s0.match( query_nodes ) ) {
7481 query_nodes = new HashSet<PhylogenyNode>();
7482 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7485 if ( s0.match( query_nodes ) ) {
7489 query_nodes = new HashSet<PhylogenyNode>();
7490 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7491 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7493 if ( s0.match( query_nodes ) ) {
7497 query_nodes = new HashSet<PhylogenyNode>();
7498 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7499 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7500 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7501 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7502 if ( s0.match( query_nodes ) ) {
7506 catch ( final Exception e ) {
7507 e.printStackTrace();
7513 private static boolean testSubtreeDeletion() {
7515 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7516 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7517 t1.deleteSubtree( t1.getNode( "A" ), false );
7518 if ( t1.getNumberOfExternalNodes() != 5 ) {
7521 t1.toNewHampshireX();
7522 t1.deleteSubtree( t1.getNode( "E" ), false );
7523 if ( t1.getNumberOfExternalNodes() != 4 ) {
7526 t1.toNewHampshireX();
7527 t1.deleteSubtree( t1.getNode( "F" ), false );
7528 if ( t1.getNumberOfExternalNodes() != 3 ) {
7531 t1.toNewHampshireX();
7532 t1.deleteSubtree( t1.getNode( "D" ), false );
7533 t1.toNewHampshireX();
7534 if ( t1.getNumberOfExternalNodes() != 3 ) {
7537 t1.deleteSubtree( t1.getNode( "def" ), false );
7538 t1.toNewHampshireX();
7539 if ( t1.getNumberOfExternalNodes() != 2 ) {
7542 t1.deleteSubtree( t1.getNode( "B" ), false );
7543 t1.toNewHampshireX();
7544 if ( t1.getNumberOfExternalNodes() != 1 ) {
7547 t1.deleteSubtree( t1.getNode( "C" ), false );
7548 t1.toNewHampshireX();
7549 if ( t1.getNumberOfExternalNodes() != 1 ) {
7552 t1.deleteSubtree( t1.getNode( "abc" ), false );
7553 t1.toNewHampshireX();
7554 if ( t1.getNumberOfExternalNodes() != 1 ) {
7557 t1.deleteSubtree( t1.getNode( "r" ), false );
7558 if ( t1.getNumberOfExternalNodes() != 0 ) {
7561 if ( !t1.isEmpty() ) {
7564 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7565 t2.deleteSubtree( t2.getNode( "A" ), false );
7566 t2.toNewHampshireX();
7567 if ( t2.getNumberOfExternalNodes() != 5 ) {
7570 t2.deleteSubtree( t2.getNode( "abc" ), false );
7571 t2.toNewHampshireX();
7572 if ( t2.getNumberOfExternalNodes() != 3 ) {
7575 t2.deleteSubtree( t2.getNode( "def" ), false );
7576 t2.toNewHampshireX();
7577 if ( t2.getNumberOfExternalNodes() != 1 ) {
7581 catch ( final Exception e ) {
7582 e.printStackTrace( System.out );
7588 private static boolean testSupportCount() {
7590 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7591 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7592 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7593 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7594 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7595 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7596 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7598 SupportCount.count( t0_1, phylogenies_1, true, false );
7599 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7600 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7601 + "(((((A,B),C),D),E),((F,G),X))"
7602 + "(((((A,Y),B),C),D),((F,G),E))"
7603 + "(((((A,B),C),D),E),(F,G))"
7604 + "(((((A,B),C),D),E),(F,G))"
7605 + "(((((A,B),C),D),E),(F,G))"
7606 + "(((((A,B),C),D),E),(F,G),Z)"
7607 + "(((((A,B),C),D),E),(F,G))"
7608 + "((((((A,B),C),D),E),F),G)"
7609 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7611 SupportCount.count( t0_2, phylogenies_2, true, false );
7612 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7613 while ( it.hasNext() ) {
7614 final PhylogenyNode n = it.next();
7615 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7619 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7620 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7621 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7622 SupportCount.count( t0_3, phylogenies_3, true, false );
7623 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7624 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7627 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7630 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7633 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7636 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7639 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7642 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7645 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7648 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7651 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7654 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7655 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7656 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7657 SupportCount.count( t0_4, phylogenies_4, true, false );
7658 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7659 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7662 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7665 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7668 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7671 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7674 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7677 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7680 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7683 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7686 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7689 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7690 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7691 double d = SupportCount.compare( b1, a, true, true, true );
7692 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7695 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7696 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7697 d = SupportCount.compare( b2, a, true, true, true );
7698 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7701 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7702 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7703 d = SupportCount.compare( b3, a, true, true, true );
7704 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7707 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7708 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7709 d = SupportCount.compare( b4, a, true, true, false );
7710 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7714 catch ( final Exception e ) {
7715 e.printStackTrace( System.out );
7721 private static boolean testSupportTransfer() {
7723 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7724 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)",
7725 new NHXParser() )[ 0 ];
7726 final Phylogeny p2 = factory
7727 .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 ];
7728 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7731 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7734 support_transfer.moveBranchLengthsToBootstrap( p1 );
7735 support_transfer.transferSupportValues( p1, p2 );
7736 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7739 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7742 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7745 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7748 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7751 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7754 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7757 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7761 catch ( final Exception e ) {
7762 e.printStackTrace( System.out );
7768 private static boolean testUniprotTaxonomySearch() {
7770 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7772 if ( results.size() != 1 ) {
7775 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7778 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7781 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7784 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7787 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7791 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7792 if ( results.size() != 1 ) {
7795 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7798 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7801 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7804 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7807 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7811 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7812 if ( results.size() != 1 ) {
7815 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7818 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7821 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7824 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7827 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7831 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7832 if ( results.size() != 1 ) {
7835 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7838 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7841 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7844 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7847 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7850 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7853 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7856 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7857 .equals( "Nematostella vectensis" ) ) {
7858 System.out.println( results.get( 0 ).getLineage() );
7862 catch ( final IOException e ) {
7863 System.out.println();
7864 System.out.println( "the following might be due to absence internet connection:" );
7865 e.printStackTrace( System.out );
7868 catch ( final Exception e ) {
7874 private static boolean testEmblEntryRetrieval() {
7875 //The format for GenBank Accession numbers are:
7876 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7877 //Protein: 3 letters + 5 numerals
7878 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7879 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7882 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7885 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7888 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7891 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7894 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7897 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7900 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7903 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7906 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7909 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7912 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7915 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7921 private static boolean testUniprotEntryRetrieval() {
7922 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7925 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7928 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7931 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7934 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7937 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7940 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7943 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7946 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7949 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7952 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7955 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7958 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7962 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7963 if ( !entry.getAccession().equals( "P12345" ) ) {
7966 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7969 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7972 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7975 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7979 catch ( final IOException e ) {
7980 System.out.println();
7981 System.out.println( "the following might be due to absence internet connection:" );
7982 e.printStackTrace( System.out );
7985 catch ( final Exception e ) {
7991 private static boolean testWabiTxSearch() {
7994 result = TxSearch.searchSimple( "nematostella" );
7995 result = TxSearch.getTxId( "nematostella" );
7996 if ( !result.equals( "45350" ) ) {
7999 result = TxSearch.getTxName( "45350" );
8000 if ( !result.equals( "Nematostella" ) ) {
8003 result = TxSearch.getTxId( "nematostella vectensis" );
8004 if ( !result.equals( "45351" ) ) {
8007 result = TxSearch.getTxName( "45351" );
8008 if ( !result.equals( "Nematostella vectensis" ) ) {
8011 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8012 if ( !result.equals( "536089" ) ) {
8015 result = TxSearch.getTxName( "536089" );
8016 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8019 final List<String> queries = new ArrayList<String>();
8020 queries.add( "Campylobacter coli" );
8021 queries.add( "Escherichia coli" );
8022 queries.add( "Arabidopsis" );
8023 queries.add( "Trichoplax" );
8024 queries.add( "Samanea saman" );
8025 queries.add( "Kluyveromyces marxianus" );
8026 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8027 queries.add( "Bornavirus parrot/PDD/2008" );
8028 final List<RANKS> ranks = new ArrayList<RANKS>();
8029 ranks.add( RANKS.SUPERKINGDOM );
8030 ranks.add( RANKS.KINGDOM );
8031 ranks.add( RANKS.FAMILY );
8032 ranks.add( RANKS.GENUS );
8033 ranks.add( RANKS.TRIBE );
8034 result = TxSearch.searchLineage( queries, ranks );
8035 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8036 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8038 catch ( final Exception e ) {
8039 System.out.println();
8040 System.out.println( "the following might be due to absence internet connection:" );
8041 e.printStackTrace( System.out );
8047 private static boolean testAminoAcidSequence() {
8049 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8050 if ( aa1.getLength() != 13 ) {
8053 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8056 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8059 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8062 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8063 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8066 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8067 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8070 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8071 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8075 catch ( final Exception e ) {
8076 e.printStackTrace();
8082 private static boolean testCreateBalancedPhylogeny() {
8084 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8085 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8088 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8091 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8092 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8095 if ( p1.getNumberOfExternalNodes() != 100 ) {
8099 catch ( final Exception e ) {
8100 e.printStackTrace();
8106 private static boolean testFastaParser() {
8108 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8111 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8114 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8115 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8118 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8121 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8124 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8127 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8130 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8134 catch ( final Exception e ) {
8135 e.printStackTrace();
8141 private static boolean testGeneralMsaParser() {
8143 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8144 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8145 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8146 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8147 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8148 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8149 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8150 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8151 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8154 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8157 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8160 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8163 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8166 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8169 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8172 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8175 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8178 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8181 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8184 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8187 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8188 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8191 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8194 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8197 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8198 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8201 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8204 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8207 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8208 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8211 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8214 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8218 catch ( final Exception e ) {
8219 e.printStackTrace();
8225 private static boolean testMafft( final String path ) {
8227 final List<String> opts = new ArrayList<String>();
8228 opts.add( "--maxiterate" );
8230 opts.add( "--localpair" );
8231 opts.add( "--quiet" );
8233 final MsaInferrer mafft = Mafft.createInstance( path );
8234 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8235 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8238 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8242 catch ( final Exception e ) {
8243 e.printStackTrace( System.out );
8249 private static boolean testNextNodeWithCollapsing() {
8251 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8253 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8254 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8255 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8256 t0.getNode( "cd" ).setCollapse( true );
8257 t0.getNode( "cde" ).setCollapse( true );
8258 n = t0.getFirstExternalNode();
8259 while ( n != null ) {
8261 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8263 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8266 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8269 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8272 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8275 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8278 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8282 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8283 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8284 t1.getNode( "ab" ).setCollapse( true );
8285 t1.getNode( "cd" ).setCollapse( true );
8286 t1.getNode( "cde" ).setCollapse( true );
8287 n = t1.getNode( "ab" );
8288 ext = new ArrayList<PhylogenyNode>();
8289 while ( n != null ) {
8291 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8293 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8296 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8299 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8302 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8305 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8311 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8312 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8313 t2.getNode( "ab" ).setCollapse( true );
8314 t2.getNode( "cd" ).setCollapse( true );
8315 t2.getNode( "cde" ).setCollapse( true );
8316 t2.getNode( "c" ).setCollapse( true );
8317 t2.getNode( "d" ).setCollapse( true );
8318 t2.getNode( "e" ).setCollapse( true );
8319 t2.getNode( "gh" ).setCollapse( true );
8320 n = t2.getNode( "ab" );
8321 ext = new ArrayList<PhylogenyNode>();
8322 while ( n != null ) {
8324 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8326 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8329 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8332 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8335 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8341 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8342 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8343 t3.getNode( "ab" ).setCollapse( true );
8344 t3.getNode( "cd" ).setCollapse( true );
8345 t3.getNode( "cde" ).setCollapse( true );
8346 t3.getNode( "c" ).setCollapse( true );
8347 t3.getNode( "d" ).setCollapse( true );
8348 t3.getNode( "e" ).setCollapse( true );
8349 t3.getNode( "gh" ).setCollapse( true );
8350 t3.getNode( "fgh" ).setCollapse( true );
8351 n = t3.getNode( "ab" );
8352 ext = new ArrayList<PhylogenyNode>();
8353 while ( n != null ) {
8355 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8357 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8360 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8363 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8369 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8370 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8371 t4.getNode( "ab" ).setCollapse( true );
8372 t4.getNode( "cd" ).setCollapse( true );
8373 t4.getNode( "cde" ).setCollapse( true );
8374 t4.getNode( "c" ).setCollapse( true );
8375 t4.getNode( "d" ).setCollapse( true );
8376 t4.getNode( "e" ).setCollapse( true );
8377 t4.getNode( "gh" ).setCollapse( true );
8378 t4.getNode( "fgh" ).setCollapse( true );
8379 t4.getNode( "abcdefgh" ).setCollapse( true );
8380 n = t4.getNode( "abcdefgh" );
8381 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8386 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8387 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8389 n = t5.getFirstExternalNode();
8390 while ( n != null ) {
8392 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8394 if ( ext.size() != 8 ) {
8397 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8400 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8403 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8406 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8409 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8412 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8415 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8418 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8423 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8424 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8426 t6.getNode( "ab" ).setCollapse( true );
8427 n = t6.getNode( "ab" );
8428 while ( n != null ) {
8430 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8432 if ( ext.size() != 7 ) {
8435 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8438 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8441 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8444 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8447 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8450 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8453 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8458 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8459 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8461 t7.getNode( "cd" ).setCollapse( true );
8462 n = t7.getNode( "a" );
8463 while ( n != null ) {
8465 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8467 if ( ext.size() != 7 ) {
8470 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8473 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8476 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8479 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8482 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8485 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8488 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8493 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8494 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8496 t8.getNode( "cd" ).setCollapse( true );
8497 t8.getNode( "c" ).setCollapse( true );
8498 t8.getNode( "d" ).setCollapse( true );
8499 n = t8.getNode( "a" );
8500 while ( n != null ) {
8502 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8504 if ( ext.size() != 7 ) {
8507 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8510 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8513 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8514 System.out.println( "2 fail" );
8517 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8520 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8523 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8526 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8531 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8532 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8534 t9.getNode( "gh" ).setCollapse( true );
8535 n = t9.getNode( "a" );
8536 while ( n != null ) {
8538 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8540 if ( ext.size() != 7 ) {
8543 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8546 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8549 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8552 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8555 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8558 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8561 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8566 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8567 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8569 t10.getNode( "gh" ).setCollapse( true );
8570 t10.getNode( "g" ).setCollapse( true );
8571 t10.getNode( "h" ).setCollapse( true );
8572 n = t10.getNode( "a" );
8573 while ( n != null ) {
8575 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8577 if ( ext.size() != 7 ) {
8580 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8583 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8586 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8589 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8592 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8595 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8598 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8603 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8604 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8606 t11.getNode( "gh" ).setCollapse( true );
8607 t11.getNode( "fgh" ).setCollapse( true );
8608 n = t11.getNode( "a" );
8609 while ( n != null ) {
8611 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8613 if ( ext.size() != 6 ) {
8616 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8619 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8622 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8625 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8628 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8631 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8636 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8637 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8639 t12.getNode( "gh" ).setCollapse( true );
8640 t12.getNode( "fgh" ).setCollapse( true );
8641 t12.getNode( "g" ).setCollapse( true );
8642 t12.getNode( "h" ).setCollapse( true );
8643 t12.getNode( "f" ).setCollapse( true );
8644 n = t12.getNode( "a" );
8645 while ( n != null ) {
8647 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8649 if ( ext.size() != 6 ) {
8652 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8655 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8658 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8661 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8664 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8667 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8672 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8673 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8675 t13.getNode( "ab" ).setCollapse( true );
8676 t13.getNode( "b" ).setCollapse( true );
8677 t13.getNode( "fgh" ).setCollapse( true );
8678 t13.getNode( "gh" ).setCollapse( true );
8679 n = t13.getNode( "ab" );
8680 while ( n != null ) {
8682 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8684 if ( ext.size() != 5 ) {
8687 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8690 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8693 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8696 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8699 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8704 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8705 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8707 t14.getNode( "ab" ).setCollapse( true );
8708 t14.getNode( "a" ).setCollapse( true );
8709 t14.getNode( "fgh" ).setCollapse( true );
8710 t14.getNode( "gh" ).setCollapse( true );
8711 n = t14.getNode( "ab" );
8712 while ( n != null ) {
8714 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8716 if ( ext.size() != 5 ) {
8719 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8722 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8725 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8728 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8731 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8736 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" );
8737 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8739 t15.getNode( "ab" ).setCollapse( true );
8740 t15.getNode( "a" ).setCollapse( true );
8741 t15.getNode( "fgh" ).setCollapse( true );
8742 t15.getNode( "gh" ).setCollapse( true );
8743 n = t15.getNode( "ab" );
8744 while ( n != null ) {
8746 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8748 if ( ext.size() != 6 ) {
8751 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8754 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8757 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8760 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8763 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8766 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8771 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" );
8772 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8774 t16.getNode( "ab" ).setCollapse( true );
8775 t16.getNode( "a" ).setCollapse( true );
8776 t16.getNode( "fgh" ).setCollapse( true );
8777 t16.getNode( "gh" ).setCollapse( true );
8778 t16.getNode( "cd" ).setCollapse( true );
8779 t16.getNode( "cde" ).setCollapse( true );
8780 t16.getNode( "d" ).setCollapse( true );
8781 t16.getNode( "x" ).setCollapse( true );
8782 n = t16.getNode( "ab" );
8783 while ( n != null ) {
8785 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8787 if ( ext.size() != 4 ) {
8790 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8793 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8796 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8799 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8803 catch ( final Exception e ) {
8804 e.printStackTrace( System.out );
8810 private static boolean testMsaQualityMethod() {
8812 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8813 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8814 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8815 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8816 final List<Sequence> l = new ArrayList<Sequence>();
8821 final Msa msa = BasicMsa.createInstance( l );
8822 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8825 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8828 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8831 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8835 catch ( final Exception e ) {
8836 e.printStackTrace( System.out );
8842 private static boolean testSequenceIdParsing() {
8844 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8845 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8846 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8848 System.out.println( "value =" + id.getValue() );
8849 System.out.println( "provider=" + id.getProvider() );
8854 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8855 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8856 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8858 System.out.println( "value =" + id.getValue() );
8859 System.out.println( "provider=" + id.getProvider() );
8864 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8865 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8866 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8868 System.out.println( "value =" + id.getValue() );
8869 System.out.println( "provider=" + id.getProvider() );
8874 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8875 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8876 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8878 System.out.println( "value =" + id.getValue() );
8879 System.out.println( "provider=" + id.getProvider() );
8884 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8885 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8886 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8888 System.out.println( "value =" + id.getValue() );
8889 System.out.println( "provider=" + id.getProvider() );
8894 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8895 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8896 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8898 System.out.println( "value =" + id.getValue() );
8899 System.out.println( "provider=" + id.getProvider() );
8904 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8905 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8906 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8908 System.out.println( "value =" + id.getValue() );
8909 System.out.println( "provider=" + id.getProvider() );
8914 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8915 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8916 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8918 System.out.println( "value =" + id.getValue() );
8919 System.out.println( "provider=" + id.getProvider() );
8924 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8925 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8926 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8928 System.out.println( "value =" + id.getValue() );
8929 System.out.println( "provider=" + id.getProvider() );
8934 id = SequenceIdParser.parse( "P4A123" );
8935 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8936 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8938 System.out.println( "value =" + id.getValue() );
8939 System.out.println( "provider=" + id.getProvider() );
8944 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
8945 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8946 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8948 System.out.println( "value =" + id.getValue() );
8949 System.out.println( "provider=" + id.getProvider() );
8954 id = SequenceIdParser.parse( "XP_12345" );
8956 System.out.println( "value =" + id.getValue() );
8957 System.out.println( "provider=" + id.getProvider() );
8960 // lcl_91970_unknown_
8962 catch ( final Exception e ) {
8963 e.printStackTrace( System.out );