2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.datastructures.IntMatrix;
42 import org.forester.development.DevelopmentTools;
43 import org.forester.evoinference.TestPhylogenyReconstruction;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
45 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
46 import org.forester.go.TestGo;
47 import org.forester.io.parsers.FastaParser;
48 import org.forester.io.parsers.GeneralMsaParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser;
50 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
51 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
52 import org.forester.io.parsers.nexus.NexusCharactersParser;
53 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
54 import org.forester.io.parsers.nhx.NHXParser;
55 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
56 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
57 import org.forester.io.parsers.tol.TolParser;
58 import org.forester.io.parsers.util.ParserUtils;
59 import org.forester.io.writers.PhylogenyWriter;
60 import org.forester.msa.BasicMsa;
61 import org.forester.msa.Mafft;
62 import org.forester.msa.Msa;
63 import org.forester.msa.MsaInferrer;
64 import org.forester.msa.MsaMethods;
65 import org.forester.pccx.TestPccx;
66 import org.forester.phylogeny.Phylogeny;
67 import org.forester.phylogeny.PhylogenyBranch;
68 import org.forester.phylogeny.PhylogenyMethods;
69 import org.forester.phylogeny.PhylogenyNode;
70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
71 import org.forester.phylogeny.data.BinaryCharacters;
72 import org.forester.phylogeny.data.BranchWidth;
73 import org.forester.phylogeny.data.Confidence;
74 import org.forester.phylogeny.data.Distribution;
75 import org.forester.phylogeny.data.DomainArchitecture;
76 import org.forester.phylogeny.data.Event;
77 import org.forester.phylogeny.data.Identifier;
78 import org.forester.phylogeny.data.PhylogenyData;
79 import org.forester.phylogeny.data.PhylogenyDataUtil;
80 import org.forester.phylogeny.data.Polygon;
81 import org.forester.phylogeny.data.PropertiesMap;
82 import org.forester.phylogeny.data.Property;
83 import org.forester.phylogeny.data.Property.AppliesTo;
84 import org.forester.phylogeny.data.ProteinDomain;
85 import org.forester.phylogeny.data.Taxonomy;
86 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
87 import org.forester.phylogeny.factories.PhylogenyFactory;
88 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
89 import org.forester.protein.Protein;
90 import org.forester.sdi.GSDI;
91 import org.forester.sdi.RIO;
92 import org.forester.sdi.SDI;
93 import org.forester.sdi.SDIR;
94 import org.forester.sdi.SDIse;
95 import org.forester.sdi.TestGSDI;
96 import org.forester.sequence.BasicSequence;
97 import org.forester.sequence.Sequence;
98 import org.forester.surfacing.TestSurfacing;
99 import org.forester.tools.ConfidenceAssessor;
100 import org.forester.tools.SupportCount;
101 import org.forester.tools.TreeSplitMatrix;
102 import org.forester.util.AsciiHistogram;
103 import org.forester.util.BasicDescriptiveStatistics;
104 import org.forester.util.BasicTable;
105 import org.forester.util.BasicTableParser;
106 import org.forester.util.DescriptiveStatistics;
107 import org.forester.util.ForesterConstants;
108 import org.forester.util.ForesterUtil;
109 import org.forester.util.GeneralTable;
110 import org.forester.util.SequenceIdParser;
111 import org.forester.ws.seqdb.SequenceDatabaseEntry;
112 import org.forester.ws.seqdb.SequenceDbWsTools;
113 import org.forester.ws.seqdb.UniProtTaxonomy;
114 import org.forester.ws.wabi.TxSearch;
115 import org.forester.ws.wabi.TxSearch.RANKS;
116 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
117 import org.forester.ws.wabi.TxSearch.TAX_RANK;
119 @SuppressWarnings( "unused")
120 public final class Test {
122 private final static double ZERO_DIFF = 1.0E-9;
123 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "test_data"
125 + ForesterUtil.getFileSeparator();
126 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
127 + ForesterUtil.getFileSeparator() + "resources"
128 + ForesterUtil.getFileSeparator();
129 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
130 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
133 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
134 + ForesterConstants.PHYLO_XML_VERSION + "/"
135 + ForesterConstants.PHYLO_XML_XSD;
137 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
138 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
142 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
143 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
144 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
147 public static boolean isEqual( final double a, final double b ) {
148 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
151 public static void main( final String[] args ) {
152 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
153 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
155 Locale.setDefault( Locale.US );
156 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
159 System.out.print( "[Test if directory with files for testing exists/is readable: " );
160 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
161 System.out.println( "OK.]" );
164 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
165 System.out.println( "Testing aborted." );
168 System.out.print( "[Test if resources directory exists/is readable: " );
169 if ( testDir( PATH_TO_RESOURCES ) ) {
170 System.out.println( "OK.]" );
173 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
174 System.out.println( "Testing aborted." );
177 final long start_time = new Date().getTime();
178 System.out.print( "Sequence id parsing: " );
179 if ( testSequenceIdParsing() ) {
180 System.out.println( "OK." );
184 System.out.println( "failed." );
187 System.out.print( "Hmmscan output parser: " );
188 if ( testHmmscanOutputParser() ) {
189 System.out.println( "OK." );
193 System.out.println( "failed." );
196 System.out.print( "Basic node methods: " );
197 if ( Test.testBasicNodeMethods() ) {
198 System.out.println( "OK." );
202 System.out.println( "failed." );
205 System.out.print( "Taxonomy extraction: " );
206 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
207 System.out.println( "OK." );
211 System.out.println( "failed." );
214 System.out.print( "Basic node construction and parsing of NHX (node level): " );
215 if ( Test.testNHXNodeParsing() ) {
216 System.out.println( "OK." );
220 System.out.println( "failed." );
223 System.out.print( "NH parsing: " );
224 if ( Test.testNHParsing() ) {
225 System.out.println( "OK." );
229 System.out.println( "failed." );
232 System.out.print( "Conversion to NHX (node level): " );
233 if ( Test.testNHXconversion() ) {
234 System.out.println( "OK." );
238 System.out.println( "failed." );
241 System.out.print( "NHX parsing: " );
242 if ( Test.testNHXParsing() ) {
243 System.out.println( "OK." );
247 System.out.println( "failed." );
250 System.out.print( "NHX parsing with quotes: " );
251 if ( Test.testNHXParsingQuotes() ) {
252 System.out.println( "OK." );
256 System.out.println( "failed." );
259 System.out.print( "NHX parsing (MrBayes): " );
260 if ( Test.testNHXParsingMB() ) {
261 System.out.println( "OK." );
265 System.out.println( "failed." );
268 System.out.print( "Nexus characters parsing: " );
269 if ( Test.testNexusCharactersParsing() ) {
270 System.out.println( "OK." );
274 System.out.println( "failed." );
277 System.out.print( "Nexus tree parsing: " );
278 if ( Test.testNexusTreeParsing() ) {
279 System.out.println( "OK." );
283 System.out.println( "failed." );
286 System.out.print( "Nexus tree parsing (translating): " );
287 if ( Test.testNexusTreeParsingTranslating() ) {
288 System.out.println( "OK." );
292 System.out.println( "failed." );
295 System.out.print( "Nexus matrix parsing: " );
296 if ( Test.testNexusMatrixParsing() ) {
297 System.out.println( "OK." );
301 System.out.println( "failed." );
304 System.out.print( "Basic phyloXML parsing: " );
305 if ( Test.testBasicPhyloXMLparsing() ) {
306 System.out.println( "OK." );
310 System.out.println( "failed." );
313 System.out.print( "Basic phyloXML parsing (validating against schema): " );
314 if ( testBasicPhyloXMLparsingValidating() ) {
315 System.out.println( "OK." );
319 System.out.println( "failed." );
322 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
323 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
324 System.out.println( "OK." );
328 System.out.println( "failed." );
331 System.out.print( "phyloXML Distribution Element: " );
332 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
333 System.out.println( "OK." );
337 System.out.println( "failed." );
340 System.out.print( "Tol XML parsing: " );
341 if ( Test.testBasicTolXMLparsing() ) {
342 System.out.println( "OK." );
346 System.out.println( "failed." );
349 System.out.print( "Copying of node data: " );
350 if ( Test.testCopyOfNodeData() ) {
351 System.out.println( "OK." );
355 System.out.println( "failed." );
358 System.out.print( "Basic tree methods: " );
359 if ( Test.testBasicTreeMethods() ) {
360 System.out.println( "OK." );
364 System.out.println( "failed." );
367 System.out.print( "Postorder Iterator: " );
368 if ( Test.testPostOrderIterator() ) {
369 System.out.println( "OK." );
373 System.out.println( "failed." );
376 System.out.print( "Preorder Iterator: " );
377 if ( Test.testPreOrderIterator() ) {
378 System.out.println( "OK." );
382 System.out.println( "failed." );
385 System.out.print( "Levelorder Iterator: " );
386 if ( Test.testLevelOrderIterator() ) {
387 System.out.println( "OK." );
391 System.out.println( "failed." );
394 System.out.print( "Re-id methods: " );
395 if ( Test.testReIdMethods() ) {
396 System.out.println( "OK." );
400 System.out.println( "failed." );
403 System.out.print( "Methods on last external nodes: " );
404 if ( Test.testLastExternalNodeMethods() ) {
405 System.out.println( "OK." );
409 System.out.println( "failed." );
412 System.out.print( "Methods on external nodes: " );
413 if ( Test.testExternalNodeRelatedMethods() ) {
414 System.out.println( "OK." );
418 System.out.println( "failed." );
421 System.out.print( "Deletion of external nodes: " );
422 if ( Test.testDeletionOfExternalNodes() ) {
423 System.out.println( "OK." );
427 System.out.println( "failed." );
430 System.out.print( "Subtree deletion: " );
431 if ( Test.testSubtreeDeletion() ) {
432 System.out.println( "OK." );
436 System.out.println( "failed." );
439 System.out.print( "Phylogeny branch: " );
440 if ( Test.testPhylogenyBranch() ) {
441 System.out.println( "OK." );
445 System.out.println( "failed." );
448 System.out.print( "Rerooting: " );
449 if ( Test.testRerooting() ) {
450 System.out.println( "OK." );
454 System.out.println( "failed." );
457 System.out.print( "Mipoint rooting: " );
458 if ( Test.testMidpointrooting() ) {
459 System.out.println( "OK." );
463 System.out.println( "failed." );
466 System.out.print( "Support count: " );
467 if ( Test.testSupportCount() ) {
468 System.out.println( "OK." );
472 System.out.println( "failed." );
475 System.out.print( "Support transfer: " );
476 if ( Test.testSupportTransfer() ) {
477 System.out.println( "OK." );
481 System.out.println( "failed." );
484 System.out.print( "Finding of LCA: " );
485 if ( Test.testGetLCA() ) {
486 System.out.println( "OK." );
490 System.out.println( "failed." );
493 System.out.print( "Finding of LCA 2: " );
494 if ( Test.testGetLCA2() ) {
495 System.out.println( "OK." );
499 System.out.println( "failed." );
502 System.out.print( "Calculation of distance between nodes: " );
503 if ( Test.testGetDistance() ) {
504 System.out.println( "OK." );
508 System.out.println( "failed." );
511 System.out.print( "SDIse: " );
512 if ( Test.testSDIse() ) {
513 System.out.println( "OK." );
517 System.out.println( "failed." );
520 System.out.print( "SDIunrooted: " );
521 if ( Test.testSDIunrooted() ) {
522 System.out.println( "OK." );
526 System.out.println( "failed." );
529 System.out.print( "GSDI: " );
530 if ( TestGSDI.test() ) {
531 System.out.println( "OK." );
535 System.out.println( "failed." );
538 System.out.print( "Ortholog table: " );
539 if ( Test.testOrthologTable() ) {
540 System.out.println( "OK." );
544 System.out.println( "failed." );
547 System.out.print( "Descriptive statistics: " );
548 if ( Test.testDescriptiveStatistics() ) {
549 System.out.println( "OK." );
553 System.out.println( "failed." );
556 System.out.print( "Data objects and methods: " );
557 if ( Test.testDataObjects() ) {
558 System.out.println( "OK." );
562 System.out.println( "failed." );
565 System.out.print( "Properties map: " );
566 if ( Test.testPropertiesMap() ) {
567 System.out.println( "OK." );
571 System.out.println( "failed." );
574 System.out.print( "Phylogeny reconstruction:" );
575 System.out.println();
576 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
577 System.out.println( "OK." );
581 System.out.println( "failed." );
584 System.out.print( "Analysis of domain architectures: " );
585 System.out.println();
586 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
587 System.out.println( "OK." );
591 System.out.println( "failed." );
594 System.out.print( "GO: " );
595 System.out.println();
596 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
597 System.out.println( "OK." );
601 System.out.println( "failed." );
604 System.out.print( "Modeling tools: " );
605 if ( TestPccx.test() ) {
606 System.out.println( "OK." );
610 System.out.println( "failed." );
613 System.out.print( "Split Matrix strict: " );
614 if ( Test.testSplitStrict() ) {
615 System.out.println( "OK." );
619 System.out.println( "failed." );
622 System.out.print( "Split Matrix: " );
623 if ( Test.testSplit() ) {
624 System.out.println( "OK." );
628 System.out.println( "failed." );
631 System.out.print( "Confidence Assessor: " );
632 if ( Test.testConfidenceAssessor() ) {
633 System.out.println( "OK." );
637 System.out.println( "failed." );
640 System.out.print( "Basic table: " );
641 if ( Test.testBasicTable() ) {
642 System.out.println( "OK." );
646 System.out.println( "failed." );
649 System.out.print( "General table: " );
650 if ( Test.testGeneralTable() ) {
651 System.out.println( "OK." );
655 System.out.println( "failed." );
658 System.out.print( "Amino acid sequence: " );
659 if ( Test.testAminoAcidSequence() ) {
660 System.out.println( "OK." );
664 System.out.println( "failed." );
667 System.out.print( "General MSA parser: " );
668 if ( Test.testGeneralMsaParser() ) {
669 System.out.println( "OK." );
673 System.out.println( "failed." );
676 System.out.print( "Fasta parser for msa: " );
677 if ( Test.testFastaParser() ) {
678 System.out.println( "OK." );
682 System.out.println( "failed." );
685 System.out.print( "Creation of balanced phylogeny: " );
686 if ( Test.testCreateBalancedPhylogeny() ) {
687 System.out.println( "OK." );
691 System.out.println( "failed." );
694 System.out.print( "EMBL Entry Retrieval: " );
695 if ( Test.testEmblEntryRetrieval() ) {
696 System.out.println( "OK." );
700 System.out.println( "failed." );
703 System.out.print( "Uniprot Entry Retrieval: " );
704 if ( Test.testUniprotEntryRetrieval() ) {
705 System.out.println( "OK." );
709 System.out.println( "failed." );
712 System.out.print( "Uniprot Taxonomy Search: " );
713 if ( Test.testUniprotTaxonomySearch() ) {
714 System.out.println( "OK." );
718 System.out.println( "failed." );
723 final String os = ForesterUtil.OS_NAME.toLowerCase();
724 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
725 path = "/usr/local/bin/mafft";
727 else if ( os.indexOf( "win" ) >= 0 ) {
728 path = "C:\\Program Files\\mafft-win\\mafft.bat";
731 path = "/home/czmasek/bin/mafft";
733 if ( !MsaInferrer.isInstalled( path ) ) {
736 if ( !MsaInferrer.isInstalled( path ) ) {
737 path = "/usr/local/bin/mafft";
739 if ( MsaInferrer.isInstalled( path ) ) {
740 System.out.print( "MAFFT (external program): " );
741 if ( Test.testMafft( path ) ) {
742 System.out.println( "OK." );
746 System.out.println( "failed [will not count towards failed tests]" );
750 System.out.print( "Next nodes with collapsed: " );
751 if ( Test.testNextNodeWithCollapsing() ) {
752 System.out.println( "OK." );
756 System.out.println( "failed." );
759 System.out.print( "Simple MSA quality: " );
760 if ( Test.testMsaQualityMethod() ) {
761 System.out.println( "OK." );
765 System.out.println( "failed." );
768 System.out.println();
769 final Runtime rt = java.lang.Runtime.getRuntime();
770 final long free_memory = rt.freeMemory() / 1000000;
771 final long total_memory = rt.totalMemory() / 1000000;
772 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
773 + free_memory + "MB, total memory: " + total_memory + "MB)" );
774 System.out.println();
775 System.out.println( "Successful tests: " + succeeded );
776 System.out.println( "Failed tests: " + failed );
777 System.out.println();
779 System.out.println( "OK." );
782 System.out.println( "Not OK." );
786 private static boolean testExtractTaxonomyCodeFromNodeName() {
788 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
791 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
794 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
797 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
798 .equals( "MOUSE" ) ) {
801 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
802 .equals( "MOUSE" ) ) {
805 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
806 .equals( "MOUSE" ) ) {
809 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
812 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
815 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
819 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
823 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
827 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
830 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
833 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
836 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
840 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
841 .equals( "MOUSE" ) ) {
844 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
845 .equals( "MOUSE" ) ) {
849 catch ( final Exception e ) {
850 e.printStackTrace( System.out );
856 private static boolean testBasicNodeMethods() {
858 if ( PhylogenyNode.getNodeCount() != 0 ) {
861 final PhylogenyNode n1 = new PhylogenyNode();
862 final PhylogenyNode n2 = PhylogenyNode
863 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
864 final PhylogenyNode n3 = PhylogenyNode
865 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
866 final PhylogenyNode n4 = PhylogenyNode
867 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
868 if ( n1.isHasAssignedEvent() ) {
871 if ( PhylogenyNode.getNodeCount() != 4 ) {
874 if ( n3.getIndicator() != 0 ) {
877 if ( n3.getNumberOfExternalNodes() != 1 ) {
880 if ( !n3.isExternal() ) {
883 if ( !n3.isRoot() ) {
886 if ( !n4.getName().equals( "n4" ) ) {
890 catch ( final Exception e ) {
891 e.printStackTrace( System.out );
897 private static boolean testBasicPhyloXMLparsing() {
899 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
900 final PhyloXmlParser xml_parser = new PhyloXmlParser();
901 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
903 if ( xml_parser.getErrorCount() > 0 ) {
904 System.out.println( xml_parser.getErrorMessages().toString() );
907 if ( phylogenies_0.length != 4 ) {
910 final Phylogeny t1 = phylogenies_0[ 0 ];
911 final Phylogeny t2 = phylogenies_0[ 1 ];
912 final Phylogeny t3 = phylogenies_0[ 2 ];
913 final Phylogeny t4 = phylogenies_0[ 3 ];
914 if ( t1.getNumberOfExternalNodes() != 1 ) {
917 if ( !t1.isRooted() ) {
920 if ( t1.isRerootable() ) {
923 if ( !t1.getType().equals( "gene_tree" ) ) {
926 if ( t2.getNumberOfExternalNodes() != 2 ) {
929 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
932 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
935 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
938 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
941 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
944 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
947 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
948 .startsWith( "actgtgggggt" ) ) {
951 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
952 .startsWith( "ctgtgatgcat" ) ) {
955 if ( t3.getNumberOfExternalNodes() != 4 ) {
958 if ( !t1.getName().equals( "t1" ) ) {
961 if ( !t2.getName().equals( "t2" ) ) {
964 if ( !t3.getName().equals( "t3" ) ) {
967 if ( !t4.getName().equals( "t4" ) ) {
970 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
973 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
976 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
979 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
980 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
983 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
986 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
989 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
992 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
993 .equals( "apoptosis" ) ) {
996 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
997 .equals( "GO:0006915" ) ) {
1000 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1001 .equals( "UniProtKB" ) ) {
1004 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1005 .equals( "experimental" ) ) {
1008 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1009 .equals( "function" ) ) {
1012 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1013 .getValue() != 1 ) {
1016 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1017 .getType().equals( "ml" ) ) {
1020 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1021 .equals( "apoptosis" ) ) {
1024 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1025 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1028 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1029 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1032 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1033 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1036 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1037 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1040 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1041 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1044 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1045 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1048 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1049 .equals( "GO:0005829" ) ) {
1052 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1053 .equals( "intracellular organelle" ) ) {
1056 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1059 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1060 .equals( "UniProt link" ) ) ) {
1063 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1067 catch ( final Exception e ) {
1068 e.printStackTrace( System.out );
1074 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1076 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1077 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1078 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1079 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1082 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1084 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1086 if ( xml_parser.getErrorCount() > 0 ) {
1087 System.out.println( xml_parser.getErrorMessages().toString() );
1090 if ( phylogenies_0.length != 4 ) {
1093 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1094 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1095 if ( phylogenies_t1.length != 1 ) {
1098 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1099 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1102 if ( !t1_rt.isRooted() ) {
1105 if ( t1_rt.isRerootable() ) {
1108 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1111 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1112 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1113 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1114 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1117 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1120 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1123 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1126 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1127 .startsWith( "actgtgggggt" ) ) {
1130 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1131 .startsWith( "ctgtgatgcat" ) ) {
1134 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1135 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1136 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1137 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1138 if ( phylogenies_1.length != 1 ) {
1141 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1142 if ( !t3_rt.getName().equals( "t3" ) ) {
1145 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1148 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1151 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1154 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1157 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1158 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1161 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1164 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1167 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1168 .equals( "UniProtKB" ) ) {
1171 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1172 .equals( "apoptosis" ) ) {
1175 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1176 .equals( "GO:0006915" ) ) {
1179 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1180 .equals( "UniProtKB" ) ) {
1183 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1184 .equals( "experimental" ) ) {
1187 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1188 .equals( "function" ) ) {
1191 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1192 .getValue() != 1 ) {
1195 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1196 .getType().equals( "ml" ) ) {
1199 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1200 .equals( "apoptosis" ) ) {
1203 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1204 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1207 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1208 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1211 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1212 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1215 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1216 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1219 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1220 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1223 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1224 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1228 .equals( "GO:0005829" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1232 .equals( "intracellular organelle" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1238 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1239 .equals( "UniProt link" ) ) ) {
1242 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1249 .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
1252 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1255 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1258 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1261 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1264 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1265 .equals( "ncbi" ) ) {
1268 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1271 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1272 .getName().equals( "B" ) ) {
1275 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1276 .getFrom() != 21 ) {
1279 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1282 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1283 .getLength() != 24 ) {
1286 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1287 .getConfidence() != 2144 ) {
1290 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1291 .equals( "pfam" ) ) {
1294 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1297 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1300 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1303 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1306 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1307 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1310 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1313 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1316 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1319 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1322 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1325 if ( taxbb.getSynonyms().size() != 2 ) {
1328 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1331 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1334 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1337 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1340 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1343 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1344 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1348 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1351 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1354 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1357 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1360 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1363 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1366 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1370 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1373 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1374 .equalsIgnoreCase( "435" ) ) {
1377 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1380 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1381 .equalsIgnoreCase( "443.7" ) ) {
1384 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1387 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1390 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1391 .equalsIgnoreCase( "433" ) ) {
1395 catch ( final Exception e ) {
1396 e.printStackTrace( System.out );
1402 private static boolean testBasicPhyloXMLparsingValidating() {
1404 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1405 PhyloXmlParser xml_parser = null;
1407 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1409 catch ( final Exception e ) {
1410 // Do nothing -- means were not running from jar.
1412 if ( xml_parser == null ) {
1413 xml_parser = new PhyloXmlParser();
1414 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1415 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1418 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1421 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1423 if ( xml_parser.getErrorCount() > 0 ) {
1424 System.out.println( xml_parser.getErrorMessages().toString() );
1427 if ( phylogenies_0.length != 4 ) {
1430 final Phylogeny t1 = phylogenies_0[ 0 ];
1431 final Phylogeny t2 = phylogenies_0[ 1 ];
1432 final Phylogeny t3 = phylogenies_0[ 2 ];
1433 final Phylogeny t4 = phylogenies_0[ 3 ];
1434 if ( !t1.getName().equals( "t1" ) ) {
1437 if ( !t2.getName().equals( "t2" ) ) {
1440 if ( !t3.getName().equals( "t3" ) ) {
1443 if ( !t4.getName().equals( "t4" ) ) {
1446 if ( t1.getNumberOfExternalNodes() != 1 ) {
1449 if ( t2.getNumberOfExternalNodes() != 2 ) {
1452 if ( t3.getNumberOfExternalNodes() != 4 ) {
1455 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1456 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1457 if ( xml_parser.getErrorCount() > 0 ) {
1458 System.out.println( "errors:" );
1459 System.out.println( xml_parser.getErrorMessages().toString() );
1462 if ( phylogenies_1.length != 4 ) {
1465 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1467 if ( xml_parser.getErrorCount() > 0 ) {
1468 System.out.println( "errors:" );
1469 System.out.println( xml_parser.getErrorMessages().toString() );
1472 if ( phylogenies_2.length != 1 ) {
1475 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1478 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1480 if ( xml_parser.getErrorCount() > 0 ) {
1481 System.out.println( xml_parser.getErrorMessages().toString() );
1484 if ( phylogenies_3.length != 2 ) {
1487 final Phylogeny a = phylogenies_3[ 0 ];
1488 if ( !a.getName().equals( "tree 4" ) ) {
1491 if ( a.getNumberOfExternalNodes() != 3 ) {
1494 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1497 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1500 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1502 if ( xml_parser.getErrorCount() > 0 ) {
1503 System.out.println( xml_parser.getErrorMessages().toString() );
1506 if ( phylogenies_4.length != 1 ) {
1509 final Phylogeny s = phylogenies_4[ 0 ];
1510 if ( s.getNumberOfExternalNodes() != 6 ) {
1513 s.getNode( "first" );
1515 s.getNode( "\"<a'b&c'd\">\"" );
1516 s.getNode( "'''\"" );
1517 s.getNode( "\"\"\"" );
1518 s.getNode( "dick & doof" );
1520 catch ( final Exception e ) {
1521 e.printStackTrace( System.out );
1527 private static boolean testBasicTable() {
1529 final BasicTable<String> t0 = new BasicTable<String>();
1530 if ( t0.getNumberOfColumns() != 0 ) {
1533 if ( t0.getNumberOfRows() != 0 ) {
1536 t0.setValue( 3, 2, "23" );
1537 t0.setValue( 10, 1, "error" );
1538 t0.setValue( 10, 1, "110" );
1539 t0.setValue( 9, 1, "19" );
1540 t0.setValue( 1, 10, "101" );
1541 t0.setValue( 10, 10, "1010" );
1542 t0.setValue( 100, 10, "10100" );
1543 t0.setValue( 0, 0, "00" );
1544 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1547 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1550 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1553 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1556 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1559 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1562 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1565 if ( t0.getNumberOfColumns() != 101 ) {
1568 if ( t0.getNumberOfRows() != 11 ) {
1571 if ( t0.getValueAsString( 49, 4 ) != null ) {
1574 final String l = ForesterUtil.getLineSeparator();
1575 final StringBuffer source = new StringBuffer();
1576 source.append( "" + l );
1577 source.append( "# 1 1 1 1 1 1 1 1" + l );
1578 source.append( " 00 01 02 03" + l );
1579 source.append( " 10 11 12 13 " + l );
1580 source.append( "20 21 22 23 " + l );
1581 source.append( " 30 31 32 33" + l );
1582 source.append( "40 41 42 43" + l );
1583 source.append( " # 1 1 1 1 1 " + l );
1584 source.append( "50 51 52 53 54" + l );
1585 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1586 if ( t1.getNumberOfColumns() != 5 ) {
1589 if ( t1.getNumberOfRows() != 6 ) {
1592 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1595 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1598 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1601 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1604 final StringBuffer source1 = new StringBuffer();
1605 source1.append( "" + l );
1606 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1607 source1.append( " 00; 01 ;02;03" + l );
1608 source1.append( " 10; 11; 12; 13 " + l );
1609 source1.append( "20; 21; 22; 23 " + l );
1610 source1.append( " 30; 31; 32; 33" + l );
1611 source1.append( "40;41;42;43" + l );
1612 source1.append( " # 1 1 1 1 1 " + l );
1613 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1614 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1615 if ( t2.getNumberOfColumns() != 5 ) {
1618 if ( t2.getNumberOfRows() != 6 ) {
1621 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1624 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1627 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1630 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1633 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1636 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1639 final StringBuffer source2 = new StringBuffer();
1640 source2.append( "" + l );
1641 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1642 source2.append( " 00; 01 ;02;03" + l );
1643 source2.append( " 10; 11; 12; 13 " + l );
1644 source2.append( "20; 21; 22; 23 " + l );
1645 source2.append( " " + l );
1646 source2.append( " 30; 31; 32; 33" + l );
1647 source2.append( "40;41;42;43" + l );
1648 source2.append( " comment: 1 1 1 1 1 " + l );
1649 source2.append( ";;;50 ; 52; 53;;54 " + l );
1650 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1656 if ( tl.size() != 2 ) {
1659 final BasicTable<String> t3 = tl.get( 0 );
1660 final BasicTable<String> t4 = tl.get( 1 );
1661 if ( t3.getNumberOfColumns() != 4 ) {
1664 if ( t3.getNumberOfRows() != 3 ) {
1667 if ( t4.getNumberOfColumns() != 4 ) {
1670 if ( t4.getNumberOfRows() != 3 ) {
1673 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1676 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1680 catch ( final Exception e ) {
1681 e.printStackTrace( System.out );
1687 private static boolean testBasicTolXMLparsing() {
1689 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1690 final TolParser parser = new TolParser();
1691 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1692 if ( parser.getErrorCount() > 0 ) {
1693 System.out.println( parser.getErrorMessages().toString() );
1696 if ( phylogenies_0.length != 1 ) {
1699 final Phylogeny t1 = phylogenies_0[ 0 ];
1700 if ( t1.getNumberOfExternalNodes() != 5 ) {
1703 if ( !t1.isRooted() ) {
1706 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1709 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1712 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1715 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1718 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1719 if ( parser.getErrorCount() > 0 ) {
1720 System.out.println( parser.getErrorMessages().toString() );
1723 if ( phylogenies_1.length != 1 ) {
1726 final Phylogeny t2 = phylogenies_1[ 0 ];
1727 if ( t2.getNumberOfExternalNodes() != 664 ) {
1730 if ( !t2.isRooted() ) {
1733 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1736 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1739 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1742 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1745 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1748 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1749 .equals( "Aquifex" ) ) {
1752 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1753 if ( parser.getErrorCount() > 0 ) {
1754 System.out.println( parser.getErrorMessages().toString() );
1757 if ( phylogenies_2.length != 1 ) {
1760 final Phylogeny t3 = phylogenies_2[ 0 ];
1761 if ( t3.getNumberOfExternalNodes() != 184 ) {
1764 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1767 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1770 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1773 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1774 if ( parser.getErrorCount() > 0 ) {
1775 System.out.println( parser.getErrorMessages().toString() );
1778 if ( phylogenies_3.length != 1 ) {
1781 final Phylogeny t4 = phylogenies_3[ 0 ];
1782 if ( t4.getNumberOfExternalNodes() != 1 ) {
1785 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1788 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1791 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1794 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1795 if ( parser.getErrorCount() > 0 ) {
1796 System.out.println( parser.getErrorMessages().toString() );
1799 if ( phylogenies_4.length != 1 ) {
1802 final Phylogeny t5 = phylogenies_4[ 0 ];
1803 if ( t5.getNumberOfExternalNodes() != 13 ) {
1806 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1809 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1812 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1816 catch ( final Exception e ) {
1817 e.printStackTrace( System.out );
1823 private static boolean testBasicTreeMethods() {
1825 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1826 final Phylogeny t1 = factory.create();
1827 if ( !t1.isEmpty() ) {
1830 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1831 if ( t2.getNumberOfExternalNodes() != 4 ) {
1834 if ( t2.getHeight() != 8.5 ) {
1837 if ( !t2.isCompletelyBinary() ) {
1840 if ( t2.isEmpty() ) {
1843 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1844 if ( t3.getNumberOfExternalNodes() != 5 ) {
1847 if ( t3.getHeight() != 11 ) {
1850 if ( t3.isCompletelyBinary() ) {
1853 final PhylogenyNode n = t3.getNode( "ABC" );
1854 final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
1855 if ( t4.getNumberOfExternalNodes() != 9 ) {
1858 if ( t4.getHeight() != 11 ) {
1861 if ( t4.isCompletelyBinary() ) {
1864 final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1865 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1866 if ( t5.getNumberOfExternalNodes() != 8 ) {
1869 if ( t5.getHeight() != 15 ) {
1872 final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1873 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1874 if ( t6.getHeight() != 15 ) {
1877 final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
1878 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1879 if ( t7.getHeight() != 15 ) {
1882 final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
1883 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1884 if ( t8.getNumberOfExternalNodes() != 10 ) {
1887 if ( t8.getHeight() != 15 ) {
1890 final char[] a9 = new char[] {};
1891 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1892 if ( t9.getHeight() != 0 ) {
1895 final char[] a10 = new char[] { 'a', ':', '6' };
1896 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1897 if ( t10.getHeight() != 6 ) {
1901 catch ( final Exception e ) {
1902 e.printStackTrace( System.out );
1908 private static boolean testConfidenceAssessor() {
1910 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1911 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1912 final Phylogeny[] ev0 = factory
1913 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1915 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1916 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1919 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1922 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1923 final Phylogeny[] ev1 = factory
1924 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1926 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1927 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1930 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1933 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1934 final Phylogeny[] ev_b = factory
1935 .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
1937 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1938 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1941 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1945 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1946 final Phylogeny[] ev1x = factory
1947 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1949 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1950 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1953 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1956 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1957 final Phylogeny[] ev_bx = factory
1958 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
1960 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1961 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1964 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1968 final Phylogeny[] t2 = factory
1969 .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
1971 final Phylogeny[] ev2 = factory
1972 .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);",
1974 for( final Phylogeny target : t2 ) {
1975 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
1978 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
1979 new NHXParser() )[ 0 ];
1980 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
1981 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
1982 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1985 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
1988 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1992 catch ( final Exception e ) {
1993 e.printStackTrace();
1999 private static boolean testCopyOfNodeData() {
2001 final PhylogenyNode n1 = PhylogenyNode
2002 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2003 final PhylogenyNode n2 = n1.copyNodeData();
2004 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2008 catch ( final Exception e ) {
2009 e.printStackTrace();
2015 private static boolean testDataObjects() {
2017 final Confidence s0 = new Confidence();
2018 final Confidence s1 = new Confidence();
2019 if ( !s0.isEqual( s1 ) ) {
2022 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2023 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2024 if ( s2.isEqual( s1 ) ) {
2027 if ( !s2.isEqual( s3 ) ) {
2030 final Confidence s4 = ( Confidence ) s3.copy();
2031 if ( !s4.isEqual( s3 ) ) {
2038 final Taxonomy t1 = new Taxonomy();
2039 final Taxonomy t2 = new Taxonomy();
2040 final Taxonomy t3 = new Taxonomy();
2041 final Taxonomy t4 = new Taxonomy();
2042 final Taxonomy t5 = new Taxonomy();
2043 t1.setIdentifier( new Identifier( "ecoli" ) );
2044 t1.setTaxonomyCode( "ECOLI" );
2045 t1.setScientificName( "E. coli" );
2046 t1.setCommonName( "coli" );
2047 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2048 if ( !t1.isEqual( t0 ) ) {
2051 t2.setIdentifier( new Identifier( "ecoli" ) );
2052 t2.setTaxonomyCode( "OTHER" );
2053 t2.setScientificName( "what" );
2054 t2.setCommonName( "something" );
2055 if ( !t1.isEqual( t2 ) ) {
2058 t2.setIdentifier( new Identifier( "nemve" ) );
2059 if ( t1.isEqual( t2 ) ) {
2062 t1.setIdentifier( null );
2063 t3.setTaxonomyCode( "ECOLI" );
2064 t3.setScientificName( "what" );
2065 t3.setCommonName( "something" );
2066 if ( !t1.isEqual( t3 ) ) {
2069 t1.setIdentifier( null );
2070 t1.setTaxonomyCode( "" );
2071 t4.setScientificName( "E. ColI" );
2072 t4.setCommonName( "something" );
2073 if ( !t1.isEqual( t4 ) ) {
2076 t4.setScientificName( "B. subtilis" );
2077 t4.setCommonName( "something" );
2078 if ( t1.isEqual( t4 ) ) {
2081 t1.setIdentifier( null );
2082 t1.setTaxonomyCode( "" );
2083 t1.setScientificName( "" );
2084 t5.setCommonName( "COLI" );
2085 if ( !t1.isEqual( t5 ) ) {
2088 t5.setCommonName( "vibrio" );
2089 if ( t1.isEqual( t5 ) ) {
2094 final Identifier id0 = new Identifier( "123", "pfam" );
2095 final Identifier id1 = ( Identifier ) id0.copy();
2096 if ( !id1.isEqual( id1 ) ) {
2099 if ( !id1.isEqual( id0 ) ) {
2102 if ( !id0.isEqual( id1 ) ) {
2109 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2110 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2111 if ( !pd1.isEqual( pd1 ) ) {
2114 if ( !pd1.isEqual( pd0 ) ) {
2119 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2120 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2121 if ( !pd3.isEqual( pd3 ) ) {
2124 if ( !pd2.isEqual( pd3 ) ) {
2127 if ( !pd0.isEqual( pd3 ) ) {
2132 // DomainArchitecture
2133 // ------------------
2134 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2135 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2136 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2137 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2138 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2139 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2144 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2145 if ( ds0.getNumberOfDomains() != 4 ) {
2148 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2149 if ( !ds0.isEqual( ds0 ) ) {
2152 if ( !ds0.isEqual( ds1 ) ) {
2155 if ( ds1.getNumberOfDomains() != 4 ) {
2158 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2163 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2164 if ( ds0.isEqual( ds2 ) ) {
2170 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2171 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2172 System.out.println( ds3.toNHX() );
2175 if ( ds3.getNumberOfDomains() != 3 ) {
2180 final Event e1 = new Event( Event.EventType.fusion );
2181 if ( e1.isDuplication() ) {
2184 if ( !e1.isFusion() ) {
2187 if ( !e1.asText().toString().equals( "fusion" ) ) {
2190 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2193 final Event e11 = new Event( Event.EventType.fusion );
2194 if ( !e11.isEqual( e1 ) ) {
2197 if ( !e11.toNHX().toString().equals( "" ) ) {
2200 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2201 if ( e2.isDuplication() ) {
2204 if ( !e2.isSpeciationOrDuplication() ) {
2207 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2210 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2213 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2216 if ( e11.isEqual( e2 ) ) {
2219 final Event e2c = ( Event ) e2.copy();
2220 if ( !e2c.isEqual( e2 ) ) {
2223 Event e3 = new Event( 1, 2, 3 );
2224 if ( e3.isDuplication() ) {
2227 if ( e3.isSpeciation() ) {
2230 if ( e3.isGeneLoss() ) {
2233 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2236 final Event e3c = ( Event ) e3.copy();
2237 final Event e3cc = ( Event ) e3c.copy();
2238 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2242 if ( !e3c.isEqual( e3cc ) ) {
2245 Event e4 = new Event( 1, 2, 3 );
2246 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2249 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2252 final Event e4c = ( Event ) e4.copy();
2254 final Event e4cc = ( Event ) e4c.copy();
2255 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2258 if ( !e4c.isEqual( e4cc ) ) {
2261 final Event e5 = new Event();
2262 if ( !e5.isUnassigned() ) {
2265 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2268 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2271 final Event e6 = new Event( 1, 0, 0 );
2272 if ( !e6.asText().toString().equals( "duplication" ) ) {
2275 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2278 final Event e7 = new Event( 0, 1, 0 );
2279 if ( !e7.asText().toString().equals( "speciation" ) ) {
2282 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2285 final Event e8 = new Event( 0, 0, 1 );
2286 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2289 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2293 catch ( final Exception e ) {
2294 e.printStackTrace( System.out );
2300 private static boolean testDeletionOfExternalNodes() {
2302 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2303 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2304 final PhylogenyWriter w = new PhylogenyWriter();
2305 if ( t0.isEmpty() ) {
2308 if ( t0.getNumberOfExternalNodes() != 1 ) {
2311 t0.deleteSubtree( t0.getNode( "A" ), false );
2312 if ( t0.getNumberOfExternalNodes() != 0 ) {
2315 if ( !t0.isEmpty() ) {
2318 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2319 if ( t1.getNumberOfExternalNodes() != 2 ) {
2322 t1.deleteSubtree( t1.getNode( "A" ), false );
2323 if ( t1.getNumberOfExternalNodes() != 1 ) {
2326 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2329 t1.deleteSubtree( t1.getNode( "B" ), false );
2330 if ( t1.getNumberOfExternalNodes() != 1 ) {
2333 t1.deleteSubtree( t1.getNode( "r" ), false );
2334 if ( !t1.isEmpty() ) {
2337 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2338 if ( t2.getNumberOfExternalNodes() != 3 ) {
2341 t2.deleteSubtree( t2.getNode( "B" ), false );
2342 if ( t2.getNumberOfExternalNodes() != 2 ) {
2345 t2.toNewHampshireX();
2346 PhylogenyNode n = t2.getNode( "A" );
2347 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2350 t2.deleteSubtree( t2.getNode( "A" ), false );
2351 if ( t2.getNumberOfExternalNodes() != 2 ) {
2354 t2.deleteSubtree( t2.getNode( "C" ), true );
2355 if ( t2.getNumberOfExternalNodes() != 1 ) {
2358 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2359 if ( t3.getNumberOfExternalNodes() != 4 ) {
2362 t3.deleteSubtree( t3.getNode( "B" ), true );
2363 if ( t3.getNumberOfExternalNodes() != 3 ) {
2366 n = t3.getNode( "A" );
2367 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2370 n = n.getNextExternalNode();
2371 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2374 t3.deleteSubtree( t3.getNode( "A" ), true );
2375 if ( t3.getNumberOfExternalNodes() != 2 ) {
2378 n = t3.getNode( "C" );
2379 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2382 t3.deleteSubtree( t3.getNode( "C" ), true );
2383 if ( t3.getNumberOfExternalNodes() != 1 ) {
2386 t3.deleteSubtree( t3.getNode( "D" ), true );
2387 if ( t3.getNumberOfExternalNodes() != 0 ) {
2390 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2391 if ( t4.getNumberOfExternalNodes() != 6 ) {
2394 t4.deleteSubtree( t4.getNode( "B2" ), true );
2395 if ( t4.getNumberOfExternalNodes() != 5 ) {
2398 String s = w.toNewHampshire( t4, false, true ).toString();
2399 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2402 t4.deleteSubtree( t4.getNode( "B11" ), true );
2403 if ( t4.getNumberOfExternalNodes() != 4 ) {
2406 t4.deleteSubtree( t4.getNode( "C" ), true );
2407 if ( t4.getNumberOfExternalNodes() != 3 ) {
2410 n = t4.getNode( "A" );
2411 n = n.getNextExternalNode();
2412 if ( !n.getName().equals( "B12" ) ) {
2415 n = n.getNextExternalNode();
2416 if ( !n.getName().equals( "D" ) ) {
2419 s = w.toNewHampshire( t4, false, true ).toString();
2420 if ( !s.equals( "((A,B12),D);" ) ) {
2423 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2424 t5.deleteSubtree( t5.getNode( "A" ), true );
2425 if ( t5.getNumberOfExternalNodes() != 5 ) {
2428 s = w.toNewHampshire( t5, false, true ).toString();
2429 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2432 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2433 t6.deleteSubtree( t6.getNode( "B11" ), true );
2434 if ( t6.getNumberOfExternalNodes() != 5 ) {
2437 s = w.toNewHampshire( t6, false, false ).toString();
2438 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2441 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2442 t7.deleteSubtree( t7.getNode( "B12" ), true );
2443 if ( t7.getNumberOfExternalNodes() != 5 ) {
2446 s = w.toNewHampshire( t7, false, true ).toString();
2447 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2450 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2451 t8.deleteSubtree( t8.getNode( "B2" ), true );
2452 if ( t8.getNumberOfExternalNodes() != 5 ) {
2455 s = w.toNewHampshire( t8, false, false ).toString();
2456 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2459 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2460 t9.deleteSubtree( t9.getNode( "C" ), true );
2461 if ( t9.getNumberOfExternalNodes() != 5 ) {
2464 s = w.toNewHampshire( t9, false, true ).toString();
2465 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2468 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2469 t10.deleteSubtree( t10.getNode( "D" ), true );
2470 if ( t10.getNumberOfExternalNodes() != 5 ) {
2473 s = w.toNewHampshire( t10, false, true ).toString();
2474 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2477 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2478 t11.deleteSubtree( t11.getNode( "A" ), true );
2479 if ( t11.getNumberOfExternalNodes() != 2 ) {
2482 s = w.toNewHampshire( t11, false, true ).toString();
2483 if ( !s.equals( "(B,C);" ) ) {
2486 t11.deleteSubtree( t11.getNode( "C" ), true );
2487 if ( t11.getNumberOfExternalNodes() != 1 ) {
2490 s = w.toNewHampshire( t11, false, false ).toString();
2491 if ( !s.equals( "B;" ) ) {
2494 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2495 t12.deleteSubtree( t12.getNode( "B2" ), true );
2496 if ( t12.getNumberOfExternalNodes() != 8 ) {
2499 s = w.toNewHampshire( t12, false, true ).toString();
2500 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2503 t12.deleteSubtree( t12.getNode( "B3" ), true );
2504 if ( t12.getNumberOfExternalNodes() != 7 ) {
2507 s = w.toNewHampshire( t12, false, true ).toString();
2508 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2511 t12.deleteSubtree( t12.getNode( "C3" ), true );
2512 if ( t12.getNumberOfExternalNodes() != 6 ) {
2515 s = w.toNewHampshire( t12, false, true ).toString();
2516 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2519 t12.deleteSubtree( t12.getNode( "A1" ), true );
2520 if ( t12.getNumberOfExternalNodes() != 5 ) {
2523 s = w.toNewHampshire( t12, false, true ).toString();
2524 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2527 t12.deleteSubtree( t12.getNode( "B1" ), true );
2528 if ( t12.getNumberOfExternalNodes() != 4 ) {
2531 s = w.toNewHampshire( t12, false, true ).toString();
2532 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2535 t12.deleteSubtree( t12.getNode( "A3" ), true );
2536 if ( t12.getNumberOfExternalNodes() != 3 ) {
2539 s = w.toNewHampshire( t12, false, true ).toString();
2540 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2543 t12.deleteSubtree( t12.getNode( "A2" ), true );
2544 if ( t12.getNumberOfExternalNodes() != 2 ) {
2547 s = w.toNewHampshire( t12, false, true ).toString();
2548 if ( !s.equals( "(C1,C2);" ) ) {
2551 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2552 t13.deleteSubtree( t13.getNode( "D" ), true );
2553 if ( t13.getNumberOfExternalNodes() != 4 ) {
2556 s = w.toNewHampshire( t13, false, true ).toString();
2557 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2560 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2561 t14.deleteSubtree( t14.getNode( "E" ), true );
2562 if ( t14.getNumberOfExternalNodes() != 5 ) {
2565 s = w.toNewHampshire( t14, false, true ).toString();
2566 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2569 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2570 t15.deleteSubtree( t15.getNode( "B2" ), true );
2571 if ( t15.getNumberOfExternalNodes() != 11 ) {
2574 t15.deleteSubtree( t15.getNode( "B1" ), true );
2575 if ( t15.getNumberOfExternalNodes() != 10 ) {
2578 t15.deleteSubtree( t15.getNode( "B3" ), true );
2579 if ( t15.getNumberOfExternalNodes() != 9 ) {
2582 t15.deleteSubtree( t15.getNode( "B4" ), true );
2583 if ( t15.getNumberOfExternalNodes() != 8 ) {
2586 t15.deleteSubtree( t15.getNode( "A1" ), true );
2587 if ( t15.getNumberOfExternalNodes() != 7 ) {
2590 t15.deleteSubtree( t15.getNode( "C4" ), true );
2591 if ( t15.getNumberOfExternalNodes() != 6 ) {
2595 catch ( final Exception e ) {
2596 e.printStackTrace( System.out );
2602 private static boolean testDescriptiveStatistics() {
2604 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2605 dss1.addValue( 82 );
2606 dss1.addValue( 78 );
2607 dss1.addValue( 70 );
2608 dss1.addValue( 58 );
2609 dss1.addValue( 42 );
2610 if ( dss1.getN() != 5 ) {
2613 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2616 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2619 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2622 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2625 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2628 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2631 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2634 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2637 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2640 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2643 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2646 dss1.addValue( 123 );
2647 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2650 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2653 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2656 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2657 dss2.addValue( -1.85 );
2658 dss2.addValue( 57.5 );
2659 dss2.addValue( 92.78 );
2660 dss2.addValue( 57.78 );
2661 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2664 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2667 final double[] a = dss2.getDataAsDoubleArray();
2668 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2671 dss2.addValue( -100 );
2672 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2675 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2678 final double[] ds = new double[ 14 ];
2693 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2694 if ( bins.length != 4 ) {
2697 if ( bins[ 0 ] != 2 ) {
2700 if ( bins[ 1 ] != 3 ) {
2703 if ( bins[ 2 ] != 4 ) {
2706 if ( bins[ 3 ] != 5 ) {
2709 final double[] ds1 = new double[ 9 ];
2719 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2720 if ( bins1.length != 4 ) {
2723 if ( bins1[ 0 ] != 2 ) {
2726 if ( bins1[ 1 ] != 3 ) {
2729 if ( bins1[ 2 ] != 0 ) {
2732 if ( bins1[ 3 ] != 4 ) {
2735 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2736 if ( bins1_1.length != 3 ) {
2739 if ( bins1_1[ 0 ] != 3 ) {
2742 if ( bins1_1[ 1 ] != 2 ) {
2745 if ( bins1_1[ 2 ] != 4 ) {
2748 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2749 if ( bins1_2.length != 3 ) {
2752 if ( bins1_2[ 0 ] != 2 ) {
2755 if ( bins1_2[ 1 ] != 2 ) {
2758 if ( bins1_2[ 2 ] != 2 ) {
2761 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2775 dss3.addValue( 10 );
2776 dss3.addValue( 10 );
2777 dss3.addValue( 10 );
2778 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2779 histo.toStringBuffer( 10, '=', 40, 5 );
2780 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2782 catch ( final Exception e ) {
2783 e.printStackTrace( System.out );
2789 private static boolean testDir( final String file ) {
2791 final File f = new File( file );
2792 if ( !f.exists() ) {
2795 if ( !f.isDirectory() ) {
2798 if ( !f.canRead() ) {
2802 catch ( final Exception e ) {
2808 private static boolean testExternalNodeRelatedMethods() {
2810 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2811 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2812 PhylogenyNode n = t1.getNode( "A" );
2813 n = n.getNextExternalNode();
2814 if ( !n.getName().equals( "B" ) ) {
2817 n = n.getNextExternalNode();
2818 if ( !n.getName().equals( "C" ) ) {
2821 n = n.getNextExternalNode();
2822 if ( !n.getName().equals( "D" ) ) {
2825 n = t1.getNode( "B" );
2826 while ( !n.isLastExternalNode() ) {
2827 n = n.getNextExternalNode();
2829 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2830 n = t2.getNode( "A" );
2831 n = n.getNextExternalNode();
2832 if ( !n.getName().equals( "B" ) ) {
2835 n = n.getNextExternalNode();
2836 if ( !n.getName().equals( "C" ) ) {
2839 n = n.getNextExternalNode();
2840 if ( !n.getName().equals( "D" ) ) {
2843 n = t2.getNode( "B" );
2844 while ( !n.isLastExternalNode() ) {
2845 n = n.getNextExternalNode();
2847 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2848 n = t3.getNode( "A" );
2849 n = n.getNextExternalNode();
2850 if ( !n.getName().equals( "B" ) ) {
2853 n = n.getNextExternalNode();
2854 if ( !n.getName().equals( "C" ) ) {
2857 n = n.getNextExternalNode();
2858 if ( !n.getName().equals( "D" ) ) {
2861 n = n.getNextExternalNode();
2862 if ( !n.getName().equals( "E" ) ) {
2865 n = n.getNextExternalNode();
2866 if ( !n.getName().equals( "F" ) ) {
2869 n = n.getNextExternalNode();
2870 if ( !n.getName().equals( "G" ) ) {
2873 n = n.getNextExternalNode();
2874 if ( !n.getName().equals( "H" ) ) {
2877 n = t3.getNode( "B" );
2878 while ( !n.isLastExternalNode() ) {
2879 n = n.getNextExternalNode();
2881 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2882 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2883 final PhylogenyNode node = iter.next();
2885 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2886 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2887 final PhylogenyNode node = iter.next();
2890 catch ( final Exception e ) {
2891 e.printStackTrace( System.out );
2897 private static boolean testGeneralTable() {
2899 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2900 t0.setValue( 3, 2, "23" );
2901 t0.setValue( 10, 1, "error" );
2902 t0.setValue( 10, 1, "110" );
2903 t0.setValue( 9, 1, "19" );
2904 t0.setValue( 1, 10, "101" );
2905 t0.setValue( 10, 10, "1010" );
2906 t0.setValue( 100, 10, "10100" );
2907 t0.setValue( 0, 0, "00" );
2908 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2911 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2914 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2917 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2920 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2923 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2926 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2929 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2932 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2935 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2936 t1.setValue( "3", "2", "23" );
2937 t1.setValue( "10", "1", "error" );
2938 t1.setValue( "10", "1", "110" );
2939 t1.setValue( "9", "1", "19" );
2940 t1.setValue( "1", "10", "101" );
2941 t1.setValue( "10", "10", "1010" );
2942 t1.setValue( "100", "10", "10100" );
2943 t1.setValue( "0", "0", "00" );
2944 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2945 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2948 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2951 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2954 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2957 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2960 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
2963 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
2966 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
2969 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
2972 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
2976 catch ( final Exception e ) {
2977 e.printStackTrace( System.out );
2983 private static boolean testGetDistance() {
2985 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2986 final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
2987 new NHXParser() )[ 0 ];
2988 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
2989 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
2992 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
2995 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
2998 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3001 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3004 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3007 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3010 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3013 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3016 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3019 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3022 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3025 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3028 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3031 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3034 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3037 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3040 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3043 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3046 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3049 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3052 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3055 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3058 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3061 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3064 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3067 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3070 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3073 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3076 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3079 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3082 final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
3083 new NHXParser() )[ 0 ];
3084 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3087 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3090 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3093 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3096 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3099 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3102 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3105 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3108 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3111 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3114 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3118 catch ( final Exception e ) {
3119 e.printStackTrace( System.out );
3125 private static boolean testGetLCA() {
3127 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3128 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3129 new NHXParser() )[ 0 ];
3130 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3131 if ( !A.getName().equals( "A" ) ) {
3134 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3135 if ( !gh.getName().equals( "gh" ) ) {
3138 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3139 if ( !ab.getName().equals( "ab" ) ) {
3142 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3143 if ( !ab2.getName().equals( "ab" ) ) {
3146 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3147 if ( !gh2.getName().equals( "gh" ) ) {
3150 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3151 if ( !gh3.getName().equals( "gh" ) ) {
3154 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3155 if ( !abc.getName().equals( "abc" ) ) {
3158 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3159 if ( !abc2.getName().equals( "abc" ) ) {
3162 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3163 if ( !abcd.getName().equals( "abcd" ) ) {
3166 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3167 if ( !abcd2.getName().equals( "abcd" ) ) {
3170 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3171 if ( !abcdef.getName().equals( "abcdef" ) ) {
3174 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3175 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3178 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3179 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3182 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3183 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3186 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3187 if ( !abcde.getName().equals( "abcde" ) ) {
3190 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3191 if ( !abcde2.getName().equals( "abcde" ) ) {
3194 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3195 if ( !r.getName().equals( "abcdefgh" ) ) {
3198 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3199 if ( !r2.getName().equals( "abcdefgh" ) ) {
3202 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3203 if ( !r3.getName().equals( "abcdefgh" ) ) {
3206 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3207 if ( !abcde3.getName().equals( "abcde" ) ) {
3210 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3211 if ( !abcde4.getName().equals( "abcde" ) ) {
3214 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3215 if ( !ab3.getName().equals( "ab" ) ) {
3218 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3219 if ( !ab4.getName().equals( "ab" ) ) {
3222 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3223 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3224 if ( !cd.getName().equals( "cd" ) ) {
3227 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3228 if ( !cd2.getName().equals( "cd" ) ) {
3231 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3232 if ( !cde.getName().equals( "cde" ) ) {
3235 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3236 if ( !cde2.getName().equals( "cde" ) ) {
3239 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3240 if ( !cdef.getName().equals( "cdef" ) ) {
3243 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3244 if ( !cdef2.getName().equals( "cdef" ) ) {
3247 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3248 if ( !cdef3.getName().equals( "cdef" ) ) {
3251 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3252 if ( !rt.getName().equals( "r" ) ) {
3255 final Phylogeny p3 = factory
3256 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3257 new NHXParser() )[ 0 ];
3258 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3259 if ( !bc_3.getName().equals( "bc" ) ) {
3262 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3263 if ( !ac_3.getName().equals( "abc" ) ) {
3266 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3267 if ( !ad_3.getName().equals( "abcde" ) ) {
3270 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3271 if ( !af_3.getName().equals( "abcdef" ) ) {
3274 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3275 if ( !ag_3.getName().equals( "" ) ) {
3278 if ( !ag_3.isRoot() ) {
3281 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3282 if ( !al_3.getName().equals( "" ) ) {
3285 if ( !al_3.isRoot() ) {
3288 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3289 if ( !kl_3.getName().equals( "" ) ) {
3292 if ( !kl_3.isRoot() ) {
3295 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3296 if ( !fl_3.getName().equals( "" ) ) {
3299 if ( !fl_3.isRoot() ) {
3302 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3303 if ( !gk_3.getName().equals( "ghijk" ) ) {
3306 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3307 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3308 if ( !r_4.getName().equals( "r" ) ) {
3311 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3312 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3313 if ( !r_5.getName().equals( "root" ) ) {
3316 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3317 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3318 if ( !r_6.getName().equals( "rot" ) ) {
3321 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3322 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3323 if ( !r_7.getName().equals( "rott" ) ) {
3327 catch ( final Exception e ) {
3328 e.printStackTrace( System.out );
3334 private static boolean testGetLCA2() {
3336 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3337 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3338 new NHXParser() )[ 0 ];
3339 PhylogenyMethods.preOrderReId( p1 );
3340 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3341 p1.getNode( "A" ) );
3342 if ( !A.getName().equals( "A" ) ) {
3345 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3346 p1.getNode( "gh" ) );
3347 if ( !gh.getName().equals( "gh" ) ) {
3350 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3351 p1.getNode( "B" ) );
3352 if ( !ab.getName().equals( "ab" ) ) {
3355 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3356 p1.getNode( "A" ) );
3357 if ( !ab2.getName().equals( "ab" ) ) {
3360 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3361 p1.getNode( "G" ) );
3362 if ( !gh2.getName().equals( "gh" ) ) {
3365 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3366 p1.getNode( "H" ) );
3367 if ( !gh3.getName().equals( "gh" ) ) {
3370 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3371 p1.getNode( "A" ) );
3372 if ( !abc.getName().equals( "abc" ) ) {
3375 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3376 p1.getNode( "C" ) );
3377 if ( !abc2.getName().equals( "abc" ) ) {
3380 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3381 p1.getNode( "D" ) );
3382 if ( !abcd.getName().equals( "abcd" ) ) {
3385 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3386 p1.getNode( "A" ) );
3387 if ( !abcd2.getName().equals( "abcd" ) ) {
3390 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3391 p1.getNode( "F" ) );
3392 if ( !abcdef.getName().equals( "abcdef" ) ) {
3395 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3396 p1.getNode( "A" ) );
3397 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3400 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3401 p1.getNode( "F" ) );
3402 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3405 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3406 p1.getNode( "ab" ) );
3407 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3410 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3411 p1.getNode( "E" ) );
3412 if ( !abcde.getName().equals( "abcde" ) ) {
3415 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3416 p1.getNode( "A" ) );
3417 if ( !abcde2.getName().equals( "abcde" ) ) {
3420 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3421 p1.getNode( "abcdefgh" ) );
3422 if ( !r.getName().equals( "abcdefgh" ) ) {
3425 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3426 p1.getNode( "H" ) );
3427 if ( !r2.getName().equals( "abcdefgh" ) ) {
3430 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3431 p1.getNode( "A" ) );
3432 if ( !r3.getName().equals( "abcdefgh" ) ) {
3435 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3436 p1.getNode( "abcde" ) );
3437 if ( !abcde3.getName().equals( "abcde" ) ) {
3440 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3441 p1.getNode( "E" ) );
3442 if ( !abcde4.getName().equals( "abcde" ) ) {
3445 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3446 p1.getNode( "B" ) );
3447 if ( !ab3.getName().equals( "ab" ) ) {
3450 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3451 p1.getNode( "ab" ) );
3452 if ( !ab4.getName().equals( "ab" ) ) {
3455 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3456 PhylogenyMethods.preOrderReId( p2 );
3457 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3458 p2.getNode( "d" ) );
3459 if ( !cd.getName().equals( "cd" ) ) {
3462 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3463 p2.getNode( "c" ) );
3464 if ( !cd2.getName().equals( "cd" ) ) {
3467 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3468 p2.getNode( "e" ) );
3469 if ( !cde.getName().equals( "cde" ) ) {
3472 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3473 p2.getNode( "c" ) );
3474 if ( !cde2.getName().equals( "cde" ) ) {
3477 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3478 p2.getNode( "f" ) );
3479 if ( !cdef.getName().equals( "cdef" ) ) {
3482 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3483 p2.getNode( "f" ) );
3484 if ( !cdef2.getName().equals( "cdef" ) ) {
3487 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3488 p2.getNode( "d" ) );
3489 if ( !cdef3.getName().equals( "cdef" ) ) {
3492 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3493 p2.getNode( "a" ) );
3494 if ( !rt.getName().equals( "r" ) ) {
3497 final Phylogeny p3 = factory
3498 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3499 new NHXParser() )[ 0 ];
3500 PhylogenyMethods.preOrderReId( p3 );
3501 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3502 p3.getNode( "c" ) );
3503 if ( !bc_3.getName().equals( "bc" ) ) {
3506 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3507 p3.getNode( "c" ) );
3508 if ( !ac_3.getName().equals( "abc" ) ) {
3511 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3512 p3.getNode( "d" ) );
3513 if ( !ad_3.getName().equals( "abcde" ) ) {
3516 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3517 p3.getNode( "f" ) );
3518 if ( !af_3.getName().equals( "abcdef" ) ) {
3521 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3522 p3.getNode( "g" ) );
3523 if ( !ag_3.getName().equals( "" ) ) {
3526 if ( !ag_3.isRoot() ) {
3529 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3530 p3.getNode( "l" ) );
3531 if ( !al_3.getName().equals( "" ) ) {
3534 if ( !al_3.isRoot() ) {
3537 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3538 p3.getNode( "l" ) );
3539 if ( !kl_3.getName().equals( "" ) ) {
3542 if ( !kl_3.isRoot() ) {
3545 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3546 p3.getNode( "l" ) );
3547 if ( !fl_3.getName().equals( "" ) ) {
3550 if ( !fl_3.isRoot() ) {
3553 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3554 p3.getNode( "k" ) );
3555 if ( !gk_3.getName().equals( "ghijk" ) ) {
3558 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3559 PhylogenyMethods.preOrderReId( p4 );
3560 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3561 p4.getNode( "c" ) );
3562 if ( !r_4.getName().equals( "r" ) ) {
3565 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3566 PhylogenyMethods.preOrderReId( p5 );
3567 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3568 p5.getNode( "c" ) );
3569 if ( !r_5.getName().equals( "root" ) ) {
3572 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3573 PhylogenyMethods.preOrderReId( p6 );
3574 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3575 p6.getNode( "a" ) );
3576 if ( !r_6.getName().equals( "rot" ) ) {
3579 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3580 PhylogenyMethods.preOrderReId( p7 );
3581 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3582 p7.getNode( "e" ) );
3583 if ( !r_7.getName().equals( "rott" ) ) {
3586 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3587 p7.getNode( "a" ) );
3588 if ( !r_71.getName().equals( "rott" ) ) {
3591 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3592 p7.getNode( "rott" ) );
3593 if ( !r_72.getName().equals( "rott" ) ) {
3596 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3597 p7.getNode( "a" ) );
3598 if ( !r_73.getName().equals( "rott" ) ) {
3601 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3602 p7.getNode( "rott" ) );
3603 if ( !r_74.getName().equals( "rott" ) ) {
3606 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3607 p7.getNode( "e" ) );
3608 if ( !r_75.getName().equals( "e" ) ) {
3612 catch ( final Exception e ) {
3613 e.printStackTrace( System.out );
3619 private static boolean testHmmscanOutputParser() {
3620 final String test_dir = Test.PATH_TO_TEST_DATA;
3622 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3623 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3625 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3626 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3627 final List<Protein> proteins = parser2.parse();
3628 if ( parser2.getProteinsEncountered() != 4 ) {
3631 if ( proteins.size() != 4 ) {
3634 if ( parser2.getDomainsEncountered() != 69 ) {
3637 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3640 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3643 final Protein p1 = proteins.get( 0 );
3644 if ( p1.getNumberOfProteinDomains() != 15 ) {
3647 if ( p1.getLength() != 850 ) {
3650 final Protein p2 = proteins.get( 1 );
3651 if ( p2.getNumberOfProteinDomains() != 51 ) {
3654 if ( p2.getLength() != 1291 ) {
3657 final Protein p3 = proteins.get( 2 );
3658 if ( p3.getNumberOfProteinDomains() != 2 ) {
3661 final Protein p4 = proteins.get( 3 );
3662 if ( p4.getNumberOfProteinDomains() != 1 ) {
3665 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3668 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3671 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3674 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3677 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3680 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3683 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3686 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3689 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3693 catch ( final Exception e ) {
3694 e.printStackTrace( System.out );
3700 private static boolean testLastExternalNodeMethods() {
3702 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3703 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3704 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3705 final PhylogenyNode n1 = t0.getNode( "A" );
3706 if ( n1.isLastExternalNode() ) {
3709 final PhylogenyNode n2 = t0.getNode( "B" );
3710 if ( n2.isLastExternalNode() ) {
3713 final PhylogenyNode n3 = t0.getNode( "C" );
3714 if ( n3.isLastExternalNode() ) {
3717 final PhylogenyNode n4 = t0.getNode( "D" );
3718 if ( !n4.isLastExternalNode() ) {
3722 catch ( final Exception e ) {
3723 e.printStackTrace( System.out );
3729 private static boolean testLevelOrderIterator() {
3731 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3732 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3733 PhylogenyNodeIterator it0;
3734 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3737 for( it0.reset(); it0.hasNext(); ) {
3740 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3741 if ( !it.next().getName().equals( "r" ) ) {
3744 if ( !it.next().getName().equals( "ab" ) ) {
3747 if ( !it.next().getName().equals( "cd" ) ) {
3750 if ( !it.next().getName().equals( "A" ) ) {
3753 if ( !it.next().getName().equals( "B" ) ) {
3756 if ( !it.next().getName().equals( "C" ) ) {
3759 if ( !it.next().getName().equals( "D" ) ) {
3762 if ( it.hasNext() ) {
3765 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",
3766 new NHXParser() )[ 0 ];
3767 PhylogenyNodeIterator it2;
3768 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3771 for( it2.reset(); it2.hasNext(); ) {
3774 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3775 if ( !it3.next().getName().equals( "r" ) ) {
3778 if ( !it3.next().getName().equals( "abc" ) ) {
3781 if ( !it3.next().getName().equals( "defg" ) ) {
3784 if ( !it3.next().getName().equals( "A" ) ) {
3787 if ( !it3.next().getName().equals( "B" ) ) {
3790 if ( !it3.next().getName().equals( "C" ) ) {
3793 if ( !it3.next().getName().equals( "D" ) ) {
3796 if ( !it3.next().getName().equals( "E" ) ) {
3799 if ( !it3.next().getName().equals( "F" ) ) {
3802 if ( !it3.next().getName().equals( "G" ) ) {
3805 if ( !it3.next().getName().equals( "1" ) ) {
3808 if ( !it3.next().getName().equals( "2" ) ) {
3811 if ( !it3.next().getName().equals( "3" ) ) {
3814 if ( !it3.next().getName().equals( "4" ) ) {
3817 if ( !it3.next().getName().equals( "5" ) ) {
3820 if ( !it3.next().getName().equals( "6" ) ) {
3823 if ( !it3.next().getName().equals( "f1" ) ) {
3826 if ( !it3.next().getName().equals( "f2" ) ) {
3829 if ( !it3.next().getName().equals( "f3" ) ) {
3832 if ( !it3.next().getName().equals( "a" ) ) {
3835 if ( !it3.next().getName().equals( "b" ) ) {
3838 if ( !it3.next().getName().equals( "f21" ) ) {
3841 if ( !it3.next().getName().equals( "X" ) ) {
3844 if ( !it3.next().getName().equals( "Y" ) ) {
3847 if ( !it3.next().getName().equals( "Z" ) ) {
3850 if ( it3.hasNext() ) {
3853 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3854 PhylogenyNodeIterator it4;
3855 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3858 for( it4.reset(); it4.hasNext(); ) {
3861 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3862 if ( !it5.next().getName().equals( "r" ) ) {
3865 if ( !it5.next().getName().equals( "A" ) ) {
3868 if ( !it5.next().getName().equals( "B" ) ) {
3871 if ( !it5.next().getName().equals( "C" ) ) {
3874 if ( !it5.next().getName().equals( "D" ) ) {
3877 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3878 PhylogenyNodeIterator it6;
3879 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3882 for( it6.reset(); it6.hasNext(); ) {
3885 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3886 if ( !it7.next().getName().equals( "A" ) ) {
3889 if ( it.hasNext() ) {
3893 catch ( final Exception e ) {
3894 e.printStackTrace( System.out );
3900 private static boolean testMidpointrooting() {
3902 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3903 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",
3904 new NHXParser() )[ 0 ];
3905 if ( !t1.isRooted() ) {
3908 PhylogenyMethods.midpointRoot( t1 );
3909 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3912 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3915 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3918 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3921 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3924 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3927 t1.reRoot( t1.getNode( "A" ) );
3928 PhylogenyMethods.midpointRoot( t1 );
3929 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3932 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3935 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3938 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3941 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3944 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3948 catch ( final Exception e ) {
3949 e.printStackTrace( System.out );
3955 private static boolean testNexusCharactersParsing() {
3957 final NexusCharactersParser parser = new NexusCharactersParser();
3958 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3960 String[] labels = parser.getCharStateLabels();
3961 if ( labels.length != 7 ) {
3964 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3967 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3970 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3973 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3976 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3979 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3982 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3985 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3987 labels = parser.getCharStateLabels();
3988 if ( labels.length != 7 ) {
3991 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3994 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3997 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4000 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4003 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4006 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4009 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4013 catch ( final Exception e ) {
4014 e.printStackTrace( System.out );
4020 private static boolean testNexusMatrixParsing() {
4022 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4023 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4025 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4026 if ( m.getNumberOfCharacters() != 9 ) {
4029 if ( m.getNumberOfIdentifiers() != 5 ) {
4032 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4035 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4038 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4041 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4044 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4047 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4050 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4053 // if ( labels.length != 7 ) {
4056 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4059 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4062 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4065 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4068 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4071 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4074 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4077 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4079 // labels = parser.getCharStateLabels();
4080 // if ( labels.length != 7 ) {
4083 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4086 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4089 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4092 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4095 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4098 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4101 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4105 catch ( final Exception e ) {
4106 e.printStackTrace( System.out );
4112 private static boolean testNexusTreeParsing() {
4114 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4115 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4116 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4117 if ( phylogenies.length != 1 ) {
4120 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4123 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4127 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4128 if ( phylogenies.length != 1 ) {
4131 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4134 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4138 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4139 if ( phylogenies.length != 1 ) {
4142 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4145 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4148 if ( phylogenies[ 0 ].isRooted() ) {
4152 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4153 if ( phylogenies.length != 18 ) {
4156 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4159 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4162 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4165 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4168 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4171 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4174 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4177 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4180 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4183 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4186 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4189 if ( phylogenies[ 8 ].isRooted() ) {
4192 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4195 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4198 if ( !phylogenies[ 9 ].isRooted() ) {
4201 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4204 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4207 if ( !phylogenies[ 10 ].isRooted() ) {
4210 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4213 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4216 if ( phylogenies[ 11 ].isRooted() ) {
4219 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4222 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4225 if ( !phylogenies[ 12 ].isRooted() ) {
4228 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4231 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4234 if ( !phylogenies[ 13 ].isRooted() ) {
4237 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4240 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4243 if ( !phylogenies[ 14 ].isRooted() ) {
4246 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4249 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4252 if ( phylogenies[ 15 ].isRooted() ) {
4255 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4258 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4261 if ( !phylogenies[ 16 ].isRooted() ) {
4264 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4267 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4270 if ( phylogenies[ 17 ].isRooted() ) {
4273 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4277 catch ( final Exception e ) {
4278 e.printStackTrace( System.out );
4284 private static boolean testNexusTreeParsingTranslating() {
4286 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4287 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4288 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4289 if ( phylogenies.length != 1 ) {
4292 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4295 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4298 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4301 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4304 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4305 .equals( "Aranaeus" ) ) {
4309 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4310 if ( phylogenies.length != 3 ) {
4313 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4316 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4319 if ( phylogenies[ 0 ].isRooted() ) {
4322 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4325 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4328 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4329 .equals( "Aranaeus" ) ) {
4332 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4335 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4338 if ( phylogenies[ 1 ].isRooted() ) {
4341 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4344 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4347 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4348 .equals( "Aranaeus" ) ) {
4351 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4354 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4357 if ( !phylogenies[ 2 ].isRooted() ) {
4360 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4363 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4366 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4367 .equals( "Aranaeus" ) ) {
4371 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4372 if ( phylogenies.length != 3 ) {
4375 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4378 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4381 if ( phylogenies[ 0 ].isRooted() ) {
4384 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4387 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4390 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4391 .equals( "Aranaeus" ) ) {
4394 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4397 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4400 if ( phylogenies[ 1 ].isRooted() ) {
4403 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4406 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4409 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4410 .equals( "Aranaeus" ) ) {
4413 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4416 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4419 if ( !phylogenies[ 2 ].isRooted() ) {
4422 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4425 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4428 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4429 .equals( "Aranaeus" ) ) {
4433 catch ( final Exception e ) {
4434 e.printStackTrace( System.out );
4440 private static boolean testNHParsing() {
4442 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4443 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4444 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4447 final NHXParser nhxp = new NHXParser();
4448 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4449 nhxp.setReplaceUnderscores( true );
4450 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4451 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4454 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4457 final Phylogeny p1b = factory
4458 .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 ",
4459 new NHXParser() )[ 0 ];
4460 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4463 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4466 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4467 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4468 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4469 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4470 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4471 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4472 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4473 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4474 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4475 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4476 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4477 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4478 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4480 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4483 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4486 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4489 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4492 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4493 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4494 final String p16_S = "((A,B),C)";
4495 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4496 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4499 final String p17_S = "(C,(A,B))";
4500 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4501 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4504 final String p18_S = "((A,B),(C,D))";
4505 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4506 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4509 final String p19_S = "(((A,B),C),D)";
4510 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4511 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4514 final String p20_S = "(A,(B,(C,D)))";
4515 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4516 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4519 final String p21_S = "(A,(B,(C,(D,E))))";
4520 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4521 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4524 final String p22_S = "((((A,B),C),D),E)";
4525 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4526 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4529 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4530 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4531 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4534 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4535 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4536 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4539 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4540 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4541 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4542 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4545 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4548 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4549 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4550 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4551 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4552 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4553 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4554 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4555 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4556 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4557 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4560 final String p26_S = "(A,B)ab";
4561 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4562 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4565 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4566 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4568 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4571 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4572 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4573 final String p28_S3 = "(A,B)ab";
4574 final String p28_S4 = "((((A,B),C),D),;E;)";
4575 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4577 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4580 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4583 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4586 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4589 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";
4590 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4591 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4594 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";
4595 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4596 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4599 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4600 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4601 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4604 final String p33_S = "A";
4605 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4606 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4609 final String p34_S = "B;";
4610 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4611 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4614 final String p35_S = "B:0.2";
4615 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4616 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4619 final String p36_S = "(A)";
4620 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4621 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4624 final String p37_S = "((A))";
4625 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4626 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4629 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4630 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4631 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4634 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4635 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4636 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4639 final String p40_S = "(A,B,C)";
4640 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4641 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4644 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4645 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4646 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4649 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4650 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4651 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4654 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)";
4655 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4656 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4659 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)))";
4660 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4661 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4664 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4665 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4666 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4669 final String p46_S = "";
4670 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4671 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4674 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4675 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4678 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4679 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4682 final Phylogeny p49 = factory
4683 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4684 new NHXParser() )[ 0 ];
4685 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4688 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4689 if ( p50.getNode( "A" ) == null ) {
4692 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4693 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4696 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4699 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4700 .equals( "((A,B)88:2.0,C);" ) ) {
4703 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4704 if ( p51.getNode( "A(A" ) == null ) {
4707 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4708 if ( p52.getNode( "A(A" ) == null ) {
4711 final Phylogeny p53 = factory
4712 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4713 new NHXParser() )[ 0 ];
4714 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4718 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4719 if ( p54.getNode( "A" ) == null ) {
4722 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4723 .equals( "((A,B)[88],C);" ) ) {
4727 catch ( final Exception e ) {
4728 e.printStackTrace( System.out );
4734 private static boolean testNHXconversion() {
4736 final PhylogenyNode n1 = new PhylogenyNode();
4737 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4738 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4739 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4740 final PhylogenyNode n5 = PhylogenyNode
4741 .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]" );
4742 final PhylogenyNode n6 = PhylogenyNode
4743 .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]" );
4744 if ( !n1.toNewHampshireX().equals( "" ) ) {
4747 if ( !n2.toNewHampshireX().equals( "" ) ) {
4750 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4753 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4756 if ( !n5.toNewHampshireX()
4757 .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]" ) ) {
4760 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]" ) ) {
4764 catch ( final Exception e ) {
4765 e.printStackTrace( System.out );
4771 private static boolean testNHXNodeParsing() {
4773 final PhylogenyNode n1 = new PhylogenyNode();
4774 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4775 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4776 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4777 final PhylogenyNode n5 = PhylogenyNode
4778 .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]" );
4779 if ( !n3.getName().equals( "n3" ) ) {
4782 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4785 if ( n3.isDuplication() ) {
4788 if ( n3.isHasAssignedEvent() ) {
4791 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4794 if ( !n4.getName().equals( "n4" ) ) {
4797 if ( n4.getDistanceToParent() != 0.01 ) {
4800 if ( !n5.getName().equals( "n5" ) ) {
4803 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4806 if ( n5.getDistanceToParent() != 0.1 ) {
4809 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4812 if ( !n5.isDuplication() ) {
4815 if ( !n5.isHasAssignedEvent() ) {
4818 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4821 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4824 final PhylogenyNode n8 = PhylogenyNode
4825 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4826 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4829 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4832 final PhylogenyNode n9 = PhylogenyNode
4833 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4834 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4837 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4840 final PhylogenyNode n10 = PhylogenyNode
4841 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4842 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4845 final PhylogenyNode n20 = PhylogenyNode
4846 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4847 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4850 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4853 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
4854 NHXParser.TAXONOMY_EXTRACTION.YES );
4855 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4858 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4861 final PhylogenyNode n20xx = PhylogenyNode
4862 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4863 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4866 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4869 final PhylogenyNode n20xxx = PhylogenyNode
4870 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4871 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4874 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4877 final PhylogenyNode n20xxxx = PhylogenyNode
4878 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4879 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4882 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4885 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
4886 NHXParser.TAXONOMY_EXTRACTION.YES );
4887 if ( !n21.getName().equals( "n21_PIG" ) ) {
4890 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4893 final PhylogenyNode n21x = PhylogenyNode
4894 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4895 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4898 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4901 final PhylogenyNode n22 = PhylogenyNode
4902 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4903 if ( !n22.getName().equals( "n22/PIG" ) ) {
4906 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4909 final PhylogenyNode n23 = PhylogenyNode
4910 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4911 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4914 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4917 final PhylogenyNode a = PhylogenyNode
4918 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4919 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4922 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4925 final PhylogenyNode b = PhylogenyNode
4926 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4927 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4930 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4933 final PhylogenyNode c = PhylogenyNode
4934 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4935 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4936 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4939 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4942 final PhylogenyNode c1 = PhylogenyNode
4943 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4944 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4945 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4948 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4951 final PhylogenyNode c2 = PhylogenyNode
4952 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4953 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4954 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4957 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
4960 final PhylogenyNode d = PhylogenyNode
4961 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4962 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4965 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4968 final PhylogenyNode e = PhylogenyNode
4969 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4970 if ( !e.getName().equals( "n10_RAT1" ) ) {
4973 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4976 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
4977 NHXParser.TAXONOMY_EXTRACTION.YES );
4978 if ( !e2.getName().equals( "n10_RAT1" ) ) {
4981 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
4984 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
4985 NHXParser.TAXONOMY_EXTRACTION.YES );
4986 if ( !e3.getName().equals( "n10_RAT~" ) ) {
4989 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
4992 final PhylogenyNode n11 = PhylogenyNode
4993 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4994 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4995 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4998 if ( n11.getDistanceToParent() != 0.4 ) {
5001 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5004 final PhylogenyNode n12 = PhylogenyNode
5005 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5006 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5007 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5010 if ( n12.getDistanceToParent() != 0.4 ) {
5013 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5016 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5017 NHXParser.TAXONOMY_EXTRACTION.YES );
5018 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5021 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5024 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5025 NHXParser.TAXONOMY_EXTRACTION.YES );
5026 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5029 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5032 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
5033 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
5034 if ( !tvu1.getRef().equals( "tag1" ) ) {
5037 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
5040 if ( !tvu1.getUnit().equals( "unit1" ) ) {
5043 if ( !tvu1.getValue().equals( "value1" ) ) {
5046 if ( !tvu3.getRef().equals( "tag3" ) ) {
5049 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
5052 if ( !tvu3.getUnit().equals( "unit3" ) ) {
5055 if ( !tvu3.getValue().equals( "value3" ) ) {
5058 if ( n1.getName().compareTo( "" ) != 0 ) {
5061 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5064 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5067 if ( n2.getName().compareTo( "" ) != 0 ) {
5070 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5073 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5076 final PhylogenyNode n00 = PhylogenyNode
5077 .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]" );
5078 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
5081 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5084 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5087 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
5090 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
5093 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
5096 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
5099 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
5102 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5103 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5106 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
5107 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
5110 final PhylogenyNode n13 = PhylogenyNode
5111 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5112 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5115 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5118 final PhylogenyNode n14 = PhylogenyNode
5119 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5120 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5123 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5126 final PhylogenyNode n15 = PhylogenyNode
5127 .createInstanceFromNhxString( "something_wicked[123]",
5128 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5129 if ( !n15.getName().equals( "something_wicked" ) ) {
5132 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5135 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5138 final PhylogenyNode n16 = PhylogenyNode
5139 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5140 if ( !n16.getName().equals( "something_wicked2" ) ) {
5143 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5146 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5149 final PhylogenyNode n17 = PhylogenyNode
5150 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5151 if ( !n17.getName().equals( "something_wicked3" ) ) {
5154 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5157 final PhylogenyNode n18 = PhylogenyNode
5158 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5159 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5162 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5165 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5169 catch ( final Exception e ) {
5170 e.printStackTrace( System.out );
5176 private static boolean testNHXParsing() {
5178 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5179 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5180 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5183 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]";
5184 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5185 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5188 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]";
5189 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5190 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5193 final Phylogeny[] p3 = factory
5194 .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]",
5196 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5199 final Phylogeny[] p4 = factory
5200 .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(]",
5202 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5205 final Phylogeny[] p5 = factory
5206 .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(((]",
5208 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5211 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)";
5212 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)";
5213 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5214 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5217 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)))";
5218 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)))";
5219 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5220 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5223 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]) ))[,,, ])))))))";
5224 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5225 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5226 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5229 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5230 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5233 final Phylogeny p10 = factory
5234 .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]",
5235 new NHXParser() )[ 0 ];
5236 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5240 catch ( final Exception e ) {
5241 e.printStackTrace( System.out );
5247 private static boolean testNHXParsingQuotes() {
5249 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5250 final NHXParser p = new NHXParser();
5251 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5252 if ( phylogenies_0.length != 5 ) {
5255 final Phylogeny phy = phylogenies_0[ 4 ];
5256 if ( phy.getNumberOfExternalNodes() != 7 ) {
5259 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5262 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5265 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5266 .getScientificName().equals( "hsapiens" ) ) {
5269 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5272 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5275 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5278 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5281 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5284 final NHXParser p1p = new NHXParser();
5285 p1p.setIgnoreQuotes( true );
5286 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5287 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5290 final NHXParser p2p = new NHXParser();
5291 p1p.setIgnoreQuotes( false );
5292 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5293 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5296 final NHXParser p3p = new NHXParser();
5297 p3p.setIgnoreQuotes( false );
5298 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5299 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5302 final NHXParser p4p = new NHXParser();
5303 p4p.setIgnoreQuotes( false );
5304 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5305 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5308 final Phylogeny p10 = factory
5309 .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]",
5310 new NHXParser() )[ 0 ];
5311 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]";
5312 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5315 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5316 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5320 final Phylogeny p12 = factory
5321 .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]",
5322 new NHXParser() )[ 0 ];
5323 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]";
5324 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5327 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5328 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5331 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;";
5332 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5335 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5336 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5340 catch ( final Exception e ) {
5341 e.printStackTrace( System.out );
5347 private static boolean testNHXParsingMB() {
5349 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5350 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5351 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5352 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5353 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5354 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5355 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5356 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5357 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5358 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5359 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5362 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5365 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5366 0.1100000000000000e+00 ) ) {
5369 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5372 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5375 final Phylogeny p2 = factory
5376 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5377 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5378 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5379 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5380 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5381 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5382 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5383 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5384 + "7.369400000000000e-02}])",
5385 new NHXParser() )[ 0 ];
5386 if ( p2.getNode( "1" ) == null ) {
5389 if ( p2.getNode( "2" ) == null ) {
5393 catch ( final Exception e ) {
5394 e.printStackTrace( System.out );
5401 private static boolean testPhylogenyBranch() {
5403 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5404 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5405 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5406 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5407 if ( !a1b1.equals( a1b1 ) ) {
5410 if ( !a1b1.equals( b1a1 ) ) {
5413 if ( !b1a1.equals( a1b1 ) ) {
5416 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5417 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5418 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5419 if ( a1_b1.equals( b1_a1 ) ) {
5422 if ( a1_b1.equals( a1_b1_ ) ) {
5425 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5426 if ( !a1_b1.equals( b1_a1_ ) ) {
5429 if ( a1_b1_.equals( b1_a1_ ) ) {
5432 if ( !a1_b1_.equals( b1_a1 ) ) {
5436 catch ( final Exception e ) {
5437 e.printStackTrace( System.out );
5443 private static boolean testPhyloXMLparsingOfDistributionElement() {
5445 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5446 PhyloXmlParser xml_parser = null;
5448 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5450 catch ( final Exception e ) {
5451 // Do nothing -- means were not running from jar.
5453 if ( xml_parser == null ) {
5454 xml_parser = new PhyloXmlParser();
5455 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5456 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5459 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5462 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5464 if ( xml_parser.getErrorCount() > 0 ) {
5465 System.out.println( xml_parser.getErrorMessages().toString() );
5468 if ( phylogenies_0.length != 1 ) {
5471 final Phylogeny t1 = phylogenies_0[ 0 ];
5472 PhylogenyNode n = null;
5473 Distribution d = null;
5474 n = t1.getNode( "root node" );
5475 if ( !n.getNodeData().isHasDistribution() ) {
5478 if ( n.getNodeData().getDistributions().size() != 1 ) {
5481 d = n.getNodeData().getDistribution();
5482 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5485 if ( d.getPoints().size() != 1 ) {
5488 if ( d.getPolygons() != null ) {
5491 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5494 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5497 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5500 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5503 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5506 n = t1.getNode( "node a" );
5507 if ( !n.getNodeData().isHasDistribution() ) {
5510 if ( n.getNodeData().getDistributions().size() != 2 ) {
5513 d = n.getNodeData().getDistribution( 1 );
5514 if ( !d.getDesc().equals( "San Diego" ) ) {
5517 if ( d.getPoints().size() != 1 ) {
5520 if ( d.getPolygons() != null ) {
5523 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5526 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5529 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5532 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5535 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5538 n = t1.getNode( "node bb" );
5539 if ( !n.getNodeData().isHasDistribution() ) {
5542 if ( n.getNodeData().getDistributions().size() != 1 ) {
5545 d = n.getNodeData().getDistribution( 0 );
5546 if ( d.getPoints().size() != 3 ) {
5549 if ( d.getPolygons().size() != 2 ) {
5552 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5555 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5558 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5561 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5564 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5567 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5570 Polygon p = d.getPolygons().get( 0 );
5571 if ( p.getPoints().size() != 3 ) {
5574 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5577 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5580 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5583 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5586 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5589 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5592 p = d.getPolygons().get( 1 );
5593 if ( p.getPoints().size() != 3 ) {
5596 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5599 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5602 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5606 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5607 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5608 if ( rt.length != 1 ) {
5611 final Phylogeny t1_rt = rt[ 0 ];
5612 n = t1_rt.getNode( "root node" );
5613 if ( !n.getNodeData().isHasDistribution() ) {
5616 if ( n.getNodeData().getDistributions().size() != 1 ) {
5619 d = n.getNodeData().getDistribution();
5620 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5623 if ( d.getPoints().size() != 1 ) {
5626 if ( d.getPolygons() != null ) {
5629 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5632 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5635 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5638 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5641 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5644 n = t1_rt.getNode( "node a" );
5645 if ( !n.getNodeData().isHasDistribution() ) {
5648 if ( n.getNodeData().getDistributions().size() != 2 ) {
5651 d = n.getNodeData().getDistribution( 1 );
5652 if ( !d.getDesc().equals( "San Diego" ) ) {
5655 if ( d.getPoints().size() != 1 ) {
5658 if ( d.getPolygons() != null ) {
5661 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5664 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5667 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5670 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5673 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5676 n = t1_rt.getNode( "node bb" );
5677 if ( !n.getNodeData().isHasDistribution() ) {
5680 if ( n.getNodeData().getDistributions().size() != 1 ) {
5683 d = n.getNodeData().getDistribution( 0 );
5684 if ( d.getPoints().size() != 3 ) {
5687 if ( d.getPolygons().size() != 2 ) {
5690 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5693 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5696 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5699 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5702 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5705 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5708 p = d.getPolygons().get( 0 );
5709 if ( p.getPoints().size() != 3 ) {
5712 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5715 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5718 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5721 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5724 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5727 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5730 p = d.getPolygons().get( 1 );
5731 if ( p.getPoints().size() != 3 ) {
5734 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5737 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5740 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5744 catch ( final Exception e ) {
5745 e.printStackTrace( System.out );
5751 private static boolean testPostOrderIterator() {
5753 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5754 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5755 PhylogenyNodeIterator it0;
5756 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5759 for( it0.reset(); it0.hasNext(); ) {
5762 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5763 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5764 if ( !it.next().getName().equals( "A" ) ) {
5767 if ( !it.next().getName().equals( "B" ) ) {
5770 if ( !it.next().getName().equals( "ab" ) ) {
5773 if ( !it.next().getName().equals( "C" ) ) {
5776 if ( !it.next().getName().equals( "D" ) ) {
5779 if ( !it.next().getName().equals( "cd" ) ) {
5782 if ( !it.next().getName().equals( "abcd" ) ) {
5785 if ( !it.next().getName().equals( "E" ) ) {
5788 if ( !it.next().getName().equals( "F" ) ) {
5791 if ( !it.next().getName().equals( "ef" ) ) {
5794 if ( !it.next().getName().equals( "G" ) ) {
5797 if ( !it.next().getName().equals( "H" ) ) {
5800 if ( !it.next().getName().equals( "gh" ) ) {
5803 if ( !it.next().getName().equals( "efgh" ) ) {
5806 if ( !it.next().getName().equals( "r" ) ) {
5809 if ( it.hasNext() ) {
5813 catch ( final Exception e ) {
5814 e.printStackTrace( System.out );
5820 private static boolean testPreOrderIterator() {
5822 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5823 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5824 PhylogenyNodeIterator it0;
5825 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5828 for( it0.reset(); it0.hasNext(); ) {
5831 PhylogenyNodeIterator it = t0.iteratorPreorder();
5832 if ( !it.next().getName().equals( "r" ) ) {
5835 if ( !it.next().getName().equals( "ab" ) ) {
5838 if ( !it.next().getName().equals( "A" ) ) {
5841 if ( !it.next().getName().equals( "B" ) ) {
5844 if ( !it.next().getName().equals( "cd" ) ) {
5847 if ( !it.next().getName().equals( "C" ) ) {
5850 if ( !it.next().getName().equals( "D" ) ) {
5853 if ( it.hasNext() ) {
5856 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5857 it = t1.iteratorPreorder();
5858 if ( !it.next().getName().equals( "r" ) ) {
5861 if ( !it.next().getName().equals( "abcd" ) ) {
5864 if ( !it.next().getName().equals( "ab" ) ) {
5867 if ( !it.next().getName().equals( "A" ) ) {
5870 if ( !it.next().getName().equals( "B" ) ) {
5873 if ( !it.next().getName().equals( "cd" ) ) {
5876 if ( !it.next().getName().equals( "C" ) ) {
5879 if ( !it.next().getName().equals( "D" ) ) {
5882 if ( !it.next().getName().equals( "efgh" ) ) {
5885 if ( !it.next().getName().equals( "ef" ) ) {
5888 if ( !it.next().getName().equals( "E" ) ) {
5891 if ( !it.next().getName().equals( "F" ) ) {
5894 if ( !it.next().getName().equals( "gh" ) ) {
5897 if ( !it.next().getName().equals( "G" ) ) {
5900 if ( !it.next().getName().equals( "H" ) ) {
5903 if ( it.hasNext() ) {
5907 catch ( final Exception e ) {
5908 e.printStackTrace( System.out );
5914 private static boolean testPropertiesMap() {
5916 final PropertiesMap pm = new PropertiesMap();
5917 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5918 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5919 final Property p2 = new Property( "something:else",
5921 "improbable:research",
5924 pm.addProperty( p0 );
5925 pm.addProperty( p1 );
5926 pm.addProperty( p2 );
5927 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5930 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5933 if ( pm.getProperties().size() != 3 ) {
5936 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5939 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5942 if ( pm.getProperties().size() != 3 ) {
5945 pm.removeProperty( "dimensions:diameter" );
5946 if ( pm.getProperties().size() != 2 ) {
5949 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5952 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5956 catch ( final Exception e ) {
5957 e.printStackTrace( System.out );
5963 private static boolean testReIdMethods() {
5965 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5966 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5967 final int count = PhylogenyNode.getNodeCount();
5969 if ( p.getNode( "r" ).getId() != count ) {
5972 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
5975 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
5978 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
5981 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
5984 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
5987 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
5990 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
5993 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
5996 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
5999 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6002 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6005 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6008 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6011 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6015 catch ( final Exception e ) {
6016 e.printStackTrace( System.out );
6022 private static boolean testRerooting() {
6024 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6025 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",
6026 new NHXParser() )[ 0 ];
6027 if ( !t1.isRooted() ) {
6030 t1.reRoot( t1.getNode( "D" ) );
6031 t1.reRoot( t1.getNode( "CD" ) );
6032 t1.reRoot( t1.getNode( "A" ) );
6033 t1.reRoot( t1.getNode( "B" ) );
6034 t1.reRoot( t1.getNode( "AB" ) );
6035 t1.reRoot( t1.getNode( "D" ) );
6036 t1.reRoot( t1.getNode( "C" ) );
6037 t1.reRoot( t1.getNode( "CD" ) );
6038 t1.reRoot( t1.getNode( "A" ) );
6039 t1.reRoot( t1.getNode( "B" ) );
6040 t1.reRoot( t1.getNode( "AB" ) );
6041 t1.reRoot( t1.getNode( "D" ) );
6042 t1.reRoot( t1.getNode( "D" ) );
6043 t1.reRoot( t1.getNode( "C" ) );
6044 t1.reRoot( t1.getNode( "A" ) );
6045 t1.reRoot( t1.getNode( "B" ) );
6046 t1.reRoot( t1.getNode( "AB" ) );
6047 t1.reRoot( t1.getNode( "C" ) );
6048 t1.reRoot( t1.getNode( "D" ) );
6049 t1.reRoot( t1.getNode( "CD" ) );
6050 t1.reRoot( t1.getNode( "D" ) );
6051 t1.reRoot( t1.getNode( "A" ) );
6052 t1.reRoot( t1.getNode( "B" ) );
6053 t1.reRoot( t1.getNode( "AB" ) );
6054 t1.reRoot( t1.getNode( "C" ) );
6055 t1.reRoot( t1.getNode( "D" ) );
6056 t1.reRoot( t1.getNode( "CD" ) );
6057 t1.reRoot( t1.getNode( "D" ) );
6058 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6061 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6064 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6067 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6070 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6073 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6076 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",
6077 new NHXParser() )[ 0 ];
6078 t2.reRoot( t2.getNode( "A" ) );
6079 t2.reRoot( t2.getNode( "D" ) );
6080 t2.reRoot( t2.getNode( "ABC" ) );
6081 t2.reRoot( t2.getNode( "A" ) );
6082 t2.reRoot( t2.getNode( "B" ) );
6083 t2.reRoot( t2.getNode( "D" ) );
6084 t2.reRoot( t2.getNode( "C" ) );
6085 t2.reRoot( t2.getNode( "ABC" ) );
6086 t2.reRoot( t2.getNode( "A" ) );
6087 t2.reRoot( t2.getNode( "B" ) );
6088 t2.reRoot( t2.getNode( "AB" ) );
6089 t2.reRoot( t2.getNode( "AB" ) );
6090 t2.reRoot( t2.getNode( "D" ) );
6091 t2.reRoot( t2.getNode( "C" ) );
6092 t2.reRoot( t2.getNode( "B" ) );
6093 t2.reRoot( t2.getNode( "AB" ) );
6094 t2.reRoot( t2.getNode( "D" ) );
6095 t2.reRoot( t2.getNode( "D" ) );
6096 t2.reRoot( t2.getNode( "ABC" ) );
6097 t2.reRoot( t2.getNode( "A" ) );
6098 t2.reRoot( t2.getNode( "B" ) );
6099 t2.reRoot( t2.getNode( "AB" ) );
6100 t2.reRoot( t2.getNode( "D" ) );
6101 t2.reRoot( t2.getNode( "C" ) );
6102 t2.reRoot( t2.getNode( "ABC" ) );
6103 t2.reRoot( t2.getNode( "A" ) );
6104 t2.reRoot( t2.getNode( "B" ) );
6105 t2.reRoot( t2.getNode( "AB" ) );
6106 t2.reRoot( t2.getNode( "D" ) );
6107 t2.reRoot( t2.getNode( "D" ) );
6108 t2.reRoot( t2.getNode( "C" ) );
6109 t2.reRoot( t2.getNode( "A" ) );
6110 t2.reRoot( t2.getNode( "B" ) );
6111 t2.reRoot( t2.getNode( "AB" ) );
6112 t2.reRoot( t2.getNode( "C" ) );
6113 t2.reRoot( t2.getNode( "D" ) );
6114 t2.reRoot( t2.getNode( "ABC" ) );
6115 t2.reRoot( t2.getNode( "D" ) );
6116 t2.reRoot( t2.getNode( "A" ) );
6117 t2.reRoot( t2.getNode( "B" ) );
6118 t2.reRoot( t2.getNode( "AB" ) );
6119 t2.reRoot( t2.getNode( "C" ) );
6120 t2.reRoot( t2.getNode( "D" ) );
6121 t2.reRoot( t2.getNode( "ABC" ) );
6122 t2.reRoot( t2.getNode( "D" ) );
6123 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6126 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6129 t2.reRoot( t2.getNode( "ABC" ) );
6130 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6133 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6136 t2.reRoot( t2.getNode( "AB" ) );
6137 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6140 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6143 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6146 t2.reRoot( t2.getNode( "AB" ) );
6147 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6150 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6153 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6156 t2.reRoot( t2.getNode( "D" ) );
6157 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6160 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6163 t2.reRoot( t2.getNode( "ABC" ) );
6164 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6167 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6170 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6171 new NHXParser() )[ 0 ];
6172 t3.reRoot( t3.getNode( "B" ) );
6173 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6176 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6179 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6182 t3.reRoot( t3.getNode( "B" ) );
6183 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6186 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6189 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6192 t3.reRoot( t3.getRoot() );
6193 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6196 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6199 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6203 catch ( final Exception e ) {
6204 e.printStackTrace( System.out );
6210 private static boolean testSDIse() {
6212 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6213 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6214 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6215 gene1.setRooted( true );
6216 species1.setRooted( true );
6217 final SDI sdi = new SDIse( gene1, species1 );
6218 if ( !gene1.getRoot().isDuplication() ) {
6221 final Phylogeny species2 = factory
6222 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6223 new NHXParser() )[ 0 ];
6224 final Phylogeny gene2 = factory
6225 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6226 new NHXParser() )[ 0 ];
6227 species2.setRooted( true );
6228 gene2.setRooted( true );
6229 final SDI sdi2 = new SDIse( gene2, species2 );
6230 if ( sdi2.getDuplicationsSum() != 0 ) {
6233 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6236 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6239 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6242 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6245 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6248 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6251 final Phylogeny species3 = factory
6252 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6253 new NHXParser() )[ 0 ];
6254 final Phylogeny gene3 = factory
6255 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6256 new NHXParser() )[ 0 ];
6257 species3.setRooted( true );
6258 gene3.setRooted( true );
6259 final SDI sdi3 = new SDIse( gene3, species3 );
6260 if ( sdi3.getDuplicationsSum() != 1 ) {
6263 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6266 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6269 final Phylogeny species4 = factory
6270 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6271 new NHXParser() )[ 0 ];
6272 final Phylogeny gene4 = factory
6273 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6274 new NHXParser() )[ 0 ];
6275 species4.setRooted( true );
6276 gene4.setRooted( true );
6277 final SDI sdi4 = new SDIse( gene4, species4 );
6278 if ( sdi4.getDuplicationsSum() != 1 ) {
6281 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6284 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6287 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6290 if ( species4.getNumberOfExternalNodes() != 6 ) {
6293 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6296 final Phylogeny species5 = factory
6297 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6298 new NHXParser() )[ 0 ];
6299 final Phylogeny gene5 = factory
6300 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6301 new NHXParser() )[ 0 ];
6302 species5.setRooted( true );
6303 gene5.setRooted( true );
6304 final SDI sdi5 = new SDIse( gene5, species5 );
6305 if ( sdi5.getDuplicationsSum() != 2 ) {
6308 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6311 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6314 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6317 if ( species5.getNumberOfExternalNodes() != 6 ) {
6320 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6323 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6324 // Conjecture for Comparing Molecular Phylogenies"
6325 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6326 final Phylogeny species6 = factory
6327 .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,"
6328 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6329 new NHXParser() )[ 0 ];
6330 final Phylogeny gene6 = factory
6331 .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,"
6332 + "((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,"
6333 + "(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;",
6334 new NHXParser() )[ 0 ];
6335 species6.setRooted( true );
6336 gene6.setRooted( true );
6337 final SDI sdi6 = new SDIse( gene6, species6 );
6338 if ( sdi6.getDuplicationsSum() != 3 ) {
6341 if ( !gene6.getNode( "r" ).isDuplication() ) {
6344 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6347 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6350 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6353 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6356 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6359 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6362 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6365 sdi6.computeMappingCostL();
6366 if ( sdi6.computeMappingCostL() != 17 ) {
6369 if ( species6.getNumberOfExternalNodes() != 9 ) {
6372 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6375 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6376 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6377 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6378 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6379 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6380 species7.setRooted( true );
6381 final Phylogeny gene7_1 = Test
6382 .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])" );
6383 gene7_1.setRooted( true );
6384 final SDI sdi7 = new SDIse( gene7_1, species7 );
6385 if ( sdi7.getDuplicationsSum() != 0 ) {
6388 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6391 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6394 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6397 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6400 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6403 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6406 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6409 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6412 final Phylogeny gene7_2 = Test
6413 .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])" );
6414 gene7_2.setRooted( true );
6415 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6416 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6419 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6422 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6425 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6428 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6431 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6434 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6437 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6440 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6443 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6447 catch ( final Exception e ) {
6453 private static boolean testSDIunrooted() {
6455 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6456 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6457 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6458 final Iterator<PhylogenyBranch> iter = l.iterator();
6459 PhylogenyBranch br = iter.next();
6460 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6463 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6467 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6470 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6474 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6477 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6481 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6484 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6488 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6491 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6495 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6498 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6502 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6505 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6509 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6512 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6516 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6519 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6523 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6526 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6530 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6533 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6537 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6540 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6544 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6547 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6551 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6554 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6558 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6561 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6564 if ( iter.hasNext() ) {
6567 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6568 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6569 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6571 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6574 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6578 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6581 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6585 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6588 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6591 if ( iter1.hasNext() ) {
6594 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6595 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6596 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6598 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6601 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6605 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6608 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6612 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6615 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6618 if ( iter2.hasNext() ) {
6621 final Phylogeny species0 = factory
6622 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6623 new NHXParser() )[ 0 ];
6624 final Phylogeny gene1 = factory
6625 .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])",
6626 new NHXParser() )[ 0 ];
6627 species0.setRooted( true );
6628 gene1.setRooted( true );
6629 final SDIR sdi_unrooted = new SDIR();
6630 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6631 if ( sdi_unrooted.getCount() != 1 ) {
6634 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6637 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6640 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6643 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6646 final Phylogeny gene2 = factory
6647 .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])",
6648 new NHXParser() )[ 0 ];
6649 gene2.setRooted( true );
6650 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6651 if ( sdi_unrooted.getCount() != 1 ) {
6654 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6657 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6660 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6663 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6666 final Phylogeny species6 = factory
6667 .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,"
6668 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6669 new NHXParser() )[ 0 ];
6670 final Phylogeny gene6 = factory
6671 .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],"
6672 + "(((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],"
6673 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6674 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6675 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6676 new NHXParser() )[ 0 ];
6677 species6.setRooted( true );
6678 gene6.setRooted( true );
6679 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6680 if ( sdi_unrooted.getCount() != 1 ) {
6683 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6686 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6689 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6692 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6695 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6698 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6701 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6704 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6707 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6710 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6713 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6716 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6720 final Phylogeny species7 = factory
6721 .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,"
6722 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6723 new NHXParser() )[ 0 ];
6724 final Phylogeny gene7 = factory
6725 .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],"
6726 + "(((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],"
6727 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6728 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6729 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6730 new NHXParser() )[ 0 ];
6731 species7.setRooted( true );
6732 gene7.setRooted( true );
6733 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6734 if ( sdi_unrooted.getCount() != 1 ) {
6737 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6740 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6743 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6746 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6749 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6752 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6755 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6758 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6761 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6764 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6767 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6770 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6774 final Phylogeny species8 = factory
6775 .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,"
6776 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6777 new NHXParser() )[ 0 ];
6778 final Phylogeny gene8 = factory
6779 .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],"
6780 + "(((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],"
6781 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6782 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6783 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6784 new NHXParser() )[ 0 ];
6785 species8.setRooted( true );
6786 gene8.setRooted( true );
6787 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6788 if ( sdi_unrooted.getCount() != 1 ) {
6791 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6794 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6797 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6800 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6803 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6806 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6809 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6812 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6815 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6818 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6821 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6824 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6829 catch ( final Exception e ) {
6830 e.printStackTrace( System.out );
6836 private static boolean testOrthologTable() {
6838 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6839 final Phylogeny s1 = factory.create( Test.PATH_TO_TEST_DATA + "rio_species.xml", new PhyloXmlParser() )[ 0 ];
6840 final NHXParser p = new NHXParser();
6841 p.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
6842 final Phylogeny g1[] = factory.create( new File( Test.PATH_TO_TEST_DATA
6843 + "rio_Bcl-2_e1_20_mafft_05_40_fme.mlt" ), p );
6844 for( final Phylogeny gt : g1 ) {
6845 gt.setRooted( true );
6846 final GSDI sdi = new GSDI( gt, s1, true, true, true );
6848 final IntMatrix m = RIO.calculateOrthologTable( g1 );
6849 // System.out.println( m.toString() );
6851 catch ( final Exception e ) {
6852 e.printStackTrace();
6858 private static boolean testSplit() {
6860 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6861 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6862 //Archaeopteryx.createApplication( p0 );
6863 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6864 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6865 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6866 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6867 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6868 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6869 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6870 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6871 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6872 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6873 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6874 // System.out.println( s0.toString() );
6876 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6877 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6879 if ( s0.match( query_nodes ) ) {
6882 query_nodes = new HashSet<PhylogenyNode>();
6883 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6890 if ( !s0.match( query_nodes ) ) {
6894 query_nodes = new HashSet<PhylogenyNode>();
6895 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6898 if ( !s0.match( query_nodes ) ) {
6902 query_nodes = new HashSet<PhylogenyNode>();
6903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6907 if ( !s0.match( query_nodes ) ) {
6911 query_nodes = new HashSet<PhylogenyNode>();
6912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6916 if ( !s0.match( query_nodes ) ) {
6920 query_nodes = new HashSet<PhylogenyNode>();
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6924 if ( !s0.match( query_nodes ) ) {
6928 query_nodes = new HashSet<PhylogenyNode>();
6929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6931 if ( !s0.match( query_nodes ) ) {
6935 query_nodes = new HashSet<PhylogenyNode>();
6936 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6937 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6941 if ( !s0.match( query_nodes ) ) {
6945 query_nodes = new HashSet<PhylogenyNode>();
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6949 if ( !s0.match( query_nodes ) ) {
6953 query_nodes = new HashSet<PhylogenyNode>();
6954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6958 if ( !s0.match( query_nodes ) ) {
6962 query_nodes = new HashSet<PhylogenyNode>();
6963 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6965 if ( s0.match( query_nodes ) ) {
6969 query_nodes = new HashSet<PhylogenyNode>();
6970 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6971 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6974 if ( s0.match( query_nodes ) ) {
6978 query_nodes = new HashSet<PhylogenyNode>();
6979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6984 if ( s0.match( query_nodes ) ) {
6988 query_nodes = new HashSet<PhylogenyNode>();
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6992 if ( s0.match( query_nodes ) ) {
6996 query_nodes = new HashSet<PhylogenyNode>();
6997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6999 if ( s0.match( query_nodes ) ) {
7003 query_nodes = new HashSet<PhylogenyNode>();
7004 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7006 if ( s0.match( query_nodes ) ) {
7010 query_nodes = new HashSet<PhylogenyNode>();
7011 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7013 if ( s0.match( query_nodes ) ) {
7017 query_nodes = new HashSet<PhylogenyNode>();
7018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7019 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7020 if ( s0.match( query_nodes ) ) {
7024 query_nodes = new HashSet<PhylogenyNode>();
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
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( "G" ) );
7034 if ( s0.match( query_nodes ) ) {
7038 query_nodes = new HashSet<PhylogenyNode>();
7039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
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 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7050 if ( s0.match( query_nodes ) ) {
7054 query_nodes = new HashSet<PhylogenyNode>();
7055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7056 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7057 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7058 if ( s0.match( query_nodes ) ) {
7062 query_nodes = new HashSet<PhylogenyNode>();
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7067 if ( s0.match( query_nodes ) ) {
7071 // query_nodes = new HashSet<PhylogenyNode>();
7072 // query_nodes.add( new PhylogenyNode( "X" ) );
7073 // query_nodes.add( new PhylogenyNode( "Y" ) );
7074 // query_nodes.add( new PhylogenyNode( "A" ) );
7075 // query_nodes.add( new PhylogenyNode( "B" ) );
7076 // query_nodes.add( new PhylogenyNode( "C" ) );
7077 // query_nodes.add( new PhylogenyNode( "D" ) );
7078 // query_nodes.add( new PhylogenyNode( "E" ) );
7079 // query_nodes.add( new PhylogenyNode( "F" ) );
7080 // query_nodes.add( new PhylogenyNode( "G" ) );
7081 // if ( !s0.match( query_nodes ) ) {
7084 // query_nodes = new HashSet<PhylogenyNode>();
7085 // query_nodes.add( new PhylogenyNode( "X" ) );
7086 // query_nodes.add( new PhylogenyNode( "Y" ) );
7087 // query_nodes.add( new PhylogenyNode( "A" ) );
7088 // query_nodes.add( new PhylogenyNode( "B" ) );
7089 // query_nodes.add( new PhylogenyNode( "C" ) );
7090 // if ( !s0.match( query_nodes ) ) {
7094 // query_nodes = new HashSet<PhylogenyNode>();
7095 // query_nodes.add( new PhylogenyNode( "X" ) );
7096 // query_nodes.add( new PhylogenyNode( "Y" ) );
7097 // query_nodes.add( new PhylogenyNode( "D" ) );
7098 // query_nodes.add( new PhylogenyNode( "E" ) );
7099 // query_nodes.add( new PhylogenyNode( "F" ) );
7100 // query_nodes.add( new PhylogenyNode( "G" ) );
7101 // if ( !s0.match( query_nodes ) ) {
7105 // query_nodes = new HashSet<PhylogenyNode>();
7106 // query_nodes.add( new PhylogenyNode( "X" ) );
7107 // query_nodes.add( new PhylogenyNode( "Y" ) );
7108 // query_nodes.add( new PhylogenyNode( "A" ) );
7109 // query_nodes.add( new PhylogenyNode( "B" ) );
7110 // query_nodes.add( new PhylogenyNode( "C" ) );
7111 // query_nodes.add( new PhylogenyNode( "D" ) );
7112 // if ( !s0.match( query_nodes ) ) {
7116 // query_nodes = new HashSet<PhylogenyNode>();
7117 // query_nodes.add( new PhylogenyNode( "X" ) );
7118 // query_nodes.add( new PhylogenyNode( "Y" ) );
7119 // query_nodes.add( new PhylogenyNode( "E" ) );
7120 // query_nodes.add( new PhylogenyNode( "F" ) );
7121 // query_nodes.add( new PhylogenyNode( "G" ) );
7122 // if ( !s0.match( query_nodes ) ) {
7126 // query_nodes = new HashSet<PhylogenyNode>();
7127 // query_nodes.add( new PhylogenyNode( "X" ) );
7128 // query_nodes.add( new PhylogenyNode( "Y" ) );
7129 // query_nodes.add( new PhylogenyNode( "F" ) );
7130 // query_nodes.add( new PhylogenyNode( "G" ) );
7131 // if ( !s0.match( query_nodes ) ) {
7135 query_nodes = new HashSet<PhylogenyNode>();
7136 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7137 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7140 if ( s0.match( query_nodes ) ) {
7144 query_nodes = new HashSet<PhylogenyNode>();
7145 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7147 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7148 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7149 if ( s0.match( query_nodes ) ) {
7152 ///////////////////////////
7154 query_nodes = new HashSet<PhylogenyNode>();
7155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7159 if ( s0.match( query_nodes ) ) {
7163 query_nodes = new HashSet<PhylogenyNode>();
7164 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7165 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7168 if ( s0.match( query_nodes ) ) {
7172 query_nodes = new HashSet<PhylogenyNode>();
7173 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7177 if ( s0.match( query_nodes ) ) {
7181 query_nodes = new HashSet<PhylogenyNode>();
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7184 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7186 if ( s0.match( query_nodes ) ) {
7190 query_nodes = new HashSet<PhylogenyNode>();
7191 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7192 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7195 if ( s0.match( query_nodes ) ) {
7199 query_nodes = new HashSet<PhylogenyNode>();
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7203 if ( s0.match( query_nodes ) ) {
7207 query_nodes = new HashSet<PhylogenyNode>();
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7209 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7210 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7211 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7212 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7213 if ( s0.match( query_nodes ) ) {
7217 query_nodes = new HashSet<PhylogenyNode>();
7218 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7223 if ( s0.match( query_nodes ) ) {
7227 query_nodes = new HashSet<PhylogenyNode>();
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7230 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7232 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7233 if ( s0.match( query_nodes ) ) {
7237 query_nodes = new HashSet<PhylogenyNode>();
7238 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7239 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7240 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7241 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7242 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7244 if ( s0.match( query_nodes ) ) {
7248 catch ( final Exception e ) {
7249 e.printStackTrace();
7255 private static boolean testSplitStrict() {
7257 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7258 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7259 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7260 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7261 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7262 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7263 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7264 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7265 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7266 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7267 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7268 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7269 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7271 if ( s0.match( query_nodes ) ) {
7274 query_nodes = new HashSet<PhylogenyNode>();
7275 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7276 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7277 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7278 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7279 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7280 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7281 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7282 if ( !s0.match( query_nodes ) ) {
7286 query_nodes = new HashSet<PhylogenyNode>();
7287 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7288 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7289 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7290 if ( !s0.match( query_nodes ) ) {
7294 query_nodes = new HashSet<PhylogenyNode>();
7295 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7297 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7298 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7299 if ( !s0.match( query_nodes ) ) {
7303 query_nodes = new HashSet<PhylogenyNode>();
7304 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7305 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7306 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7307 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7308 if ( !s0.match( query_nodes ) ) {
7312 query_nodes = new HashSet<PhylogenyNode>();
7313 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7314 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7315 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7316 if ( !s0.match( query_nodes ) ) {
7320 query_nodes = new HashSet<PhylogenyNode>();
7321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7322 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7323 if ( !s0.match( query_nodes ) ) {
7327 query_nodes = new HashSet<PhylogenyNode>();
7328 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7329 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7330 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7332 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7333 if ( !s0.match( query_nodes ) ) {
7337 query_nodes = new HashSet<PhylogenyNode>();
7338 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7341 if ( !s0.match( query_nodes ) ) {
7345 query_nodes = new HashSet<PhylogenyNode>();
7346 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7347 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7350 if ( !s0.match( query_nodes ) ) {
7354 query_nodes = new HashSet<PhylogenyNode>();
7355 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7357 if ( s0.match( query_nodes ) ) {
7361 query_nodes = new HashSet<PhylogenyNode>();
7362 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7363 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7366 if ( s0.match( query_nodes ) ) {
7370 query_nodes = new HashSet<PhylogenyNode>();
7371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7375 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7376 if ( s0.match( query_nodes ) ) {
7380 query_nodes = new HashSet<PhylogenyNode>();
7381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7383 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7384 if ( s0.match( query_nodes ) ) {
7388 query_nodes = new HashSet<PhylogenyNode>();
7389 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7391 if ( s0.match( query_nodes ) ) {
7395 query_nodes = new HashSet<PhylogenyNode>();
7396 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7397 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7398 if ( s0.match( query_nodes ) ) {
7402 query_nodes = new HashSet<PhylogenyNode>();
7403 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7404 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7405 if ( s0.match( query_nodes ) ) {
7409 query_nodes = new HashSet<PhylogenyNode>();
7410 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7411 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7412 if ( s0.match( query_nodes ) ) {
7416 query_nodes = new HashSet<PhylogenyNode>();
7417 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7418 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
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( "G" ) );
7426 if ( s0.match( query_nodes ) ) {
7430 query_nodes = new HashSet<PhylogenyNode>();
7431 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7432 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
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 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7442 if ( s0.match( query_nodes ) ) {
7446 query_nodes = new HashSet<PhylogenyNode>();
7447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7448 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7449 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7450 if ( s0.match( query_nodes ) ) {
7454 query_nodes = new HashSet<PhylogenyNode>();
7455 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7456 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7457 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7458 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7459 if ( s0.match( query_nodes ) ) {
7463 catch ( final Exception e ) {
7464 e.printStackTrace();
7470 private static boolean testSubtreeDeletion() {
7472 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7473 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7474 t1.deleteSubtree( t1.getNode( "A" ), false );
7475 if ( t1.getNumberOfExternalNodes() != 5 ) {
7478 t1.toNewHampshireX();
7479 t1.deleteSubtree( t1.getNode( "E" ), false );
7480 if ( t1.getNumberOfExternalNodes() != 4 ) {
7483 t1.toNewHampshireX();
7484 t1.deleteSubtree( t1.getNode( "F" ), false );
7485 if ( t1.getNumberOfExternalNodes() != 3 ) {
7488 t1.toNewHampshireX();
7489 t1.deleteSubtree( t1.getNode( "D" ), false );
7490 t1.toNewHampshireX();
7491 if ( t1.getNumberOfExternalNodes() != 3 ) {
7494 t1.deleteSubtree( t1.getNode( "def" ), false );
7495 t1.toNewHampshireX();
7496 if ( t1.getNumberOfExternalNodes() != 2 ) {
7499 t1.deleteSubtree( t1.getNode( "B" ), false );
7500 t1.toNewHampshireX();
7501 if ( t1.getNumberOfExternalNodes() != 1 ) {
7504 t1.deleteSubtree( t1.getNode( "C" ), false );
7505 t1.toNewHampshireX();
7506 if ( t1.getNumberOfExternalNodes() != 1 ) {
7509 t1.deleteSubtree( t1.getNode( "abc" ), false );
7510 t1.toNewHampshireX();
7511 if ( t1.getNumberOfExternalNodes() != 1 ) {
7514 t1.deleteSubtree( t1.getNode( "r" ), false );
7515 if ( t1.getNumberOfExternalNodes() != 0 ) {
7518 if ( !t1.isEmpty() ) {
7521 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7522 t2.deleteSubtree( t2.getNode( "A" ), false );
7523 t2.toNewHampshireX();
7524 if ( t2.getNumberOfExternalNodes() != 5 ) {
7527 t2.deleteSubtree( t2.getNode( "abc" ), false );
7528 t2.toNewHampshireX();
7529 if ( t2.getNumberOfExternalNodes() != 3 ) {
7532 t2.deleteSubtree( t2.getNode( "def" ), false );
7533 t2.toNewHampshireX();
7534 if ( t2.getNumberOfExternalNodes() != 1 ) {
7538 catch ( final Exception e ) {
7539 e.printStackTrace( System.out );
7545 private static boolean testSupportCount() {
7547 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7548 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7549 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7550 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7551 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7552 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7553 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7555 SupportCount.count( t0_1, phylogenies_1, true, false );
7556 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7557 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7558 + "(((((A,B),C),D),E),((F,G),X))"
7559 + "(((((A,Y),B),C),D),((F,G),E))"
7560 + "(((((A,B),C),D),E),(F,G))"
7561 + "(((((A,B),C),D),E),(F,G))"
7562 + "(((((A,B),C),D),E),(F,G))"
7563 + "(((((A,B),C),D),E),(F,G),Z)"
7564 + "(((((A,B),C),D),E),(F,G))"
7565 + "((((((A,B),C),D),E),F),G)"
7566 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7568 SupportCount.count( t0_2, phylogenies_2, true, false );
7569 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7570 while ( it.hasNext() ) {
7571 final PhylogenyNode n = it.next();
7572 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7576 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7577 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7578 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7579 SupportCount.count( t0_3, phylogenies_3, true, false );
7580 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7581 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7584 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7587 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7590 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7593 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7596 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7599 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7602 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7605 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7608 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7611 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7612 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7613 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7614 SupportCount.count( t0_4, phylogenies_4, true, false );
7615 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7616 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7619 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7622 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7625 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7628 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7631 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7634 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7637 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7640 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7643 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7646 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7647 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7648 double d = SupportCount.compare( b1, a, true, true, true );
7649 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7652 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7653 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7654 d = SupportCount.compare( b2, a, true, true, true );
7655 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7658 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7659 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7660 d = SupportCount.compare( b3, a, true, true, true );
7661 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7664 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7665 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7666 d = SupportCount.compare( b4, a, true, true, false );
7667 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7671 catch ( final Exception e ) {
7672 e.printStackTrace( System.out );
7678 private static boolean testSupportTransfer() {
7680 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7681 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)",
7682 new NHXParser() )[ 0 ];
7683 final Phylogeny p2 = factory
7684 .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 ];
7685 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7688 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7691 support_transfer.moveBranchLengthsToBootstrap( p1 );
7692 support_transfer.transferSupportValues( p1, p2 );
7693 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7696 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7699 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7702 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7705 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7708 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7711 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7714 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7718 catch ( final Exception e ) {
7719 e.printStackTrace( System.out );
7725 private static boolean testUniprotTaxonomySearch() {
7727 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7729 if ( results.size() != 1 ) {
7732 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7735 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7738 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7741 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7744 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7748 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7749 if ( results.size() != 1 ) {
7752 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7755 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7758 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7761 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7764 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7768 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7769 if ( results.size() != 1 ) {
7772 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7775 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7778 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7781 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7784 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7788 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7789 if ( results.size() != 1 ) {
7792 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7795 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7798 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7801 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7804 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7807 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7810 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7813 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7814 .equals( "Nematostella vectensis" ) ) {
7815 System.out.println( results.get( 0 ).getLineage() );
7819 catch ( final IOException e ) {
7820 System.out.println();
7821 System.out.println( "the following might be due to absence internet connection:" );
7822 e.printStackTrace( System.out );
7825 catch ( final Exception e ) {
7831 private static boolean testEmblEntryRetrieval() {
7832 //The format for GenBank Accession numbers are:
7833 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7834 //Protein: 3 letters + 5 numerals
7835 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7836 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7839 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7842 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7845 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7848 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7851 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7854 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7857 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7860 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7863 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7866 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7869 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7872 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7878 private static boolean testUniprotEntryRetrieval() {
7879 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7882 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7885 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7888 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7891 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7894 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7897 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7900 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7903 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7906 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7909 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7912 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7915 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7919 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7920 if ( !entry.getAccession().equals( "P12345" ) ) {
7923 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7926 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7929 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7932 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7936 catch ( final IOException e ) {
7937 System.out.println();
7938 System.out.println( "the following might be due to absence internet connection:" );
7939 e.printStackTrace( System.out );
7942 catch ( final Exception e ) {
7948 private static boolean testWabiTxSearch() {
7951 result = TxSearch.searchSimple( "nematostella" );
7952 result = TxSearch.getTxId( "nematostella" );
7953 if ( !result.equals( "45350" ) ) {
7956 result = TxSearch.getTxName( "45350" );
7957 if ( !result.equals( "Nematostella" ) ) {
7960 result = TxSearch.getTxId( "nematostella vectensis" );
7961 if ( !result.equals( "45351" ) ) {
7964 result = TxSearch.getTxName( "45351" );
7965 if ( !result.equals( "Nematostella vectensis" ) ) {
7968 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7969 if ( !result.equals( "536089" ) ) {
7972 result = TxSearch.getTxName( "536089" );
7973 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7976 final List<String> queries = new ArrayList<String>();
7977 queries.add( "Campylobacter coli" );
7978 queries.add( "Escherichia coli" );
7979 queries.add( "Arabidopsis" );
7980 queries.add( "Trichoplax" );
7981 queries.add( "Samanea saman" );
7982 queries.add( "Kluyveromyces marxianus" );
7983 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7984 queries.add( "Bornavirus parrot/PDD/2008" );
7985 final List<RANKS> ranks = new ArrayList<RANKS>();
7986 ranks.add( RANKS.SUPERKINGDOM );
7987 ranks.add( RANKS.KINGDOM );
7988 ranks.add( RANKS.FAMILY );
7989 ranks.add( RANKS.GENUS );
7990 ranks.add( RANKS.TRIBE );
7991 result = TxSearch.searchLineage( queries, ranks );
7992 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7993 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7995 catch ( final Exception e ) {
7996 System.out.println();
7997 System.out.println( "the following might be due to absence internet connection:" );
7998 e.printStackTrace( System.out );
8004 private static boolean testAminoAcidSequence() {
8006 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8007 if ( aa1.getLength() != 13 ) {
8010 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8013 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8016 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8019 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8020 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8023 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8024 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8027 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8028 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8032 catch ( final Exception e ) {
8033 e.printStackTrace();
8039 private static boolean testCreateBalancedPhylogeny() {
8041 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8042 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8045 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8048 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8049 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8052 if ( p1.getNumberOfExternalNodes() != 100 ) {
8056 catch ( final Exception e ) {
8057 e.printStackTrace();
8063 private static boolean testFastaParser() {
8065 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8068 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8071 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8072 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8075 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8078 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8081 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8084 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8087 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8091 catch ( final Exception e ) {
8092 e.printStackTrace();
8098 private static boolean testGeneralMsaParser() {
8100 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8101 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8102 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8103 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8104 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8105 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8106 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8107 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8108 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8111 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8114 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8117 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8120 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8123 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8126 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8129 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8132 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8135 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8138 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8141 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8144 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8145 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8148 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8151 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8154 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8155 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8158 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8161 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8164 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8165 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8168 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8171 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8175 catch ( final Exception e ) {
8176 e.printStackTrace();
8182 private static boolean testMafft( final String path ) {
8184 final List<String> opts = new ArrayList<String>();
8185 opts.add( "--maxiterate" );
8187 opts.add( "--localpair" );
8188 opts.add( "--quiet" );
8190 final MsaInferrer mafft = Mafft.createInstance( path );
8191 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8192 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8195 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8199 catch ( final Exception e ) {
8200 e.printStackTrace( System.out );
8206 private static boolean testNextNodeWithCollapsing() {
8208 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8210 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8211 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8212 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8213 t0.getNode( "cd" ).setCollapse( true );
8214 t0.getNode( "cde" ).setCollapse( true );
8215 n = t0.getFirstExternalNode();
8216 while ( n != null ) {
8218 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8220 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8223 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8226 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8229 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8232 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8235 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8239 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8240 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8241 t1.getNode( "ab" ).setCollapse( true );
8242 t1.getNode( "cd" ).setCollapse( true );
8243 t1.getNode( "cde" ).setCollapse( true );
8244 n = t1.getNode( "ab" );
8245 ext = new ArrayList<PhylogenyNode>();
8246 while ( n != null ) {
8248 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8250 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8253 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8256 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8259 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8262 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8268 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8269 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8270 t2.getNode( "ab" ).setCollapse( true );
8271 t2.getNode( "cd" ).setCollapse( true );
8272 t2.getNode( "cde" ).setCollapse( true );
8273 t2.getNode( "c" ).setCollapse( true );
8274 t2.getNode( "d" ).setCollapse( true );
8275 t2.getNode( "e" ).setCollapse( true );
8276 t2.getNode( "gh" ).setCollapse( true );
8277 n = t2.getNode( "ab" );
8278 ext = new ArrayList<PhylogenyNode>();
8279 while ( n != null ) {
8281 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8283 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8286 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8289 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8292 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8298 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8299 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8300 t3.getNode( "ab" ).setCollapse( true );
8301 t3.getNode( "cd" ).setCollapse( true );
8302 t3.getNode( "cde" ).setCollapse( true );
8303 t3.getNode( "c" ).setCollapse( true );
8304 t3.getNode( "d" ).setCollapse( true );
8305 t3.getNode( "e" ).setCollapse( true );
8306 t3.getNode( "gh" ).setCollapse( true );
8307 t3.getNode( "fgh" ).setCollapse( true );
8308 n = t3.getNode( "ab" );
8309 ext = new ArrayList<PhylogenyNode>();
8310 while ( n != null ) {
8312 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8314 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8317 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8320 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8326 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8327 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8328 t4.getNode( "ab" ).setCollapse( true );
8329 t4.getNode( "cd" ).setCollapse( true );
8330 t4.getNode( "cde" ).setCollapse( true );
8331 t4.getNode( "c" ).setCollapse( true );
8332 t4.getNode( "d" ).setCollapse( true );
8333 t4.getNode( "e" ).setCollapse( true );
8334 t4.getNode( "gh" ).setCollapse( true );
8335 t4.getNode( "fgh" ).setCollapse( true );
8336 t4.getNode( "abcdefgh" ).setCollapse( true );
8337 n = t4.getNode( "abcdefgh" );
8338 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8343 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8344 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8346 n = t5.getFirstExternalNode();
8347 while ( n != null ) {
8349 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8351 if ( ext.size() != 8 ) {
8354 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8357 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8360 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8363 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8366 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8369 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8372 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8375 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8380 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8381 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8383 t6.getNode( "ab" ).setCollapse( true );
8384 n = t6.getNode( "ab" );
8385 while ( n != null ) {
8387 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8389 if ( ext.size() != 7 ) {
8392 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8395 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8398 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8401 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8404 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8407 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8410 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8415 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8416 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8418 t7.getNode( "cd" ).setCollapse( true );
8419 n = t7.getNode( "a" );
8420 while ( n != null ) {
8422 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8424 if ( ext.size() != 7 ) {
8427 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8430 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8433 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8436 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8439 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8442 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8445 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8450 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8451 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8453 t8.getNode( "cd" ).setCollapse( true );
8454 t8.getNode( "c" ).setCollapse( true );
8455 t8.getNode( "d" ).setCollapse( true );
8456 n = t8.getNode( "a" );
8457 while ( n != null ) {
8459 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8461 if ( ext.size() != 7 ) {
8464 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8467 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8470 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8471 System.out.println( "2 fail" );
8474 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8477 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8480 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8483 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8488 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8489 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8491 t9.getNode( "gh" ).setCollapse( true );
8492 n = t9.getNode( "a" );
8493 while ( n != null ) {
8495 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8497 if ( ext.size() != 7 ) {
8500 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8503 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8506 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8509 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8512 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8515 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8518 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8523 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8524 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8526 t10.getNode( "gh" ).setCollapse( true );
8527 t10.getNode( "g" ).setCollapse( true );
8528 t10.getNode( "h" ).setCollapse( true );
8529 n = t10.getNode( "a" );
8530 while ( n != null ) {
8532 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8534 if ( ext.size() != 7 ) {
8537 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8540 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8543 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8546 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8549 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8552 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8555 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8560 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8561 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8563 t11.getNode( "gh" ).setCollapse( true );
8564 t11.getNode( "fgh" ).setCollapse( true );
8565 n = t11.getNode( "a" );
8566 while ( n != null ) {
8568 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8570 if ( ext.size() != 6 ) {
8573 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8576 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8579 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8582 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8585 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8588 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8593 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8594 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8596 t12.getNode( "gh" ).setCollapse( true );
8597 t12.getNode( "fgh" ).setCollapse( true );
8598 t12.getNode( "g" ).setCollapse( true );
8599 t12.getNode( "h" ).setCollapse( true );
8600 t12.getNode( "f" ).setCollapse( true );
8601 n = t12.getNode( "a" );
8602 while ( n != null ) {
8604 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8606 if ( ext.size() != 6 ) {
8609 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8612 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8615 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8618 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8621 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8624 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8629 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8630 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8632 t13.getNode( "ab" ).setCollapse( true );
8633 t13.getNode( "b" ).setCollapse( true );
8634 t13.getNode( "fgh" ).setCollapse( true );
8635 t13.getNode( "gh" ).setCollapse( true );
8636 n = t13.getNode( "ab" );
8637 while ( n != null ) {
8639 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8641 if ( ext.size() != 5 ) {
8644 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8647 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8650 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8653 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8656 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8661 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8662 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8664 t14.getNode( "ab" ).setCollapse( true );
8665 t14.getNode( "a" ).setCollapse( true );
8666 t14.getNode( "fgh" ).setCollapse( true );
8667 t14.getNode( "gh" ).setCollapse( true );
8668 n = t14.getNode( "ab" );
8669 while ( n != null ) {
8671 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8673 if ( ext.size() != 5 ) {
8676 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8679 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8682 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8685 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8688 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8693 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" );
8694 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8696 t15.getNode( "ab" ).setCollapse( true );
8697 t15.getNode( "a" ).setCollapse( true );
8698 t15.getNode( "fgh" ).setCollapse( true );
8699 t15.getNode( "gh" ).setCollapse( true );
8700 n = t15.getNode( "ab" );
8701 while ( n != null ) {
8703 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8705 if ( ext.size() != 6 ) {
8708 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8711 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8714 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8717 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8720 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8723 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8728 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" );
8729 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8731 t16.getNode( "ab" ).setCollapse( true );
8732 t16.getNode( "a" ).setCollapse( true );
8733 t16.getNode( "fgh" ).setCollapse( true );
8734 t16.getNode( "gh" ).setCollapse( true );
8735 t16.getNode( "cd" ).setCollapse( true );
8736 t16.getNode( "cde" ).setCollapse( true );
8737 t16.getNode( "d" ).setCollapse( true );
8738 t16.getNode( "x" ).setCollapse( true );
8739 n = t16.getNode( "ab" );
8740 while ( n != null ) {
8742 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8744 if ( ext.size() != 4 ) {
8747 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8750 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8753 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8756 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8760 catch ( final Exception e ) {
8761 e.printStackTrace( System.out );
8767 private static boolean testMsaQualityMethod() {
8769 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8770 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8771 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8772 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8773 final List<Sequence> l = new ArrayList<Sequence>();
8778 final Msa msa = BasicMsa.createInstance( l );
8779 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8782 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8785 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8788 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8792 catch ( final Exception e ) {
8793 e.printStackTrace( System.out );
8799 private static boolean testSequenceIdParsing() {
8801 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8802 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8803 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8805 System.out.println( "value =" + id.getValue() );
8806 System.out.println( "provider=" + id.getProvider() );
8811 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8812 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8813 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8815 System.out.println( "value =" + id.getValue() );
8816 System.out.println( "provider=" + id.getProvider() );
8821 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8822 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8823 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8825 System.out.println( "value =" + id.getValue() );
8826 System.out.println( "provider=" + id.getProvider() );
8831 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8832 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8833 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8835 System.out.println( "value =" + id.getValue() );
8836 System.out.println( "provider=" + id.getProvider() );
8841 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8842 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8843 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8845 System.out.println( "value =" + id.getValue() );
8846 System.out.println( "provider=" + id.getProvider() );
8851 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8852 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8853 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8855 System.out.println( "value =" + id.getValue() );
8856 System.out.println( "provider=" + id.getProvider() );
8861 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8862 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8863 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8865 System.out.println( "value =" + id.getValue() );
8866 System.out.println( "provider=" + id.getProvider() );
8871 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8872 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8873 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8875 System.out.println( "value =" + id.getValue() );
8876 System.out.println( "provider=" + id.getProvider() );
8881 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8882 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8883 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8885 System.out.println( "value =" + id.getValue() );
8886 System.out.println( "provider=" + id.getProvider() );
8891 id = SequenceIdParser.parse( "P4A123" );
8892 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8893 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8895 System.out.println( "value =" + id.getValue() );
8896 System.out.println( "provider=" + id.getProvider() );
8901 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
8902 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8903 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8905 System.out.println( "value =" + id.getValue() );
8906 System.out.println( "provider=" + id.getProvider() );
8911 id = SequenceIdParser.parse( "XP_12345" );
8913 System.out.println( "value =" + id.getValue() );
8914 System.out.println( "provider=" + id.getProvider() );
8917 // lcl_91970_unknown_
8919 catch ( final Exception e ) {
8920 e.printStackTrace( System.out );