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: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
56 import org.forester.io.parsers.tol.TolParser;
57 import org.forester.io.parsers.util.ParserUtils;
58 import org.forester.io.writers.PhylogenyWriter;
59 import org.forester.msa.BasicMsa;
60 import org.forester.msa.Mafft;
61 import org.forester.msa.Msa;
62 import org.forester.msa.MsaInferrer;
63 import org.forester.msa.MsaMethods;
64 import org.forester.pccx.TestPccx;
65 import org.forester.phylogeny.Phylogeny;
66 import org.forester.phylogeny.PhylogenyBranch;
67 import org.forester.phylogeny.PhylogenyMethods;
68 import org.forester.phylogeny.PhylogenyNode;
69 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
70 import org.forester.phylogeny.data.BinaryCharacters;
71 import org.forester.phylogeny.data.BranchWidth;
72 import org.forester.phylogeny.data.Confidence;
73 import org.forester.phylogeny.data.Distribution;
74 import org.forester.phylogeny.data.DomainArchitecture;
75 import org.forester.phylogeny.data.Event;
76 import org.forester.phylogeny.data.Identifier;
77 import org.forester.phylogeny.data.PhylogenyData;
78 import org.forester.phylogeny.data.PhylogenyDataUtil;
79 import org.forester.phylogeny.data.Polygon;
80 import org.forester.phylogeny.data.PropertiesMap;
81 import org.forester.phylogeny.data.Property;
82 import org.forester.phylogeny.data.Property.AppliesTo;
83 import org.forester.phylogeny.data.ProteinDomain;
84 import org.forester.phylogeny.data.Taxonomy;
85 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
86 import org.forester.phylogeny.factories.PhylogenyFactory;
87 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
88 import org.forester.protein.Protein;
89 import org.forester.rio.TestRIO;
90 import org.forester.sdi.SDI;
91 import org.forester.sdi.SDIR;
92 import org.forester.sdi.TestGSDI;
93 import org.forester.sequence.BasicSequence;
94 import org.forester.sequence.Sequence;
95 import org.forester.surfacing.TestSurfacing;
96 import org.forester.tools.ConfidenceAssessor;
97 import org.forester.tools.SupportCount;
98 import org.forester.tools.TreeSplitMatrix;
99 import org.forester.util.AsciiHistogram;
100 import org.forester.util.BasicDescriptiveStatistics;
101 import org.forester.util.BasicTable;
102 import org.forester.util.BasicTableParser;
103 import org.forester.util.DescriptiveStatistics;
104 import org.forester.util.ForesterConstants;
105 import org.forester.util.ForesterUtil;
106 import org.forester.util.GeneralTable;
107 import org.forester.util.SequenceIdParser;
108 import org.forester.ws.seqdb.SequenceDatabaseEntry;
109 import org.forester.ws.seqdb.SequenceDbWsTools;
110 import org.forester.ws.seqdb.UniProtTaxonomy;
111 import org.forester.ws.wabi.TxSearch;
112 import org.forester.ws.wabi.TxSearch.RANKS;
113 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
114 import org.forester.ws.wabi.TxSearch.TAX_RANK;
116 @SuppressWarnings( "unused")
117 public final class Test {
119 private final static double ZERO_DIFF = 1.0E-9;
120 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "test_data"
122 + ForesterUtil.getFileSeparator();
123 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "resources"
125 + ForesterUtil.getFileSeparator();
126 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
127 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
130 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
134 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
135 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
139 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
140 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
143 public static boolean isEqual( final double a, final double b ) {
144 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
147 public static void main( final String[] args ) {
148 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
149 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
151 Locale.setDefault( Locale.US );
152 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
155 System.out.print( "[Test if directory with files for testing exists/is readable: " );
156 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
157 System.out.println( "OK.]" );
160 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
161 System.out.println( "Testing aborted." );
164 System.out.print( "[Test if resources directory exists/is readable: " );
165 if ( testDir( PATH_TO_RESOURCES ) ) {
166 System.out.println( "OK.]" );
169 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
170 System.out.println( "Testing aborted." );
173 final long start_time = new Date().getTime();
174 System.out.print( "Sequence id parsing: " );
175 if ( testSequenceIdParsing() ) {
176 System.out.println( "OK." );
180 System.out.println( "failed." );
183 System.out.print( "Hmmscan output parser: " );
184 if ( testHmmscanOutputParser() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node methods: " );
193 if ( Test.testBasicNodeMethods() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "Taxonomy code extraction: " );
202 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "Taxonomy extraction (general): " );
211 if ( Test.testTaxonomyExtraction() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "Basic node construction and parsing of NHX (node level): " );
220 if ( Test.testNHXNodeParsing() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NHX parsing iterating: " );
229 if ( Test.testNHParsingIter() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "NH parsing: " );
238 if ( Test.testNHParsing() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "Conversion to NHX (node level): " );
247 if ( Test.testNHXconversion() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "NHX parsing: " );
256 if ( Test.testNHXParsing() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "NHX parsing with quotes: " );
265 if ( Test.testNHXParsingQuotes() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "NHX parsing (MrBayes): " );
274 if ( Test.testNHXParsingMB() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Nexus characters parsing: " );
283 if ( Test.testNexusCharactersParsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Nexus tree parsing: " );
292 if ( Test.testNexusTreeParsing() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Nexus tree parsing (translating): " );
301 if ( Test.testNexusTreeParsingTranslating() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "Nexus matrix parsing: " );
310 if ( Test.testNexusMatrixParsing() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "Basic phyloXML parsing: " );
319 if ( Test.testBasicPhyloXMLparsing() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Basic phyloXML parsing (validating against schema): " );
328 if ( testBasicPhyloXMLparsingValidating() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
337 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "phyloXML Distribution Element: " );
346 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "Tol XML parsing: " );
355 if ( Test.testBasicTolXMLparsing() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Copying of node data: " );
364 if ( Test.testCopyOfNodeData() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Basic tree methods: " );
373 if ( Test.testBasicTreeMethods() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Postorder Iterator: " );
382 if ( Test.testPostOrderIterator() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Preorder Iterator: " );
391 if ( Test.testPreOrderIterator() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Levelorder Iterator: " );
400 if ( Test.testLevelOrderIterator() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Re-id methods: " );
409 if ( Test.testReIdMethods() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Methods on last external nodes: " );
418 if ( Test.testLastExternalNodeMethods() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Methods on external nodes: " );
427 if ( Test.testExternalNodeRelatedMethods() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Deletion of external nodes: " );
436 if ( Test.testDeletionOfExternalNodes() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Subtree deletion: " );
445 if ( Test.testSubtreeDeletion() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Phylogeny branch: " );
454 if ( Test.testPhylogenyBranch() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Rerooting: " );
463 if ( Test.testRerooting() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Mipoint rooting: " );
472 if ( Test.testMidpointrooting() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "Node removal: " );
481 if ( Test.testNodeRemoval() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "Support count: " );
490 if ( Test.testSupportCount() ) {
491 System.out.println( "OK." );
495 System.out.println( "failed." );
498 System.out.print( "Support transfer: " );
499 if ( Test.testSupportTransfer() ) {
500 System.out.println( "OK." );
504 System.out.println( "failed." );
507 System.out.print( "Finding of LCA: " );
508 if ( Test.testGetLCA() ) {
509 System.out.println( "OK." );
513 System.out.println( "failed." );
516 System.out.print( "Finding of LCA 2: " );
517 if ( Test.testGetLCA2() ) {
518 System.out.println( "OK." );
522 System.out.println( "failed." );
525 System.out.print( "Calculation of distance between nodes: " );
526 if ( Test.testGetDistance() ) {
527 System.out.println( "OK." );
531 System.out.println( "failed." );
534 System.out.print( "Descriptive statistics: " );
535 if ( Test.testDescriptiveStatistics() ) {
536 System.out.println( "OK." );
540 System.out.println( "failed." );
543 System.out.print( "Data objects and methods: " );
544 if ( Test.testDataObjects() ) {
545 System.out.println( "OK." );
549 System.out.println( "failed." );
552 System.out.print( "Properties map: " );
553 if ( Test.testPropertiesMap() ) {
554 System.out.println( "OK." );
558 System.out.println( "failed." );
561 System.out.print( "SDIse: " );
562 if ( Test.testSDIse() ) {
563 System.out.println( "OK." );
567 System.out.println( "failed." );
570 System.out.print( "SDIunrooted: " );
571 if ( Test.testSDIunrooted() ) {
572 System.out.println( "OK." );
576 System.out.println( "failed." );
579 System.out.print( "GSDI: " );
580 if ( TestGSDI.test() ) {
581 System.out.println( "OK." );
585 System.out.println( "failed." );
588 System.out.print( "RIO: " );
589 if ( TestRIO.test() ) {
590 System.out.println( "OK." );
594 System.out.println( "failed." );
597 System.out.print( "Phylogeny reconstruction:" );
598 System.out.println();
599 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
600 System.out.println( "OK." );
604 System.out.println( "failed." );
607 System.out.print( "Analysis of domain architectures: " );
608 System.out.println();
609 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
610 System.out.println( "OK." );
614 System.out.println( "failed." );
617 System.out.print( "GO: " );
618 System.out.println();
619 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
620 System.out.println( "OK." );
624 System.out.println( "failed." );
627 System.out.print( "Modeling tools: " );
628 if ( TestPccx.test() ) {
629 System.out.println( "OK." );
633 System.out.println( "failed." );
636 System.out.print( "Split Matrix strict: " );
637 if ( Test.testSplitStrict() ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "Split Matrix: " );
646 if ( Test.testSplit() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "Confidence Assessor: " );
655 if ( Test.testConfidenceAssessor() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "Basic table: " );
664 if ( Test.testBasicTable() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "General table: " );
673 if ( Test.testGeneralTable() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "Amino acid sequence: " );
682 if ( Test.testAminoAcidSequence() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
690 System.out.print( "General MSA parser: " );
691 if ( Test.testGeneralMsaParser() ) {
692 System.out.println( "OK." );
696 System.out.println( "failed." );
699 System.out.print( "Fasta parser for msa: " );
700 if ( Test.testFastaParser() ) {
701 System.out.println( "OK." );
705 System.out.println( "failed." );
708 System.out.print( "Creation of balanced phylogeny: " );
709 if ( Test.testCreateBalancedPhylogeny() ) {
710 System.out.println( "OK." );
714 System.out.println( "failed." );
717 System.out.print( "EMBL Entry Retrieval: " );
718 if ( Test.testEmblEntryRetrieval() ) {
719 System.out.println( "OK." );
723 System.out.println( "failed." );
726 System.out.print( "Uniprot Entry Retrieval: " );
727 if ( Test.testUniprotEntryRetrieval() ) {
728 System.out.println( "OK." );
732 System.out.println( "failed." );
735 System.out.print( "Uniprot Taxonomy Search: " );
736 if ( Test.testUniprotTaxonomySearch() ) {
737 System.out.println( "OK." );
741 System.out.println( "failed." );
746 final String os = ForesterUtil.OS_NAME.toLowerCase();
747 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
748 path = "/usr/local/bin/mafft";
750 else if ( os.indexOf( "win" ) >= 0 ) {
751 path = "C:\\Program Files\\mafft-win\\mafft.bat";
754 path = "/home/czmasek/bin/mafft";
756 if ( !MsaInferrer.isInstalled( path ) ) {
759 if ( !MsaInferrer.isInstalled( path ) ) {
760 path = "/usr/local/bin/mafft";
762 if ( MsaInferrer.isInstalled( path ) ) {
763 System.out.print( "MAFFT (external program): " );
764 if ( Test.testMafft( path ) ) {
765 System.out.println( "OK." );
769 System.out.println( "failed [will not count towards failed tests]" );
773 System.out.print( "Next nodes with collapsed: " );
774 if ( Test.testNextNodeWithCollapsing() ) {
775 System.out.println( "OK." );
779 System.out.println( "failed." );
782 System.out.print( "Simple MSA quality: " );
783 if ( Test.testMsaQualityMethod() ) {
784 System.out.println( "OK." );
788 System.out.println( "failed." );
791 System.out.println();
792 final Runtime rt = java.lang.Runtime.getRuntime();
793 final long free_memory = rt.freeMemory() / 1000000;
794 final long total_memory = rt.totalMemory() / 1000000;
795 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
796 + free_memory + "MB, total memory: " + total_memory + "MB)" );
797 System.out.println();
798 System.out.println( "Successful tests: " + succeeded );
799 System.out.println( "Failed tests: " + failed );
800 System.out.println();
802 System.out.println( "OK." );
805 System.out.println( "Not OK." );
809 private static boolean testExtractTaxonomyCodeFromNodeName() {
811 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
814 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
817 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
820 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
821 .equals( "MOUSE" ) ) {
824 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
825 .equals( "MOUSE" ) ) {
828 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
829 .equals( "MOUSE" ) ) {
832 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
835 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
838 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
842 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
846 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
850 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
853 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
856 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
859 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
863 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
864 .equals( "MOUSE" ) ) {
867 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
868 .equals( "MOUSE" ) ) {
872 catch ( final Exception e ) {
873 e.printStackTrace( System.out );
879 private static boolean testBasicNodeMethods() {
881 if ( PhylogenyNode.getNodeCount() != 0 ) {
884 final PhylogenyNode n1 = new PhylogenyNode();
885 final PhylogenyNode n2 = PhylogenyNode
886 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
887 final PhylogenyNode n3 = PhylogenyNode
888 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
889 final PhylogenyNode n4 = PhylogenyNode
890 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
891 if ( n1.isHasAssignedEvent() ) {
894 if ( PhylogenyNode.getNodeCount() != 4 ) {
897 if ( n3.getIndicator() != 0 ) {
900 if ( n3.getNumberOfExternalNodes() != 1 ) {
903 if ( !n3.isExternal() ) {
906 if ( !n3.isRoot() ) {
909 if ( !n4.getName().equals( "n4" ) ) {
913 catch ( final Exception e ) {
914 e.printStackTrace( System.out );
920 private static boolean testBasicPhyloXMLparsing() {
922 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
923 final PhyloXmlParser xml_parser = new PhyloXmlParser();
924 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
926 if ( xml_parser.getErrorCount() > 0 ) {
927 System.out.println( xml_parser.getErrorMessages().toString() );
930 if ( phylogenies_0.length != 4 ) {
933 final Phylogeny t1 = phylogenies_0[ 0 ];
934 final Phylogeny t2 = phylogenies_0[ 1 ];
935 final Phylogeny t3 = phylogenies_0[ 2 ];
936 final Phylogeny t4 = phylogenies_0[ 3 ];
937 if ( t1.getNumberOfExternalNodes() != 1 ) {
940 if ( !t1.isRooted() ) {
943 if ( t1.isRerootable() ) {
946 if ( !t1.getType().equals( "gene_tree" ) ) {
949 if ( t2.getNumberOfExternalNodes() != 2 ) {
952 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
955 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
958 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
961 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
964 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
967 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
970 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
971 .startsWith( "actgtgggggt" ) ) {
974 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
975 .startsWith( "ctgtgatgcat" ) ) {
978 if ( t3.getNumberOfExternalNodes() != 4 ) {
981 if ( !t1.getName().equals( "t1" ) ) {
984 if ( !t2.getName().equals( "t2" ) ) {
987 if ( !t3.getName().equals( "t3" ) ) {
990 if ( !t4.getName().equals( "t4" ) ) {
993 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
996 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
999 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1002 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1003 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1006 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1009 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1012 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1015 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1016 .equals( "apoptosis" ) ) {
1019 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1020 .equals( "GO:0006915" ) ) {
1023 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1024 .equals( "UniProtKB" ) ) {
1027 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1028 .equals( "experimental" ) ) {
1031 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1032 .equals( "function" ) ) {
1035 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1036 .getValue() != 1 ) {
1039 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1040 .getType().equals( "ml" ) ) {
1043 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1044 .equals( "apoptosis" ) ) {
1047 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1048 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1051 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1052 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1055 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1056 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1059 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1060 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1063 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1064 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1067 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1068 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1071 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1072 .equals( "GO:0005829" ) ) {
1075 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1076 .equals( "intracellular organelle" ) ) {
1079 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1082 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1083 .equals( "UniProt link" ) ) ) {
1086 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1090 catch ( final Exception e ) {
1091 e.printStackTrace( System.out );
1097 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1099 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1100 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1101 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1102 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1105 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1107 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1109 if ( xml_parser.getErrorCount() > 0 ) {
1110 System.out.println( xml_parser.getErrorMessages().toString() );
1113 if ( phylogenies_0.length != 4 ) {
1116 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1117 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1118 if ( phylogenies_t1.length != 1 ) {
1121 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1122 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1125 if ( !t1_rt.isRooted() ) {
1128 if ( t1_rt.isRerootable() ) {
1131 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1134 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1135 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1136 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1137 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1140 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1143 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1146 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1149 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1150 .startsWith( "actgtgggggt" ) ) {
1153 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1154 .startsWith( "ctgtgatgcat" ) ) {
1157 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1158 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1159 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1160 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1161 if ( phylogenies_1.length != 1 ) {
1164 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1165 if ( !t3_rt.getName().equals( "t3" ) ) {
1168 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1171 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1174 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1177 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1180 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1181 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1184 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1187 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1190 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1191 .equals( "UniProtKB" ) ) {
1194 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1195 .equals( "apoptosis" ) ) {
1198 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1199 .equals( "GO:0006915" ) ) {
1202 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1203 .equals( "UniProtKB" ) ) {
1206 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1207 .equals( "experimental" ) ) {
1210 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1211 .equals( "function" ) ) {
1214 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1215 .getValue() != 1 ) {
1218 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1219 .getType().equals( "ml" ) ) {
1222 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1223 .equals( "apoptosis" ) ) {
1226 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1227 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1230 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1231 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1234 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1235 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1238 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1239 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1242 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1243 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1246 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1247 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1250 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1251 .equals( "GO:0005829" ) ) {
1254 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1255 .equals( "intracellular organelle" ) ) {
1258 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1261 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1262 .equals( "UniProt link" ) ) ) {
1265 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1268 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1271 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1272 .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." ) ) ) {
1275 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1278 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1281 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1284 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1287 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1288 .equals( "ncbi" ) ) {
1291 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1294 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1295 .getName().equals( "B" ) ) {
1298 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1299 .getFrom() != 21 ) {
1302 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1305 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1306 .getLength() != 24 ) {
1309 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1310 .getConfidence() != 2144 ) {
1313 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1314 .equals( "pfam" ) ) {
1317 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1320 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1323 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1326 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1329 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1330 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1333 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1336 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1339 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1342 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1345 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1348 if ( taxbb.getSynonyms().size() != 2 ) {
1351 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1354 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1357 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1360 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1363 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1366 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1367 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1371 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1374 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1377 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1380 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1383 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1386 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1389 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1393 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1396 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1397 .equalsIgnoreCase( "435" ) ) {
1400 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1403 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1404 .equalsIgnoreCase( "443.7" ) ) {
1407 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1410 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1413 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1414 .equalsIgnoreCase( "433" ) ) {
1418 catch ( final Exception e ) {
1419 e.printStackTrace( System.out );
1425 private static boolean testBasicPhyloXMLparsingValidating() {
1427 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1428 PhyloXmlParser xml_parser = null;
1430 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1432 catch ( final Exception e ) {
1433 // Do nothing -- means were not running from jar.
1435 if ( xml_parser == null ) {
1436 xml_parser = new PhyloXmlParser();
1437 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1438 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1441 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1444 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1446 if ( xml_parser.getErrorCount() > 0 ) {
1447 System.out.println( xml_parser.getErrorMessages().toString() );
1450 if ( phylogenies_0.length != 4 ) {
1453 final Phylogeny t1 = phylogenies_0[ 0 ];
1454 final Phylogeny t2 = phylogenies_0[ 1 ];
1455 final Phylogeny t3 = phylogenies_0[ 2 ];
1456 final Phylogeny t4 = phylogenies_0[ 3 ];
1457 if ( !t1.getName().equals( "t1" ) ) {
1460 if ( !t2.getName().equals( "t2" ) ) {
1463 if ( !t3.getName().equals( "t3" ) ) {
1466 if ( !t4.getName().equals( "t4" ) ) {
1469 if ( t1.getNumberOfExternalNodes() != 1 ) {
1472 if ( t2.getNumberOfExternalNodes() != 2 ) {
1475 if ( t3.getNumberOfExternalNodes() != 4 ) {
1478 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1479 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1480 if ( xml_parser.getErrorCount() > 0 ) {
1481 System.out.println( "errors:" );
1482 System.out.println( xml_parser.getErrorMessages().toString() );
1485 if ( phylogenies_1.length != 4 ) {
1488 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1490 if ( xml_parser.getErrorCount() > 0 ) {
1491 System.out.println( "errors:" );
1492 System.out.println( xml_parser.getErrorMessages().toString() );
1495 if ( phylogenies_2.length != 1 ) {
1498 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1501 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1503 if ( xml_parser.getErrorCount() > 0 ) {
1504 System.out.println( xml_parser.getErrorMessages().toString() );
1507 if ( phylogenies_3.length != 2 ) {
1510 final Phylogeny a = phylogenies_3[ 0 ];
1511 if ( !a.getName().equals( "tree 4" ) ) {
1514 if ( a.getNumberOfExternalNodes() != 3 ) {
1517 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1520 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1523 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1525 if ( xml_parser.getErrorCount() > 0 ) {
1526 System.out.println( xml_parser.getErrorMessages().toString() );
1529 if ( phylogenies_4.length != 1 ) {
1532 final Phylogeny s = phylogenies_4[ 0 ];
1533 if ( s.getNumberOfExternalNodes() != 6 ) {
1536 s.getNode( "first" );
1538 s.getNode( "\"<a'b&c'd\">\"" );
1539 s.getNode( "'''\"" );
1540 s.getNode( "\"\"\"" );
1541 s.getNode( "dick & doof" );
1543 catch ( final Exception e ) {
1544 e.printStackTrace( System.out );
1550 private static boolean testBasicTable() {
1552 final BasicTable<String> t0 = new BasicTable<String>();
1553 if ( t0.getNumberOfColumns() != 0 ) {
1556 if ( t0.getNumberOfRows() != 0 ) {
1559 t0.setValue( 3, 2, "23" );
1560 t0.setValue( 10, 1, "error" );
1561 t0.setValue( 10, 1, "110" );
1562 t0.setValue( 9, 1, "19" );
1563 t0.setValue( 1, 10, "101" );
1564 t0.setValue( 10, 10, "1010" );
1565 t0.setValue( 100, 10, "10100" );
1566 t0.setValue( 0, 0, "00" );
1567 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1570 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1573 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1576 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1579 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1582 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1585 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1588 if ( t0.getNumberOfColumns() != 101 ) {
1591 if ( t0.getNumberOfRows() != 11 ) {
1594 if ( t0.getValueAsString( 49, 4 ) != null ) {
1597 final String l = ForesterUtil.getLineSeparator();
1598 final StringBuffer source = new StringBuffer();
1599 source.append( "" + l );
1600 source.append( "# 1 1 1 1 1 1 1 1" + l );
1601 source.append( " 00 01 02 03" + l );
1602 source.append( " 10 11 12 13 " + l );
1603 source.append( "20 21 22 23 " + l );
1604 source.append( " 30 31 32 33" + l );
1605 source.append( "40 41 42 43" + l );
1606 source.append( " # 1 1 1 1 1 " + l );
1607 source.append( "50 51 52 53 54" + l );
1608 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1609 if ( t1.getNumberOfColumns() != 5 ) {
1612 if ( t1.getNumberOfRows() != 6 ) {
1615 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1618 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1621 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1624 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1627 final StringBuffer source1 = new StringBuffer();
1628 source1.append( "" + l );
1629 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1630 source1.append( " 00; 01 ;02;03" + l );
1631 source1.append( " 10; 11; 12; 13 " + l );
1632 source1.append( "20; 21; 22; 23 " + l );
1633 source1.append( " 30; 31; 32; 33" + l );
1634 source1.append( "40;41;42;43" + l );
1635 source1.append( " # 1 1 1 1 1 " + l );
1636 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1637 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1638 if ( t2.getNumberOfColumns() != 5 ) {
1641 if ( t2.getNumberOfRows() != 6 ) {
1644 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1647 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1650 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1653 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1656 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1659 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1662 final StringBuffer source2 = new StringBuffer();
1663 source2.append( "" + l );
1664 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1665 source2.append( " 00; 01 ;02;03" + l );
1666 source2.append( " 10; 11; 12; 13 " + l );
1667 source2.append( "20; 21; 22; 23 " + l );
1668 source2.append( " " + l );
1669 source2.append( " 30; 31; 32; 33" + l );
1670 source2.append( "40;41;42;43" + l );
1671 source2.append( " comment: 1 1 1 1 1 " + l );
1672 source2.append( ";;;50 ; 52; 53;;54 " + l );
1673 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1679 if ( tl.size() != 2 ) {
1682 final BasicTable<String> t3 = tl.get( 0 );
1683 final BasicTable<String> t4 = tl.get( 1 );
1684 if ( t3.getNumberOfColumns() != 4 ) {
1687 if ( t3.getNumberOfRows() != 3 ) {
1690 if ( t4.getNumberOfColumns() != 4 ) {
1693 if ( t4.getNumberOfRows() != 3 ) {
1696 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1699 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1703 catch ( final Exception e ) {
1704 e.printStackTrace( System.out );
1710 private static boolean testBasicTolXMLparsing() {
1712 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1713 final TolParser parser = new TolParser();
1714 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1715 if ( parser.getErrorCount() > 0 ) {
1716 System.out.println( parser.getErrorMessages().toString() );
1719 if ( phylogenies_0.length != 1 ) {
1722 final Phylogeny t1 = phylogenies_0[ 0 ];
1723 if ( t1.getNumberOfExternalNodes() != 5 ) {
1726 if ( !t1.isRooted() ) {
1729 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1732 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1735 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1738 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1741 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1742 if ( parser.getErrorCount() > 0 ) {
1743 System.out.println( parser.getErrorMessages().toString() );
1746 if ( phylogenies_1.length != 1 ) {
1749 final Phylogeny t2 = phylogenies_1[ 0 ];
1750 if ( t2.getNumberOfExternalNodes() != 664 ) {
1753 if ( !t2.isRooted() ) {
1756 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1759 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1762 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1765 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1768 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1771 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1772 .equals( "Aquifex" ) ) {
1775 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1776 if ( parser.getErrorCount() > 0 ) {
1777 System.out.println( parser.getErrorMessages().toString() );
1780 if ( phylogenies_2.length != 1 ) {
1783 final Phylogeny t3 = phylogenies_2[ 0 ];
1784 if ( t3.getNumberOfExternalNodes() != 184 ) {
1787 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1790 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1793 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1796 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1797 if ( parser.getErrorCount() > 0 ) {
1798 System.out.println( parser.getErrorMessages().toString() );
1801 if ( phylogenies_3.length != 1 ) {
1804 final Phylogeny t4 = phylogenies_3[ 0 ];
1805 if ( t4.getNumberOfExternalNodes() != 1 ) {
1808 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1811 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1814 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1817 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1818 if ( parser.getErrorCount() > 0 ) {
1819 System.out.println( parser.getErrorMessages().toString() );
1822 if ( phylogenies_4.length != 1 ) {
1825 final Phylogeny t5 = phylogenies_4[ 0 ];
1826 if ( t5.getNumberOfExternalNodes() != 13 ) {
1829 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1832 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1835 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1839 catch ( final Exception e ) {
1840 e.printStackTrace( System.out );
1846 private static boolean testBasicTreeMethods() {
1848 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1849 final Phylogeny t1 = factory.create();
1850 if ( !t1.isEmpty() ) {
1853 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1854 if ( t2.getNumberOfExternalNodes() != 4 ) {
1857 if ( t2.getHeight() != 8.5 ) {
1860 if ( !t2.isCompletelyBinary() ) {
1863 if ( t2.isEmpty() ) {
1866 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1867 if ( t3.getNumberOfExternalNodes() != 5 ) {
1870 if ( t3.getHeight() != 11 ) {
1873 if ( t3.isCompletelyBinary() ) {
1876 final PhylogenyNode n = t3.getNode( "ABC" );
1877 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 ];
1878 if ( t4.getNumberOfExternalNodes() != 9 ) {
1881 if ( t4.getHeight() != 11 ) {
1884 if ( t4.isCompletelyBinary() ) {
1887 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)" );
1888 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1889 if ( t5.getNumberOfExternalNodes() != 8 ) {
1892 if ( t5.getHeight() != 15 ) {
1895 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)" );
1896 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1897 if ( t6.getHeight() != 15 ) {
1900 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)" );
1901 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1902 if ( t7.getHeight() != 15 ) {
1905 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)" );
1906 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1907 if ( t8.getNumberOfExternalNodes() != 10 ) {
1910 if ( t8.getHeight() != 15 ) {
1913 final char[] a9 = new char[] { 'a' };
1914 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1915 if ( t9.getHeight() != 0 ) {
1918 final char[] a10 = new char[] { 'a', ':', '6' };
1919 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1920 if ( t10.getHeight() != 6 ) {
1924 catch ( final Exception e ) {
1925 e.printStackTrace( System.out );
1931 private static boolean testConfidenceAssessor() {
1933 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1934 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1935 final Phylogeny[] ev0 = factory
1936 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1938 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1939 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1942 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1945 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1946 final Phylogeny[] ev1 = 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", ev1, t1, false, 1 );
1950 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1953 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1956 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1957 final Phylogeny[] ev_b = factory
1958 .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",
1960 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1961 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1964 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1968 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1969 final Phylogeny[] ev1x = factory
1970 .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)));",
1972 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1973 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1976 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1979 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1980 final Phylogeny[] ev_bx = factory
1981 .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",
1983 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1984 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1987 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1991 final Phylogeny[] t2 = factory
1992 .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);",
1994 final Phylogeny[] ev2 = factory
1995 .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);",
1997 for( final Phylogeny target : t2 ) {
1998 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2001 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2002 new NHXParser() )[ 0 ];
2003 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2004 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2005 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2008 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2011 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2015 catch ( final Exception e ) {
2016 e.printStackTrace();
2022 private static boolean testCopyOfNodeData() {
2024 final PhylogenyNode n1 = PhylogenyNode
2025 .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]" );
2026 final PhylogenyNode n2 = n1.copyNodeData();
2027 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2031 catch ( final Exception e ) {
2032 e.printStackTrace();
2038 private static boolean testDataObjects() {
2040 final Confidence s0 = new Confidence();
2041 final Confidence s1 = new Confidence();
2042 if ( !s0.isEqual( s1 ) ) {
2045 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2046 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2047 if ( s2.isEqual( s1 ) ) {
2050 if ( !s2.isEqual( s3 ) ) {
2053 final Confidence s4 = ( Confidence ) s3.copy();
2054 if ( !s4.isEqual( s3 ) ) {
2061 final Taxonomy t1 = new Taxonomy();
2062 final Taxonomy t2 = new Taxonomy();
2063 final Taxonomy t3 = new Taxonomy();
2064 final Taxonomy t4 = new Taxonomy();
2065 final Taxonomy t5 = new Taxonomy();
2066 t1.setIdentifier( new Identifier( "ecoli" ) );
2067 t1.setTaxonomyCode( "ECOLI" );
2068 t1.setScientificName( "E. coli" );
2069 t1.setCommonName( "coli" );
2070 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2071 if ( !t1.isEqual( t0 ) ) {
2074 t2.setIdentifier( new Identifier( "ecoli" ) );
2075 t2.setTaxonomyCode( "OTHER" );
2076 t2.setScientificName( "what" );
2077 t2.setCommonName( "something" );
2078 if ( !t1.isEqual( t2 ) ) {
2081 t2.setIdentifier( new Identifier( "nemve" ) );
2082 if ( t1.isEqual( t2 ) ) {
2085 t1.setIdentifier( null );
2086 t3.setTaxonomyCode( "ECOLI" );
2087 t3.setScientificName( "what" );
2088 t3.setCommonName( "something" );
2089 if ( !t1.isEqual( t3 ) ) {
2092 t1.setIdentifier( null );
2093 t1.setTaxonomyCode( "" );
2094 t4.setScientificName( "E. ColI" );
2095 t4.setCommonName( "something" );
2096 if ( !t1.isEqual( t4 ) ) {
2099 t4.setScientificName( "B. subtilis" );
2100 t4.setCommonName( "something" );
2101 if ( t1.isEqual( t4 ) ) {
2104 t1.setIdentifier( null );
2105 t1.setTaxonomyCode( "" );
2106 t1.setScientificName( "" );
2107 t5.setCommonName( "COLI" );
2108 if ( !t1.isEqual( t5 ) ) {
2111 t5.setCommonName( "vibrio" );
2112 if ( t1.isEqual( t5 ) ) {
2117 final Identifier id0 = new Identifier( "123", "pfam" );
2118 final Identifier id1 = ( Identifier ) id0.copy();
2119 if ( !id1.isEqual( id1 ) ) {
2122 if ( !id1.isEqual( id0 ) ) {
2125 if ( !id0.isEqual( id1 ) ) {
2132 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2133 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2134 if ( !pd1.isEqual( pd1 ) ) {
2137 if ( !pd1.isEqual( pd0 ) ) {
2142 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2143 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2144 if ( !pd3.isEqual( pd3 ) ) {
2147 if ( !pd2.isEqual( pd3 ) ) {
2150 if ( !pd0.isEqual( pd3 ) ) {
2155 // DomainArchitecture
2156 // ------------------
2157 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2158 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2159 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2160 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2161 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2162 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2167 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2168 if ( ds0.getNumberOfDomains() != 4 ) {
2171 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2172 if ( !ds0.isEqual( ds0 ) ) {
2175 if ( !ds0.isEqual( ds1 ) ) {
2178 if ( ds1.getNumberOfDomains() != 4 ) {
2181 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2186 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2187 if ( ds0.isEqual( ds2 ) ) {
2193 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2194 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2195 System.out.println( ds3.toNHX() );
2198 if ( ds3.getNumberOfDomains() != 3 ) {
2203 final Event e1 = new Event( Event.EventType.fusion );
2204 if ( e1.isDuplication() ) {
2207 if ( !e1.isFusion() ) {
2210 if ( !e1.asText().toString().equals( "fusion" ) ) {
2213 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2216 final Event e11 = new Event( Event.EventType.fusion );
2217 if ( !e11.isEqual( e1 ) ) {
2220 if ( !e11.toNHX().toString().equals( "" ) ) {
2223 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2224 if ( e2.isDuplication() ) {
2227 if ( !e2.isSpeciationOrDuplication() ) {
2230 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2233 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2236 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2239 if ( e11.isEqual( e2 ) ) {
2242 final Event e2c = ( Event ) e2.copy();
2243 if ( !e2c.isEqual( e2 ) ) {
2246 Event e3 = new Event( 1, 2, 3 );
2247 if ( e3.isDuplication() ) {
2250 if ( e3.isSpeciation() ) {
2253 if ( e3.isGeneLoss() ) {
2256 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2259 final Event e3c = ( Event ) e3.copy();
2260 final Event e3cc = ( Event ) e3c.copy();
2261 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2265 if ( !e3c.isEqual( e3cc ) ) {
2268 Event e4 = new Event( 1, 2, 3 );
2269 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2272 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2275 final Event e4c = ( Event ) e4.copy();
2277 final Event e4cc = ( Event ) e4c.copy();
2278 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2281 if ( !e4c.isEqual( e4cc ) ) {
2284 final Event e5 = new Event();
2285 if ( !e5.isUnassigned() ) {
2288 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2291 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2294 final Event e6 = new Event( 1, 0, 0 );
2295 if ( !e6.asText().toString().equals( "duplication" ) ) {
2298 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2301 final Event e7 = new Event( 0, 1, 0 );
2302 if ( !e7.asText().toString().equals( "speciation" ) ) {
2305 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2308 final Event e8 = new Event( 0, 0, 1 );
2309 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2312 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2316 catch ( final Exception e ) {
2317 e.printStackTrace( System.out );
2323 private static boolean testDeletionOfExternalNodes() {
2325 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2326 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2327 final PhylogenyWriter w = new PhylogenyWriter();
2328 if ( t0.isEmpty() ) {
2331 if ( t0.getNumberOfExternalNodes() != 1 ) {
2334 t0.deleteSubtree( t0.getNode( "A" ), false );
2335 if ( t0.getNumberOfExternalNodes() != 0 ) {
2338 if ( !t0.isEmpty() ) {
2341 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2342 if ( t1.getNumberOfExternalNodes() != 2 ) {
2345 t1.deleteSubtree( t1.getNode( "A" ), false );
2346 if ( t1.getNumberOfExternalNodes() != 1 ) {
2349 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2352 t1.deleteSubtree( t1.getNode( "B" ), false );
2353 if ( t1.getNumberOfExternalNodes() != 1 ) {
2356 t1.deleteSubtree( t1.getNode( "r" ), false );
2357 if ( !t1.isEmpty() ) {
2360 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2361 if ( t2.getNumberOfExternalNodes() != 3 ) {
2364 t2.deleteSubtree( t2.getNode( "B" ), false );
2365 if ( t2.getNumberOfExternalNodes() != 2 ) {
2368 t2.toNewHampshireX();
2369 PhylogenyNode n = t2.getNode( "A" );
2370 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2373 t2.deleteSubtree( t2.getNode( "A" ), false );
2374 if ( t2.getNumberOfExternalNodes() != 2 ) {
2377 t2.deleteSubtree( t2.getNode( "C" ), true );
2378 if ( t2.getNumberOfExternalNodes() != 1 ) {
2381 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2382 if ( t3.getNumberOfExternalNodes() != 4 ) {
2385 t3.deleteSubtree( t3.getNode( "B" ), true );
2386 if ( t3.getNumberOfExternalNodes() != 3 ) {
2389 n = t3.getNode( "A" );
2390 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2393 n = n.getNextExternalNode();
2394 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2397 t3.deleteSubtree( t3.getNode( "A" ), true );
2398 if ( t3.getNumberOfExternalNodes() != 2 ) {
2401 n = t3.getNode( "C" );
2402 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2405 t3.deleteSubtree( t3.getNode( "C" ), true );
2406 if ( t3.getNumberOfExternalNodes() != 1 ) {
2409 t3.deleteSubtree( t3.getNode( "D" ), true );
2410 if ( t3.getNumberOfExternalNodes() != 0 ) {
2413 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2414 if ( t4.getNumberOfExternalNodes() != 6 ) {
2417 t4.deleteSubtree( t4.getNode( "B2" ), true );
2418 if ( t4.getNumberOfExternalNodes() != 5 ) {
2421 String s = w.toNewHampshire( t4, false, true ).toString();
2422 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2425 t4.deleteSubtree( t4.getNode( "B11" ), true );
2426 if ( t4.getNumberOfExternalNodes() != 4 ) {
2429 t4.deleteSubtree( t4.getNode( "C" ), true );
2430 if ( t4.getNumberOfExternalNodes() != 3 ) {
2433 n = t4.getNode( "A" );
2434 n = n.getNextExternalNode();
2435 if ( !n.getName().equals( "B12" ) ) {
2438 n = n.getNextExternalNode();
2439 if ( !n.getName().equals( "D" ) ) {
2442 s = w.toNewHampshire( t4, false, true ).toString();
2443 if ( !s.equals( "((A,B12),D);" ) ) {
2446 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2447 t5.deleteSubtree( t5.getNode( "A" ), true );
2448 if ( t5.getNumberOfExternalNodes() != 5 ) {
2451 s = w.toNewHampshire( t5, false, true ).toString();
2452 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2455 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2456 t6.deleteSubtree( t6.getNode( "B11" ), true );
2457 if ( t6.getNumberOfExternalNodes() != 5 ) {
2460 s = w.toNewHampshire( t6, false, false ).toString();
2461 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2464 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2465 t7.deleteSubtree( t7.getNode( "B12" ), true );
2466 if ( t7.getNumberOfExternalNodes() != 5 ) {
2469 s = w.toNewHampshire( t7, false, true ).toString();
2470 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2473 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2474 t8.deleteSubtree( t8.getNode( "B2" ), true );
2475 if ( t8.getNumberOfExternalNodes() != 5 ) {
2478 s = w.toNewHampshire( t8, false, false ).toString();
2479 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2482 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2483 t9.deleteSubtree( t9.getNode( "C" ), true );
2484 if ( t9.getNumberOfExternalNodes() != 5 ) {
2487 s = w.toNewHampshire( t9, false, true ).toString();
2488 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2491 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2492 t10.deleteSubtree( t10.getNode( "D" ), true );
2493 if ( t10.getNumberOfExternalNodes() != 5 ) {
2496 s = w.toNewHampshire( t10, false, true ).toString();
2497 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2500 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2501 t11.deleteSubtree( t11.getNode( "A" ), true );
2502 if ( t11.getNumberOfExternalNodes() != 2 ) {
2505 s = w.toNewHampshire( t11, false, true ).toString();
2506 if ( !s.equals( "(B,C);" ) ) {
2509 t11.deleteSubtree( t11.getNode( "C" ), true );
2510 if ( t11.getNumberOfExternalNodes() != 1 ) {
2513 s = w.toNewHampshire( t11, false, false ).toString();
2514 if ( !s.equals( "B;" ) ) {
2517 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2518 t12.deleteSubtree( t12.getNode( "B2" ), true );
2519 if ( t12.getNumberOfExternalNodes() != 8 ) {
2522 s = w.toNewHampshire( t12, false, true ).toString();
2523 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2526 t12.deleteSubtree( t12.getNode( "B3" ), true );
2527 if ( t12.getNumberOfExternalNodes() != 7 ) {
2530 s = w.toNewHampshire( t12, false, true ).toString();
2531 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2534 t12.deleteSubtree( t12.getNode( "C3" ), true );
2535 if ( t12.getNumberOfExternalNodes() != 6 ) {
2538 s = w.toNewHampshire( t12, false, true ).toString();
2539 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2542 t12.deleteSubtree( t12.getNode( "A1" ), true );
2543 if ( t12.getNumberOfExternalNodes() != 5 ) {
2546 s = w.toNewHampshire( t12, false, true ).toString();
2547 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2550 t12.deleteSubtree( t12.getNode( "B1" ), true );
2551 if ( t12.getNumberOfExternalNodes() != 4 ) {
2554 s = w.toNewHampshire( t12, false, true ).toString();
2555 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2558 t12.deleteSubtree( t12.getNode( "A3" ), true );
2559 if ( t12.getNumberOfExternalNodes() != 3 ) {
2562 s = w.toNewHampshire( t12, false, true ).toString();
2563 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2566 t12.deleteSubtree( t12.getNode( "A2" ), true );
2567 if ( t12.getNumberOfExternalNodes() != 2 ) {
2570 s = w.toNewHampshire( t12, false, true ).toString();
2571 if ( !s.equals( "(C1,C2);" ) ) {
2574 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2575 t13.deleteSubtree( t13.getNode( "D" ), true );
2576 if ( t13.getNumberOfExternalNodes() != 4 ) {
2579 s = w.toNewHampshire( t13, false, true ).toString();
2580 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2583 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2584 t14.deleteSubtree( t14.getNode( "E" ), true );
2585 if ( t14.getNumberOfExternalNodes() != 5 ) {
2588 s = w.toNewHampshire( t14, false, true ).toString();
2589 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2592 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2593 t15.deleteSubtree( t15.getNode( "B2" ), true );
2594 if ( t15.getNumberOfExternalNodes() != 11 ) {
2597 t15.deleteSubtree( t15.getNode( "B1" ), true );
2598 if ( t15.getNumberOfExternalNodes() != 10 ) {
2601 t15.deleteSubtree( t15.getNode( "B3" ), true );
2602 if ( t15.getNumberOfExternalNodes() != 9 ) {
2605 t15.deleteSubtree( t15.getNode( "B4" ), true );
2606 if ( t15.getNumberOfExternalNodes() != 8 ) {
2609 t15.deleteSubtree( t15.getNode( "A1" ), true );
2610 if ( t15.getNumberOfExternalNodes() != 7 ) {
2613 t15.deleteSubtree( t15.getNode( "C4" ), true );
2614 if ( t15.getNumberOfExternalNodes() != 6 ) {
2618 catch ( final Exception e ) {
2619 e.printStackTrace( System.out );
2625 private static boolean testDescriptiveStatistics() {
2627 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2628 dss1.addValue( 82 );
2629 dss1.addValue( 78 );
2630 dss1.addValue( 70 );
2631 dss1.addValue( 58 );
2632 dss1.addValue( 42 );
2633 if ( dss1.getN() != 5 ) {
2636 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2639 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2642 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2645 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2648 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2651 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2654 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2657 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2660 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2663 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2666 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2669 dss1.addValue( 123 );
2670 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2673 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2676 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2679 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2680 dss2.addValue( -1.85 );
2681 dss2.addValue( 57.5 );
2682 dss2.addValue( 92.78 );
2683 dss2.addValue( 57.78 );
2684 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2687 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2690 final double[] a = dss2.getDataAsDoubleArray();
2691 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2694 dss2.addValue( -100 );
2695 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2698 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2701 final double[] ds = new double[ 14 ];
2716 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2717 if ( bins.length != 4 ) {
2720 if ( bins[ 0 ] != 2 ) {
2723 if ( bins[ 1 ] != 3 ) {
2726 if ( bins[ 2 ] != 4 ) {
2729 if ( bins[ 3 ] != 5 ) {
2732 final double[] ds1 = new double[ 9 ];
2742 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2743 if ( bins1.length != 4 ) {
2746 if ( bins1[ 0 ] != 2 ) {
2749 if ( bins1[ 1 ] != 3 ) {
2752 if ( bins1[ 2 ] != 0 ) {
2755 if ( bins1[ 3 ] != 4 ) {
2758 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2759 if ( bins1_1.length != 3 ) {
2762 if ( bins1_1[ 0 ] != 3 ) {
2765 if ( bins1_1[ 1 ] != 2 ) {
2768 if ( bins1_1[ 2 ] != 4 ) {
2771 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2772 if ( bins1_2.length != 3 ) {
2775 if ( bins1_2[ 0 ] != 2 ) {
2778 if ( bins1_2[ 1 ] != 2 ) {
2781 if ( bins1_2[ 2 ] != 2 ) {
2784 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2798 dss3.addValue( 10 );
2799 dss3.addValue( 10 );
2800 dss3.addValue( 10 );
2801 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2802 histo.toStringBuffer( 10, '=', 40, 5 );
2803 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2805 catch ( final Exception e ) {
2806 e.printStackTrace( System.out );
2812 private static boolean testDir( final String file ) {
2814 final File f = new File( file );
2815 if ( !f.exists() ) {
2818 if ( !f.isDirectory() ) {
2821 if ( !f.canRead() ) {
2825 catch ( final Exception e ) {
2831 private static boolean testExternalNodeRelatedMethods() {
2833 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2834 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2835 PhylogenyNode n = t1.getNode( "A" );
2836 n = n.getNextExternalNode();
2837 if ( !n.getName().equals( "B" ) ) {
2840 n = n.getNextExternalNode();
2841 if ( !n.getName().equals( "C" ) ) {
2844 n = n.getNextExternalNode();
2845 if ( !n.getName().equals( "D" ) ) {
2848 n = t1.getNode( "B" );
2849 while ( !n.isLastExternalNode() ) {
2850 n = n.getNextExternalNode();
2852 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2853 n = t2.getNode( "A" );
2854 n = n.getNextExternalNode();
2855 if ( !n.getName().equals( "B" ) ) {
2858 n = n.getNextExternalNode();
2859 if ( !n.getName().equals( "C" ) ) {
2862 n = n.getNextExternalNode();
2863 if ( !n.getName().equals( "D" ) ) {
2866 n = t2.getNode( "B" );
2867 while ( !n.isLastExternalNode() ) {
2868 n = n.getNextExternalNode();
2870 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2871 n = t3.getNode( "A" );
2872 n = n.getNextExternalNode();
2873 if ( !n.getName().equals( "B" ) ) {
2876 n = n.getNextExternalNode();
2877 if ( !n.getName().equals( "C" ) ) {
2880 n = n.getNextExternalNode();
2881 if ( !n.getName().equals( "D" ) ) {
2884 n = n.getNextExternalNode();
2885 if ( !n.getName().equals( "E" ) ) {
2888 n = n.getNextExternalNode();
2889 if ( !n.getName().equals( "F" ) ) {
2892 n = n.getNextExternalNode();
2893 if ( !n.getName().equals( "G" ) ) {
2896 n = n.getNextExternalNode();
2897 if ( !n.getName().equals( "H" ) ) {
2900 n = t3.getNode( "B" );
2901 while ( !n.isLastExternalNode() ) {
2902 n = n.getNextExternalNode();
2904 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2905 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2906 final PhylogenyNode node = iter.next();
2908 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2909 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2910 final PhylogenyNode node = iter.next();
2912 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2913 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2914 if ( !iter.next().getName().equals( "A" ) ) {
2917 if ( !iter.next().getName().equals( "B" ) ) {
2920 if ( !iter.next().getName().equals( "C" ) ) {
2923 if ( !iter.next().getName().equals( "D" ) ) {
2926 if ( !iter.next().getName().equals( "E" ) ) {
2929 if ( !iter.next().getName().equals( "F" ) ) {
2932 if ( iter.hasNext() ) {
2936 catch ( final Exception e ) {
2937 e.printStackTrace( System.out );
2943 private static boolean testGeneralTable() {
2945 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2946 t0.setValue( 3, 2, "23" );
2947 t0.setValue( 10, 1, "error" );
2948 t0.setValue( 10, 1, "110" );
2949 t0.setValue( 9, 1, "19" );
2950 t0.setValue( 1, 10, "101" );
2951 t0.setValue( 10, 10, "1010" );
2952 t0.setValue( 100, 10, "10100" );
2953 t0.setValue( 0, 0, "00" );
2954 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2957 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2960 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2963 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2966 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2969 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2972 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2975 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2978 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2981 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2982 t1.setValue( "3", "2", "23" );
2983 t1.setValue( "10", "1", "error" );
2984 t1.setValue( "10", "1", "110" );
2985 t1.setValue( "9", "1", "19" );
2986 t1.setValue( "1", "10", "101" );
2987 t1.setValue( "10", "10", "1010" );
2988 t1.setValue( "100", "10", "10100" );
2989 t1.setValue( "0", "0", "00" );
2990 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2991 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2994 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2997 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3000 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3003 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3006 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3009 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3012 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3015 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3018 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3022 catch ( final Exception e ) {
3023 e.printStackTrace( System.out );
3029 private static boolean testGetDistance() {
3031 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3032 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",
3033 new NHXParser() )[ 0 ];
3034 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3037 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3040 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3043 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3046 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3049 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3052 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3055 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3058 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3061 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3064 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3067 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3070 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3073 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3076 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3079 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3082 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3085 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3088 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3091 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3094 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3097 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3100 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3103 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3106 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3109 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3112 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3115 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3118 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3121 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3124 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3127 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",
3128 new NHXParser() )[ 0 ];
3129 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3132 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3135 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3138 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3141 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3144 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3147 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3150 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3153 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3156 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3159 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3163 catch ( final Exception e ) {
3164 e.printStackTrace( System.out );
3170 private static boolean testGetLCA() {
3172 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3173 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3174 new NHXParser() )[ 0 ];
3175 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3176 if ( !A.getName().equals( "A" ) ) {
3179 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3180 if ( !gh.getName().equals( "gh" ) ) {
3183 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3184 if ( !ab.getName().equals( "ab" ) ) {
3187 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3188 if ( !ab2.getName().equals( "ab" ) ) {
3191 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3192 if ( !gh2.getName().equals( "gh" ) ) {
3195 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3196 if ( !gh3.getName().equals( "gh" ) ) {
3199 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3200 if ( !abc.getName().equals( "abc" ) ) {
3203 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3204 if ( !abc2.getName().equals( "abc" ) ) {
3207 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3208 if ( !abcd.getName().equals( "abcd" ) ) {
3211 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3212 if ( !abcd2.getName().equals( "abcd" ) ) {
3215 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3216 if ( !abcdef.getName().equals( "abcdef" ) ) {
3219 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3220 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3223 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3224 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3227 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3228 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3231 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3232 if ( !abcde.getName().equals( "abcde" ) ) {
3235 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3236 if ( !abcde2.getName().equals( "abcde" ) ) {
3239 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3240 if ( !r.getName().equals( "abcdefgh" ) ) {
3243 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3244 if ( !r2.getName().equals( "abcdefgh" ) ) {
3247 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3248 if ( !r3.getName().equals( "abcdefgh" ) ) {
3251 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3252 if ( !abcde3.getName().equals( "abcde" ) ) {
3255 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3256 if ( !abcde4.getName().equals( "abcde" ) ) {
3259 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3260 if ( !ab3.getName().equals( "ab" ) ) {
3263 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3264 if ( !ab4.getName().equals( "ab" ) ) {
3267 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3268 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3269 if ( !cd.getName().equals( "cd" ) ) {
3272 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3273 if ( !cd2.getName().equals( "cd" ) ) {
3276 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3277 if ( !cde.getName().equals( "cde" ) ) {
3280 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3281 if ( !cde2.getName().equals( "cde" ) ) {
3284 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3285 if ( !cdef.getName().equals( "cdef" ) ) {
3288 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3289 if ( !cdef2.getName().equals( "cdef" ) ) {
3292 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3293 if ( !cdef3.getName().equals( "cdef" ) ) {
3296 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3297 if ( !rt.getName().equals( "r" ) ) {
3300 final Phylogeny p3 = factory
3301 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3302 new NHXParser() )[ 0 ];
3303 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3304 if ( !bc_3.getName().equals( "bc" ) ) {
3307 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3308 if ( !ac_3.getName().equals( "abc" ) ) {
3311 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3312 if ( !ad_3.getName().equals( "abcde" ) ) {
3315 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3316 if ( !af_3.getName().equals( "abcdef" ) ) {
3319 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3320 if ( !ag_3.getName().equals( "" ) ) {
3323 if ( !ag_3.isRoot() ) {
3326 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3327 if ( !al_3.getName().equals( "" ) ) {
3330 if ( !al_3.isRoot() ) {
3333 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3334 if ( !kl_3.getName().equals( "" ) ) {
3337 if ( !kl_3.isRoot() ) {
3340 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3341 if ( !fl_3.getName().equals( "" ) ) {
3344 if ( !fl_3.isRoot() ) {
3347 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3348 if ( !gk_3.getName().equals( "ghijk" ) ) {
3351 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3352 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3353 if ( !r_4.getName().equals( "r" ) ) {
3356 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3357 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3358 if ( !r_5.getName().equals( "root" ) ) {
3361 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3362 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3363 if ( !r_6.getName().equals( "rot" ) ) {
3366 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3367 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3368 if ( !r_7.getName().equals( "rott" ) ) {
3372 catch ( final Exception e ) {
3373 e.printStackTrace( System.out );
3379 private static boolean testGetLCA2() {
3381 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3382 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3383 PhylogenyMethods.preOrderReId( p_a );
3384 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3385 p_a.getNode( "a" ) );
3386 if ( !p_a_1.getName().equals( "a" ) ) {
3389 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3390 PhylogenyMethods.preOrderReId( p_b );
3391 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3392 p_b.getNode( "a" ) );
3393 if ( !p_b_1.getName().equals( "b" ) ) {
3396 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3397 p_b.getNode( "b" ) );
3398 if ( !p_b_2.getName().equals( "b" ) ) {
3401 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3402 PhylogenyMethods.preOrderReId( p_c );
3403 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3404 p_c.getNode( "a" ) );
3405 if ( !p_c_1.getName().equals( "b" ) ) {
3408 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3409 p_c.getNode( "c" ) );
3410 if ( !p_c_2.getName().equals( "c" ) ) {
3411 System.out.println( p_c_2.getName() );
3415 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3416 p_c.getNode( "b" ) );
3417 if ( !p_c_3.getName().equals( "b" ) ) {
3420 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3421 p_c.getNode( "a" ) );
3422 if ( !p_c_4.getName().equals( "c" ) ) {
3425 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3426 new NHXParser() )[ 0 ];
3427 PhylogenyMethods.preOrderReId( p1 );
3428 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3429 p1.getNode( "A" ) );
3430 if ( !A.getName().equals( "A" ) ) {
3433 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3434 p1.getNode( "gh" ) );
3435 if ( !gh.getName().equals( "gh" ) ) {
3438 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3439 p1.getNode( "B" ) );
3440 if ( !ab.getName().equals( "ab" ) ) {
3443 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3444 p1.getNode( "A" ) );
3445 if ( !ab2.getName().equals( "ab" ) ) {
3448 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3449 p1.getNode( "G" ) );
3450 if ( !gh2.getName().equals( "gh" ) ) {
3453 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3454 p1.getNode( "H" ) );
3455 if ( !gh3.getName().equals( "gh" ) ) {
3458 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3459 p1.getNode( "A" ) );
3460 if ( !abc.getName().equals( "abc" ) ) {
3463 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3464 p1.getNode( "C" ) );
3465 if ( !abc2.getName().equals( "abc" ) ) {
3468 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3469 p1.getNode( "D" ) );
3470 if ( !abcd.getName().equals( "abcd" ) ) {
3473 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3474 p1.getNode( "A" ) );
3475 if ( !abcd2.getName().equals( "abcd" ) ) {
3478 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3479 p1.getNode( "F" ) );
3480 if ( !abcdef.getName().equals( "abcdef" ) ) {
3483 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3484 p1.getNode( "A" ) );
3485 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3488 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3489 p1.getNode( "F" ) );
3490 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3493 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3494 p1.getNode( "ab" ) );
3495 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3498 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3499 p1.getNode( "E" ) );
3500 if ( !abcde.getName().equals( "abcde" ) ) {
3503 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3504 p1.getNode( "A" ) );
3505 if ( !abcde2.getName().equals( "abcde" ) ) {
3508 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3509 p1.getNode( "abcdefgh" ) );
3510 if ( !r.getName().equals( "abcdefgh" ) ) {
3513 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3514 p1.getNode( "H" ) );
3515 if ( !r2.getName().equals( "abcdefgh" ) ) {
3518 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3519 p1.getNode( "A" ) );
3520 if ( !r3.getName().equals( "abcdefgh" ) ) {
3523 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3524 p1.getNode( "abcde" ) );
3525 if ( !abcde3.getName().equals( "abcde" ) ) {
3528 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3529 p1.getNode( "E" ) );
3530 if ( !abcde4.getName().equals( "abcde" ) ) {
3533 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3534 p1.getNode( "B" ) );
3535 if ( !ab3.getName().equals( "ab" ) ) {
3538 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3539 p1.getNode( "ab" ) );
3540 if ( !ab4.getName().equals( "ab" ) ) {
3543 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3544 PhylogenyMethods.preOrderReId( p2 );
3545 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3546 p2.getNode( "d" ) );
3547 if ( !cd.getName().equals( "cd" ) ) {
3550 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3551 p2.getNode( "c" ) );
3552 if ( !cd2.getName().equals( "cd" ) ) {
3555 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3556 p2.getNode( "e" ) );
3557 if ( !cde.getName().equals( "cde" ) ) {
3560 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3561 p2.getNode( "c" ) );
3562 if ( !cde2.getName().equals( "cde" ) ) {
3565 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3566 p2.getNode( "f" ) );
3567 if ( !cdef.getName().equals( "cdef" ) ) {
3570 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3571 p2.getNode( "f" ) );
3572 if ( !cdef2.getName().equals( "cdef" ) ) {
3575 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3576 p2.getNode( "d" ) );
3577 if ( !cdef3.getName().equals( "cdef" ) ) {
3580 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3581 p2.getNode( "a" ) );
3582 if ( !rt.getName().equals( "r" ) ) {
3585 final Phylogeny p3 = factory
3586 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3587 new NHXParser() )[ 0 ];
3588 PhylogenyMethods.preOrderReId( p3 );
3589 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3590 p3.getNode( "c" ) );
3591 if ( !bc_3.getName().equals( "bc" ) ) {
3594 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3595 p3.getNode( "c" ) );
3596 if ( !ac_3.getName().equals( "abc" ) ) {
3599 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3600 p3.getNode( "d" ) );
3601 if ( !ad_3.getName().equals( "abcde" ) ) {
3604 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3605 p3.getNode( "f" ) );
3606 if ( !af_3.getName().equals( "abcdef" ) ) {
3609 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3610 p3.getNode( "g" ) );
3611 if ( !ag_3.getName().equals( "" ) ) {
3614 if ( !ag_3.isRoot() ) {
3617 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3618 p3.getNode( "l" ) );
3619 if ( !al_3.getName().equals( "" ) ) {
3622 if ( !al_3.isRoot() ) {
3625 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3626 p3.getNode( "l" ) );
3627 if ( !kl_3.getName().equals( "" ) ) {
3630 if ( !kl_3.isRoot() ) {
3633 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3634 p3.getNode( "l" ) );
3635 if ( !fl_3.getName().equals( "" ) ) {
3638 if ( !fl_3.isRoot() ) {
3641 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3642 p3.getNode( "k" ) );
3643 if ( !gk_3.getName().equals( "ghijk" ) ) {
3646 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3647 PhylogenyMethods.preOrderReId( p4 );
3648 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3649 p4.getNode( "c" ) );
3650 if ( !r_4.getName().equals( "r" ) ) {
3653 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3654 PhylogenyMethods.preOrderReId( p5 );
3655 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3656 p5.getNode( "c" ) );
3657 if ( !r_5.getName().equals( "root" ) ) {
3660 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3661 PhylogenyMethods.preOrderReId( p6 );
3662 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3663 p6.getNode( "a" ) );
3664 if ( !r_6.getName().equals( "rot" ) ) {
3667 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3668 PhylogenyMethods.preOrderReId( p7 );
3669 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3670 p7.getNode( "e" ) );
3671 if ( !r_7.getName().equals( "rott" ) ) {
3674 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3675 p7.getNode( "a" ) );
3676 if ( !r_71.getName().equals( "rott" ) ) {
3679 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3680 p7.getNode( "rott" ) );
3681 if ( !r_72.getName().equals( "rott" ) ) {
3684 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3685 p7.getNode( "a" ) );
3686 if ( !r_73.getName().equals( "rott" ) ) {
3689 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3690 p7.getNode( "rott" ) );
3691 if ( !r_74.getName().equals( "rott" ) ) {
3694 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3695 p7.getNode( "e" ) );
3696 if ( !r_75.getName().equals( "e" ) ) {
3700 catch ( final Exception e ) {
3701 e.printStackTrace( System.out );
3707 private static boolean testHmmscanOutputParser() {
3708 final String test_dir = Test.PATH_TO_TEST_DATA;
3710 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3711 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3713 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3714 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3715 final List<Protein> proteins = parser2.parse();
3716 if ( parser2.getProteinsEncountered() != 4 ) {
3719 if ( proteins.size() != 4 ) {
3722 if ( parser2.getDomainsEncountered() != 69 ) {
3725 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3728 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3731 final Protein p1 = proteins.get( 0 );
3732 if ( p1.getNumberOfProteinDomains() != 15 ) {
3735 if ( p1.getLength() != 850 ) {
3738 final Protein p2 = proteins.get( 1 );
3739 if ( p2.getNumberOfProteinDomains() != 51 ) {
3742 if ( p2.getLength() != 1291 ) {
3745 final Protein p3 = proteins.get( 2 );
3746 if ( p3.getNumberOfProteinDomains() != 2 ) {
3749 final Protein p4 = proteins.get( 3 );
3750 if ( p4.getNumberOfProteinDomains() != 1 ) {
3753 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3756 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3759 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3762 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3765 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3768 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3771 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3774 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3777 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3781 catch ( final Exception e ) {
3782 e.printStackTrace( System.out );
3788 private static boolean testLastExternalNodeMethods() {
3790 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3791 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3792 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3793 final PhylogenyNode n1 = t0.getNode( "A" );
3794 if ( n1.isLastExternalNode() ) {
3797 final PhylogenyNode n2 = t0.getNode( "B" );
3798 if ( n2.isLastExternalNode() ) {
3801 final PhylogenyNode n3 = t0.getNode( "C" );
3802 if ( n3.isLastExternalNode() ) {
3805 final PhylogenyNode n4 = t0.getNode( "D" );
3806 if ( !n4.isLastExternalNode() ) {
3810 catch ( final Exception e ) {
3811 e.printStackTrace( System.out );
3817 private static boolean testLevelOrderIterator() {
3819 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3820 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3821 PhylogenyNodeIterator it0;
3822 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3825 for( it0.reset(); it0.hasNext(); ) {
3828 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3829 if ( !it.next().getName().equals( "r" ) ) {
3832 if ( !it.next().getName().equals( "ab" ) ) {
3835 if ( !it.next().getName().equals( "cd" ) ) {
3838 if ( !it.next().getName().equals( "A" ) ) {
3841 if ( !it.next().getName().equals( "B" ) ) {
3844 if ( !it.next().getName().equals( "C" ) ) {
3847 if ( !it.next().getName().equals( "D" ) ) {
3850 if ( it.hasNext() ) {
3853 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",
3854 new NHXParser() )[ 0 ];
3855 PhylogenyNodeIterator it2;
3856 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3859 for( it2.reset(); it2.hasNext(); ) {
3862 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3863 if ( !it3.next().getName().equals( "r" ) ) {
3866 if ( !it3.next().getName().equals( "abc" ) ) {
3869 if ( !it3.next().getName().equals( "defg" ) ) {
3872 if ( !it3.next().getName().equals( "A" ) ) {
3875 if ( !it3.next().getName().equals( "B" ) ) {
3878 if ( !it3.next().getName().equals( "C" ) ) {
3881 if ( !it3.next().getName().equals( "D" ) ) {
3884 if ( !it3.next().getName().equals( "E" ) ) {
3887 if ( !it3.next().getName().equals( "F" ) ) {
3890 if ( !it3.next().getName().equals( "G" ) ) {
3893 if ( !it3.next().getName().equals( "1" ) ) {
3896 if ( !it3.next().getName().equals( "2" ) ) {
3899 if ( !it3.next().getName().equals( "3" ) ) {
3902 if ( !it3.next().getName().equals( "4" ) ) {
3905 if ( !it3.next().getName().equals( "5" ) ) {
3908 if ( !it3.next().getName().equals( "6" ) ) {
3911 if ( !it3.next().getName().equals( "f1" ) ) {
3914 if ( !it3.next().getName().equals( "f2" ) ) {
3917 if ( !it3.next().getName().equals( "f3" ) ) {
3920 if ( !it3.next().getName().equals( "a" ) ) {
3923 if ( !it3.next().getName().equals( "b" ) ) {
3926 if ( !it3.next().getName().equals( "f21" ) ) {
3929 if ( !it3.next().getName().equals( "X" ) ) {
3932 if ( !it3.next().getName().equals( "Y" ) ) {
3935 if ( !it3.next().getName().equals( "Z" ) ) {
3938 if ( it3.hasNext() ) {
3941 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3942 PhylogenyNodeIterator it4;
3943 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3946 for( it4.reset(); it4.hasNext(); ) {
3949 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3950 if ( !it5.next().getName().equals( "r" ) ) {
3953 if ( !it5.next().getName().equals( "A" ) ) {
3956 if ( !it5.next().getName().equals( "B" ) ) {
3959 if ( !it5.next().getName().equals( "C" ) ) {
3962 if ( !it5.next().getName().equals( "D" ) ) {
3965 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3966 PhylogenyNodeIterator it6;
3967 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3970 for( it6.reset(); it6.hasNext(); ) {
3973 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3974 if ( !it7.next().getName().equals( "A" ) ) {
3977 if ( it.hasNext() ) {
3981 catch ( final Exception e ) {
3982 e.printStackTrace( System.out );
3988 private static boolean testNodeRemoval() {
3990 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3991 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3992 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
3993 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
3996 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
3997 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
3998 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4001 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4002 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4003 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4007 catch ( final Exception e ) {
4008 e.printStackTrace( System.out );
4014 private static boolean testMidpointrooting() {
4016 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4017 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4018 PhylogenyMethods.midpointRoot( t0 );
4019 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4022 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4025 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4029 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",
4030 new NHXParser() )[ 0 ];
4031 if ( !t1.isRooted() ) {
4034 PhylogenyMethods.midpointRoot( t1 );
4035 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4038 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4041 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4044 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4047 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4050 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4053 t1.reRoot( t1.getNode( "A" ) );
4054 PhylogenyMethods.midpointRoot( t1 );
4055 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4058 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4061 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4064 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4067 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4071 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4075 catch ( final Exception e ) {
4076 e.printStackTrace( System.out );
4082 private static boolean testNexusCharactersParsing() {
4084 final NexusCharactersParser parser = new NexusCharactersParser();
4085 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4087 String[] labels = parser.getCharStateLabels();
4088 if ( labels.length != 7 ) {
4091 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4094 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4097 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4100 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4103 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4106 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4109 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4112 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4114 labels = parser.getCharStateLabels();
4115 if ( labels.length != 7 ) {
4118 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4121 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4124 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4127 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4130 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4133 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4136 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4140 catch ( final Exception e ) {
4141 e.printStackTrace( System.out );
4147 private static boolean testNexusMatrixParsing() {
4149 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4150 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4152 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4153 if ( m.getNumberOfCharacters() != 9 ) {
4156 if ( m.getNumberOfIdentifiers() != 5 ) {
4159 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4162 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4165 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4168 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4171 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4174 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4177 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4180 // if ( labels.length != 7 ) {
4183 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4186 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4189 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4192 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4195 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4198 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4201 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4204 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4206 // labels = parser.getCharStateLabels();
4207 // if ( labels.length != 7 ) {
4210 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4213 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4216 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4219 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4222 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4225 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4228 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4232 catch ( final Exception e ) {
4233 e.printStackTrace( System.out );
4239 private static boolean testNexusTreeParsing() {
4241 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4242 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4243 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4244 if ( phylogenies.length != 1 ) {
4247 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4250 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4254 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4255 if ( phylogenies.length != 1 ) {
4258 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4261 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4265 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4266 if ( phylogenies.length != 1 ) {
4269 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4272 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4275 if ( phylogenies[ 0 ].isRooted() ) {
4279 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4280 if ( phylogenies.length != 18 ) {
4283 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4286 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4289 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4292 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4295 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4298 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4301 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4304 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4307 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4310 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4313 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4316 if ( phylogenies[ 8 ].isRooted() ) {
4319 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4322 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4325 if ( !phylogenies[ 9 ].isRooted() ) {
4328 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4331 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4334 if ( !phylogenies[ 10 ].isRooted() ) {
4337 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4340 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4343 if ( phylogenies[ 11 ].isRooted() ) {
4346 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4349 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4352 if ( !phylogenies[ 12 ].isRooted() ) {
4355 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4358 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4361 if ( !phylogenies[ 13 ].isRooted() ) {
4364 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4367 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4370 if ( !phylogenies[ 14 ].isRooted() ) {
4373 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4376 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4379 if ( phylogenies[ 15 ].isRooted() ) {
4382 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4385 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4388 if ( !phylogenies[ 16 ].isRooted() ) {
4391 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4394 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4397 if ( phylogenies[ 17 ].isRooted() ) {
4400 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4404 catch ( final Exception e ) {
4405 e.printStackTrace( System.out );
4411 private static boolean testNexusTreeParsingTranslating() {
4413 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4414 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4415 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4416 if ( phylogenies.length != 1 ) {
4419 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4422 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4425 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4428 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4431 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4432 .equals( "Aranaeus" ) ) {
4436 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4437 if ( phylogenies.length != 3 ) {
4440 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4443 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4446 if ( phylogenies[ 0 ].isRooted() ) {
4449 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4452 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4455 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4456 .equals( "Aranaeus" ) ) {
4459 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4462 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4465 if ( phylogenies[ 1 ].isRooted() ) {
4468 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4471 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4474 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4475 .equals( "Aranaeus" ) ) {
4478 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4481 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4484 if ( !phylogenies[ 2 ].isRooted() ) {
4487 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4490 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4493 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4494 .equals( "Aranaeus" ) ) {
4498 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4499 if ( phylogenies.length != 3 ) {
4502 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4505 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4508 if ( phylogenies[ 0 ].isRooted() ) {
4511 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4514 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4517 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4518 .equals( "Aranaeus" ) ) {
4521 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4524 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4527 if ( phylogenies[ 1 ].isRooted() ) {
4530 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4533 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4536 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4537 .equals( "Aranaeus" ) ) {
4540 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4543 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4546 if ( !phylogenies[ 2 ].isRooted() ) {
4549 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4552 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4555 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4556 .equals( "Aranaeus" ) ) {
4560 catch ( final Exception e ) {
4561 e.printStackTrace( System.out );
4567 private static boolean testNHParsing() {
4569 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4570 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4571 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4574 final NHXParser nhxp = new NHXParser();
4575 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4576 nhxp.setReplaceUnderscores( true );
4577 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4578 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4581 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4584 final Phylogeny p1b = factory
4585 .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 ",
4586 new NHXParser() )[ 0 ];
4587 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4590 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4593 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4594 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4595 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4596 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4597 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4598 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4599 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4600 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4601 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4602 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4603 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4604 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4605 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4607 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4610 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4613 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4616 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4619 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4620 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4621 final String p16_S = "((A,B),C)";
4622 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4623 if ( p16.length != 1 ) {
4626 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4629 final String p17_S = "(C,(A,B))";
4630 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4631 if ( p17.length != 1 ) {
4634 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4637 final String p18_S = "((A,B),(C,D))";
4638 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4639 if ( p18.length != 1 ) {
4642 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4645 final String p19_S = "(((A,B),C),D)";
4646 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4647 if ( p19.length != 1 ) {
4650 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4653 final String p20_S = "(A,(B,(C,D)))";
4654 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4655 if ( p20.length != 1 ) {
4658 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4661 final String p21_S = "(A,(B,(C,(D,E))))";
4662 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4663 if ( p21.length != 1 ) {
4666 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4669 final String p22_S = "((((A,B),C),D),E)";
4670 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4671 if ( p22.length != 1 ) {
4674 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4677 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4678 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4679 if ( p23.length != 1 ) {
4680 System.out.println( "xl=" + p23.length );
4684 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4687 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4688 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4689 if ( p24.length != 1 ) {
4692 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4695 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4696 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4697 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4698 if ( p241.length != 2 ) {
4701 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4704 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4707 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4708 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4709 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4710 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4711 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4712 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4713 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4714 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4715 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4716 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4719 final String p26_S = "(A,B)ab";
4720 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4721 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4724 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4725 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
4726 if ( p27s.length != 1 ) {
4727 System.out.println( "xxl=" + p27s.length );
4731 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4732 System.out.println( p27s[ 0 ].toNewHampshireX() );
4736 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4738 if ( p27.length != 1 ) {
4739 System.out.println( "yl=" + p27.length );
4743 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4744 System.out.println( p27[ 0 ].toNewHampshireX() );
4748 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4749 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4750 final String p28_S3 = "(A,B)ab";
4751 final String p28_S4 = "((((A,B),C),D),;E;)";
4752 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4754 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4757 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4760 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4763 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4766 if ( p28.length != 4 ) {
4769 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";
4770 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4771 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4774 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";
4775 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4776 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4779 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4780 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4781 if ( ( p32.length != 0 ) ) {
4784 final String p33_S = "A";
4785 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4786 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4789 final String p34_S = "B;";
4790 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4791 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4794 final String p35_S = "B:0.2";
4795 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4796 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4799 final String p36_S = "(A)";
4800 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4801 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4804 final String p37_S = "((A))";
4805 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4806 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4809 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4810 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4811 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4814 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4815 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4816 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4819 final String p40_S = "(A,B,C)";
4820 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4821 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4824 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4825 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4826 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4829 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4830 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4831 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4834 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)";
4835 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4836 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4839 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)))";
4840 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4841 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4844 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4845 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4846 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4849 final String p46_S = "";
4850 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4851 if ( p46.length != 0 ) {
4854 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4855 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4858 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4859 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4862 final Phylogeny p49 = factory
4863 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4864 new NHXParser() )[ 0 ];
4865 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4868 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4869 if ( p50.getNode( "A" ) == null ) {
4872 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4873 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4876 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4879 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4880 .equals( "((A,B)88:2.0,C);" ) ) {
4883 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4884 if ( p51.getNode( "A(A" ) == null ) {
4887 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4888 if ( p52.getNode( "A(A" ) == null ) {
4891 final Phylogeny p53 = factory
4892 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4893 new NHXParser() )[ 0 ];
4894 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4898 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4899 if ( p54.getNode( "A" ) == null ) {
4902 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4903 .equals( "((A,B)[88],C);" ) ) {
4907 catch ( final Exception e ) {
4908 e.printStackTrace( System.out );
4914 private static boolean testNHParsingIter() {
4916 final String p0_str = "(A,B);";
4917 final NHXParser p = new NHXParser();
4918 p.setSource( p0_str );
4919 if ( !p.hasNext() ) {
4922 final Phylogeny p0 = p.next();
4923 if ( !p0.toNewHampshire().equals( p0_str ) ) {
4924 System.out.println( p0.toNewHampshire() );
4927 if ( p.hasNext() ) {
4930 if ( p.next() != null ) {
4934 final String p00_str = "(A,B)root;";
4935 p.setSource( p00_str );
4936 final Phylogeny p00 = p.next();
4937 if ( !p00.toNewHampshire().equals( p00_str ) ) {
4938 System.out.println( p00.toNewHampshire() );
4942 final String p000_str = "A;";
4943 p.setSource( p000_str );
4944 final Phylogeny p000 = p.next();
4945 if ( !p000.toNewHampshire().equals( p000_str ) ) {
4946 System.out.println( p000.toNewHampshire() );
4950 final String p0000_str = "A";
4951 p.setSource( p0000_str );
4952 final Phylogeny p0000 = p.next();
4953 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
4954 System.out.println( p0000.toNewHampshire() );
4958 p.setSource( "(A)" );
4959 final Phylogeny p00000 = p.next();
4960 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
4961 System.out.println( p00000.toNewHampshire() );
4965 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
4966 p.setSource( p1_str );
4967 if ( !p.hasNext() ) {
4970 final Phylogeny p1_0 = p.next();
4971 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
4972 System.out.println( p1_0.toNewHampshire() );
4975 if ( !p.hasNext() ) {
4978 final Phylogeny p1_1 = p.next();
4979 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
4980 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
4983 if ( !p.hasNext() ) {
4986 final Phylogeny p1_2 = p.next();
4987 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
4988 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
4991 if ( !p.hasNext() ) {
4994 final Phylogeny p1_3 = p.next();
4995 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
4996 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
4999 if ( p.hasNext() ) {
5002 if ( p.next() != null ) {
5006 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
5007 p.setSource( p2_str );
5008 if ( !p.hasNext() ) {
5011 Phylogeny p2_0 = p.next();
5012 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5013 System.out.println( p2_0.toNewHampshire() );
5016 if ( !p.hasNext() ) {
5019 Phylogeny p2_1 = p.next();
5020 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5021 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5024 if ( !p.hasNext() ) {
5027 Phylogeny p2_2 = p.next();
5028 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5029 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5032 if ( !p.hasNext() ) {
5035 Phylogeny p2_3 = p.next();
5036 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5037 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5040 if ( !p.hasNext() ) {
5043 Phylogeny p2_4 = p.next();
5044 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5045 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5048 if ( p.hasNext() ) {
5051 if ( p.next() != null ) {
5056 if ( !p.hasNext() ) {
5060 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5061 System.out.println( p2_0.toNewHampshire() );
5064 if ( !p.hasNext() ) {
5068 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5069 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5072 if ( !p.hasNext() ) {
5076 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5077 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5080 if ( !p.hasNext() ) {
5084 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5085 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5088 if ( !p.hasNext() ) {
5092 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5093 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5096 if ( p.hasNext() ) {
5099 if ( p.next() != null ) {
5103 final String p3_str = "((A,B),C)abc";
5104 p.setSource( p3_str );
5105 if ( !p.hasNext() ) {
5108 final Phylogeny p3_0 = p.next();
5109 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
5112 if ( p.hasNext() ) {
5115 if ( p.next() != null ) {
5119 final String p4_str = "((A,B)ab,C)abc";
5120 p.setSource( p4_str );
5121 if ( !p.hasNext() ) {
5124 final Phylogeny p4_0 = p.next();
5125 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
5128 if ( p.hasNext() ) {
5131 if ( p.next() != null ) {
5135 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
5136 p.setSource( p5_str );
5137 if ( !p.hasNext() ) {
5140 final Phylogeny p5_0 = p.next();
5141 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
5144 if ( p.hasNext() ) {
5147 if ( p.next() != null ) {
5151 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5152 p.setSource( p6_str );
5153 if ( !p.hasNext() ) {
5156 Phylogeny p6_0 = p.next();
5157 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5160 if ( p.hasNext() ) {
5163 if ( p.next() != null ) {
5167 if ( !p.hasNext() ) {
5171 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5174 if ( p.hasNext() ) {
5177 if ( p.next() != null ) {
5181 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5182 p.setSource( p7_str );
5183 if ( !p.hasNext() ) {
5186 Phylogeny p7_0 = p.next();
5187 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5190 if ( p.hasNext() ) {
5193 if ( p.next() != null ) {
5197 if ( !p.hasNext() ) {
5201 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5204 if ( p.hasNext() ) {
5207 if ( p.next() != null ) {
5211 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
5212 p.setSource( p8_str );
5213 if ( !p.hasNext() ) {
5216 Phylogeny p8_0 = p.next();
5217 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5220 if ( !p.hasNext() ) {
5223 if ( !p.hasNext() ) {
5226 Phylogeny p8_1 = p.next();
5227 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5230 if ( p.hasNext() ) {
5233 if ( p.next() != null ) {
5237 if ( !p.hasNext() ) {
5241 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5244 if ( !p.hasNext() ) {
5248 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5251 if ( p.hasNext() ) {
5254 if ( p.next() != null ) {
5260 if ( p.hasNext() ) {
5264 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
5265 if ( !p.hasNext() ) {
5268 Phylogeny p_27 = p.next();
5269 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5270 System.out.println( p_27.toNewHampshireX() );
5274 if ( p.hasNext() ) {
5277 if ( p.next() != null ) {
5281 if ( !p.hasNext() ) {
5285 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5286 System.out.println( p_27.toNewHampshireX() );
5290 if ( p.hasNext() ) {
5293 if ( p.next() != null ) {
5297 catch ( final Exception e ) {
5298 e.printStackTrace( System.out );
5304 private static boolean testNHXconversion() {
5306 final PhylogenyNode n1 = new PhylogenyNode();
5307 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5308 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5309 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5310 final PhylogenyNode n5 = PhylogenyNode
5311 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
5312 final PhylogenyNode n6 = PhylogenyNode
5313 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
5314 if ( !n1.toNewHampshireX().equals( "" ) ) {
5317 if ( !n2.toNewHampshireX().equals( "" ) ) {
5320 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
5323 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
5326 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
5329 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
5333 catch ( final Exception e ) {
5334 e.printStackTrace( System.out );
5340 private static boolean testTaxonomyExtraction() {
5342 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5343 NHXParser.TAXONOMY_EXTRACTION.YES );
5344 if ( n0.getNodeData().isHasTaxonomy() ) {
5347 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
5348 NHXParser.TAXONOMY_EXTRACTION.YES );
5349 if ( n1.getNodeData().isHasTaxonomy() ) {
5350 System.out.println( n1.toString() );
5353 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
5354 NHXParser.TAXONOMY_EXTRACTION.YES );
5355 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5356 System.out.println( n2.toString() );
5359 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
5360 NHXParser.TAXONOMY_EXTRACTION.YES );
5361 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5362 System.out.println( n3.toString() );
5365 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
5366 NHXParser.TAXONOMY_EXTRACTION.YES );
5367 if ( n4.getNodeData().isHasTaxonomy() ) {
5368 System.out.println( n4.toString() );
5371 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
5372 NHXParser.TAXONOMY_EXTRACTION.YES );
5373 if ( n5.getNodeData().isHasTaxonomy() ) {
5374 System.out.println( n5.toString() );
5377 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
5378 NHXParser.TAXONOMY_EXTRACTION.YES );
5379 if ( n6.getNodeData().isHasTaxonomy() ) {
5380 System.out.println( n6.toString() );
5383 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
5384 NHXParser.TAXONOMY_EXTRACTION.YES );
5385 if ( n7.getNodeData().isHasTaxonomy() ) {
5386 System.out.println( n7.toString() );
5389 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
5390 NHXParser.TAXONOMY_EXTRACTION.YES );
5391 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5392 System.out.println( n8.toString() );
5395 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
5396 NHXParser.TAXONOMY_EXTRACTION.YES );
5397 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5398 System.out.println( n9.toString() );
5401 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
5402 NHXParser.TAXONOMY_EXTRACTION.YES );
5403 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
5404 System.out.println( n10.toString() );
5407 final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
5408 NHXParser.TAXONOMY_EXTRACTION.YES );
5409 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
5410 System.out.println( n11.toString() );
5413 final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
5414 NHXParser.TAXONOMY_EXTRACTION.YES );
5415 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
5416 System.out.println( n12.toString() );
5419 final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
5420 NHXParser.TAXONOMY_EXTRACTION.YES );
5421 if ( n13.getNodeData().isHasTaxonomy() ) {
5422 System.out.println( n13.toString() );
5425 final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
5426 NHXParser.TAXONOMY_EXTRACTION.YES );
5427 if ( n14.getNodeData().isHasTaxonomy() ) {
5428 System.out.println( n14.toString() );
5431 final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
5432 NHXParser.TAXONOMY_EXTRACTION.YES );
5433 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
5434 System.out.println( n15.toString() );
5437 final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
5438 NHXParser.TAXONOMY_EXTRACTION.YES );
5439 if ( n16.getNodeData().isHasTaxonomy() ) {
5440 System.out.println( n16.toString() );
5443 final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
5444 NHXParser.TAXONOMY_EXTRACTION.YES );
5445 if ( n17.getNodeData().isHasTaxonomy() ) {
5446 System.out.println( n17.toString() );
5450 catch ( final Exception e ) {
5451 e.printStackTrace( System.out );
5457 private static boolean testNHXNodeParsing() {
5459 final PhylogenyNode n1 = new PhylogenyNode();
5460 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5461 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5462 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5463 final PhylogenyNode n5 = PhylogenyNode
5464 .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]" );
5465 if ( !n3.getName().equals( "n3" ) ) {
5468 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5471 if ( n3.isDuplication() ) {
5474 if ( n3.isHasAssignedEvent() ) {
5477 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
5480 if ( !n4.getName().equals( "n4" ) ) {
5483 if ( n4.getDistanceToParent() != 0.01 ) {
5486 if ( !n5.getName().equals( "n5" ) ) {
5489 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
5492 if ( n5.getDistanceToParent() != 0.1 ) {
5495 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
5498 if ( !n5.isDuplication() ) {
5501 if ( !n5.isHasAssignedEvent() ) {
5504 final PhylogenyNode n8 = PhylogenyNode
5505 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5506 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
5509 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
5512 final PhylogenyNode n9 = PhylogenyNode
5513 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5514 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
5517 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
5520 final PhylogenyNode n10 = PhylogenyNode
5521 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5522 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
5525 final PhylogenyNode n20 = PhylogenyNode
5526 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5527 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
5530 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
5533 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
5534 NHXParser.TAXONOMY_EXTRACTION.YES );
5535 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
5538 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
5541 final PhylogenyNode n20xx = PhylogenyNode
5542 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5543 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
5546 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
5549 final PhylogenyNode n20xxx = PhylogenyNode
5550 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5551 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
5554 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
5557 final PhylogenyNode n20xxxx = PhylogenyNode
5558 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5559 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
5562 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
5565 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
5566 NHXParser.TAXONOMY_EXTRACTION.YES );
5567 if ( !n21.getName().equals( "n21_PIG" ) ) {
5570 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
5573 final PhylogenyNode n21x = PhylogenyNode
5574 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5575 if ( !n21x.getName().equals( "n21_PIG" ) ) {
5578 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
5581 final PhylogenyNode n22 = PhylogenyNode
5582 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5583 if ( !n22.getName().equals( "n22/PIG" ) ) {
5586 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
5589 final PhylogenyNode n23 = PhylogenyNode
5590 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5591 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
5594 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
5597 final PhylogenyNode a = PhylogenyNode
5598 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5599 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
5602 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
5605 final PhylogenyNode b = PhylogenyNode
5606 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5607 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
5610 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
5613 final PhylogenyNode c = PhylogenyNode
5614 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
5615 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5616 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
5619 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
5622 final PhylogenyNode c1 = PhylogenyNode
5623 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
5624 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5625 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
5628 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
5631 final PhylogenyNode c2 = PhylogenyNode
5632 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
5633 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5634 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5637 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5640 final PhylogenyNode d = PhylogenyNode
5641 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5642 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5645 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5648 final PhylogenyNode e = PhylogenyNode
5649 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5650 if ( !e.getName().equals( "n10_RAT1" ) ) {
5653 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5656 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5657 NHXParser.TAXONOMY_EXTRACTION.YES );
5658 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5661 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5664 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5665 NHXParser.TAXONOMY_EXTRACTION.YES );
5666 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5669 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5672 final PhylogenyNode n11 = PhylogenyNode
5673 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5674 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5675 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5678 if ( n11.getDistanceToParent() != 0.4 ) {
5681 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5684 final PhylogenyNode n12 = PhylogenyNode
5685 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5686 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5687 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5690 if ( n12.getDistanceToParent() != 0.4 ) {
5693 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5696 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5697 NHXParser.TAXONOMY_EXTRACTION.YES );
5698 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5701 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5704 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5705 NHXParser.TAXONOMY_EXTRACTION.YES );
5706 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5709 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5712 if ( n1.getName().compareTo( "" ) != 0 ) {
5715 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5718 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5721 if ( n2.getName().compareTo( "" ) != 0 ) {
5724 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5727 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5730 final PhylogenyNode n00 = PhylogenyNode
5731 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
5732 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5735 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5738 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5739 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5742 final PhylogenyNode n13 = PhylogenyNode
5743 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5744 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5747 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5750 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5753 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5756 final PhylogenyNode n14 = PhylogenyNode
5757 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5758 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5761 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5764 final PhylogenyNode n15 = PhylogenyNode
5765 .createInstanceFromNhxString( "something_wicked[123]",
5766 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5767 if ( !n15.getName().equals( "something_wicked" ) ) {
5770 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5773 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5776 final PhylogenyNode n16 = PhylogenyNode
5777 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5778 if ( !n16.getName().equals( "something_wicked2" ) ) {
5781 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5784 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5787 final PhylogenyNode n17 = PhylogenyNode
5788 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5789 if ( !n17.getName().equals( "something_wicked3" ) ) {
5792 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5795 final PhylogenyNode n18 = PhylogenyNode
5796 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5797 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5800 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5803 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5806 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
5807 NHXParser.TAXONOMY_EXTRACTION.YES );
5808 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
5811 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5814 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
5815 NHXParser.TAXONOMY_EXTRACTION.YES );
5816 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
5819 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5822 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
5823 NHXParser.TAXONOMY_EXTRACTION.YES );
5824 if ( n31.getNodeData().isHasTaxonomy() ) {
5827 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5828 NHXParser.TAXONOMY_EXTRACTION.YES );
5829 if ( n32.getNodeData().isHasTaxonomy() ) {
5833 catch ( final Exception e ) {
5834 e.printStackTrace( System.out );
5840 private static boolean testNHXParsing() {
5842 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5843 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5844 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5847 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]";
5848 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5849 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5852 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]";
5853 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5854 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5857 final Phylogeny[] p3 = factory
5858 .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]",
5860 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5863 final Phylogeny[] p4 = factory
5864 .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(]",
5866 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5869 final Phylogeny[] p5 = factory
5870 .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(((]",
5872 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5875 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)";
5876 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)";
5877 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5878 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5881 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)))";
5882 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)))";
5883 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5884 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5887 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]) ))[,,, ])))))))";
5888 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5889 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5890 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5893 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5894 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5897 final Phylogeny p10 = factory
5898 .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]",
5899 new NHXParser() )[ 0 ];
5900 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5904 catch ( final Exception e ) {
5905 e.printStackTrace( System.out );
5911 private static boolean testNHXParsingQuotes() {
5913 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5914 final NHXParser p = new NHXParser();
5915 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5916 if ( phylogenies_0.length != 5 ) {
5919 final Phylogeny phy = phylogenies_0[ 4 ];
5920 if ( phy.getNumberOfExternalNodes() != 7 ) {
5923 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5926 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5929 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5930 .getScientificName().equals( "hsapiens" ) ) {
5933 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5936 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5939 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5942 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5945 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5948 final NHXParser p1p = new NHXParser();
5949 p1p.setIgnoreQuotes( true );
5950 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5951 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5954 final NHXParser p2p = new NHXParser();
5955 p1p.setIgnoreQuotes( false );
5956 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5957 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5960 final NHXParser p3p = new NHXParser();
5961 p3p.setIgnoreQuotes( false );
5962 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5963 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5966 final NHXParser p4p = new NHXParser();
5967 p4p.setIgnoreQuotes( false );
5968 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5969 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5972 final Phylogeny p10 = factory
5973 .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]",
5974 new NHXParser() )[ 0 ];
5975 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]";
5976 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5979 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5980 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5984 final Phylogeny p12 = factory
5985 .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]",
5986 new NHXParser() )[ 0 ];
5987 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]";
5988 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5991 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5992 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5995 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;";
5996 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5999 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
6000 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
6004 catch ( final Exception e ) {
6005 e.printStackTrace( System.out );
6011 private static boolean testNHXParsingMB() {
6013 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6014 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
6015 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6016 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6017 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6018 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6019 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6020 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6021 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6022 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
6023 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
6026 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
6029 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
6030 0.1100000000000000e+00 ) ) {
6033 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
6036 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
6039 final Phylogeny p2 = factory
6040 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
6041 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6042 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6043 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6044 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6045 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6046 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6047 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6048 + "7.369400000000000e-02}])",
6049 new NHXParser() )[ 0 ];
6050 if ( p2.getNode( "1" ) == null ) {
6053 if ( p2.getNode( "2" ) == null ) {
6057 catch ( final Exception e ) {
6058 e.printStackTrace( System.out );
6065 private static boolean testPhylogenyBranch() {
6067 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
6068 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
6069 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
6070 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
6071 if ( !a1b1.equals( a1b1 ) ) {
6074 if ( !a1b1.equals( b1a1 ) ) {
6077 if ( !b1a1.equals( a1b1 ) ) {
6080 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
6081 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
6082 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
6083 if ( a1_b1.equals( b1_a1 ) ) {
6086 if ( a1_b1.equals( a1_b1_ ) ) {
6089 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
6090 if ( !a1_b1.equals( b1_a1_ ) ) {
6093 if ( a1_b1_.equals( b1_a1_ ) ) {
6096 if ( !a1_b1_.equals( b1_a1 ) ) {
6100 catch ( final Exception e ) {
6101 e.printStackTrace( System.out );
6107 private static boolean testPhyloXMLparsingOfDistributionElement() {
6109 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6110 PhyloXmlParser xml_parser = null;
6112 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
6114 catch ( final Exception e ) {
6115 // Do nothing -- means were not running from jar.
6117 if ( xml_parser == null ) {
6118 xml_parser = new PhyloXmlParser();
6119 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
6120 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
6123 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
6126 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
6128 if ( xml_parser.getErrorCount() > 0 ) {
6129 System.out.println( xml_parser.getErrorMessages().toString() );
6132 if ( phylogenies_0.length != 1 ) {
6135 final Phylogeny t1 = phylogenies_0[ 0 ];
6136 PhylogenyNode n = null;
6137 Distribution d = null;
6138 n = t1.getNode( "root node" );
6139 if ( !n.getNodeData().isHasDistribution() ) {
6142 if ( n.getNodeData().getDistributions().size() != 1 ) {
6145 d = n.getNodeData().getDistribution();
6146 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6149 if ( d.getPoints().size() != 1 ) {
6152 if ( d.getPolygons() != null ) {
6155 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6158 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6161 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6164 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6167 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6170 n = t1.getNode( "node a" );
6171 if ( !n.getNodeData().isHasDistribution() ) {
6174 if ( n.getNodeData().getDistributions().size() != 2 ) {
6177 d = n.getNodeData().getDistribution( 1 );
6178 if ( !d.getDesc().equals( "San Diego" ) ) {
6181 if ( d.getPoints().size() != 1 ) {
6184 if ( d.getPolygons() != null ) {
6187 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6190 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6193 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6196 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6199 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6202 n = t1.getNode( "node bb" );
6203 if ( !n.getNodeData().isHasDistribution() ) {
6206 if ( n.getNodeData().getDistributions().size() != 1 ) {
6209 d = n.getNodeData().getDistribution( 0 );
6210 if ( d.getPoints().size() != 3 ) {
6213 if ( d.getPolygons().size() != 2 ) {
6216 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6219 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6222 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6225 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6228 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6231 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6234 Polygon p = d.getPolygons().get( 0 );
6235 if ( p.getPoints().size() != 3 ) {
6238 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6241 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6244 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6247 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6250 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6253 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6256 p = d.getPolygons().get( 1 );
6257 if ( p.getPoints().size() != 3 ) {
6260 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6263 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6266 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6270 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
6271 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
6272 if ( rt.length != 1 ) {
6275 final Phylogeny t1_rt = rt[ 0 ];
6276 n = t1_rt.getNode( "root node" );
6277 if ( !n.getNodeData().isHasDistribution() ) {
6280 if ( n.getNodeData().getDistributions().size() != 1 ) {
6283 d = n.getNodeData().getDistribution();
6284 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6287 if ( d.getPoints().size() != 1 ) {
6290 if ( d.getPolygons() != null ) {
6293 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6296 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6299 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6302 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6305 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6308 n = t1_rt.getNode( "node a" );
6309 if ( !n.getNodeData().isHasDistribution() ) {
6312 if ( n.getNodeData().getDistributions().size() != 2 ) {
6315 d = n.getNodeData().getDistribution( 1 );
6316 if ( !d.getDesc().equals( "San Diego" ) ) {
6319 if ( d.getPoints().size() != 1 ) {
6322 if ( d.getPolygons() != null ) {
6325 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6328 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6331 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6334 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6337 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6340 n = t1_rt.getNode( "node bb" );
6341 if ( !n.getNodeData().isHasDistribution() ) {
6344 if ( n.getNodeData().getDistributions().size() != 1 ) {
6347 d = n.getNodeData().getDistribution( 0 );
6348 if ( d.getPoints().size() != 3 ) {
6351 if ( d.getPolygons().size() != 2 ) {
6354 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6357 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6360 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6363 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6366 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6369 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6372 p = d.getPolygons().get( 0 );
6373 if ( p.getPoints().size() != 3 ) {
6376 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6379 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6382 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6385 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6388 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6391 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6394 p = d.getPolygons().get( 1 );
6395 if ( p.getPoints().size() != 3 ) {
6398 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6401 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6404 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6408 catch ( final Exception e ) {
6409 e.printStackTrace( System.out );
6415 private static boolean testPostOrderIterator() {
6417 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6418 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6419 PhylogenyNodeIterator it0;
6420 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
6423 for( it0.reset(); it0.hasNext(); ) {
6426 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6427 final PhylogenyNodeIterator it = t1.iteratorPostorder();
6428 if ( !it.next().getName().equals( "A" ) ) {
6431 if ( !it.next().getName().equals( "B" ) ) {
6434 if ( !it.next().getName().equals( "ab" ) ) {
6437 if ( !it.next().getName().equals( "C" ) ) {
6440 if ( !it.next().getName().equals( "D" ) ) {
6443 if ( !it.next().getName().equals( "cd" ) ) {
6446 if ( !it.next().getName().equals( "abcd" ) ) {
6449 if ( !it.next().getName().equals( "E" ) ) {
6452 if ( !it.next().getName().equals( "F" ) ) {
6455 if ( !it.next().getName().equals( "ef" ) ) {
6458 if ( !it.next().getName().equals( "G" ) ) {
6461 if ( !it.next().getName().equals( "H" ) ) {
6464 if ( !it.next().getName().equals( "gh" ) ) {
6467 if ( !it.next().getName().equals( "efgh" ) ) {
6470 if ( !it.next().getName().equals( "r" ) ) {
6473 if ( it.hasNext() ) {
6477 catch ( final Exception e ) {
6478 e.printStackTrace( System.out );
6484 private static boolean testPreOrderIterator() {
6486 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6487 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6488 PhylogenyNodeIterator it0;
6489 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
6492 for( it0.reset(); it0.hasNext(); ) {
6495 PhylogenyNodeIterator it = t0.iteratorPreorder();
6496 if ( !it.next().getName().equals( "r" ) ) {
6499 if ( !it.next().getName().equals( "ab" ) ) {
6502 if ( !it.next().getName().equals( "A" ) ) {
6505 if ( !it.next().getName().equals( "B" ) ) {
6508 if ( !it.next().getName().equals( "cd" ) ) {
6511 if ( !it.next().getName().equals( "C" ) ) {
6514 if ( !it.next().getName().equals( "D" ) ) {
6517 if ( it.hasNext() ) {
6520 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6521 it = t1.iteratorPreorder();
6522 if ( !it.next().getName().equals( "r" ) ) {
6525 if ( !it.next().getName().equals( "abcd" ) ) {
6528 if ( !it.next().getName().equals( "ab" ) ) {
6531 if ( !it.next().getName().equals( "A" ) ) {
6534 if ( !it.next().getName().equals( "B" ) ) {
6537 if ( !it.next().getName().equals( "cd" ) ) {
6540 if ( !it.next().getName().equals( "C" ) ) {
6543 if ( !it.next().getName().equals( "D" ) ) {
6546 if ( !it.next().getName().equals( "efgh" ) ) {
6549 if ( !it.next().getName().equals( "ef" ) ) {
6552 if ( !it.next().getName().equals( "E" ) ) {
6555 if ( !it.next().getName().equals( "F" ) ) {
6558 if ( !it.next().getName().equals( "gh" ) ) {
6561 if ( !it.next().getName().equals( "G" ) ) {
6564 if ( !it.next().getName().equals( "H" ) ) {
6567 if ( it.hasNext() ) {
6571 catch ( final Exception e ) {
6572 e.printStackTrace( System.out );
6578 private static boolean testPropertiesMap() {
6580 final PropertiesMap pm = new PropertiesMap();
6581 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6582 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6583 final Property p2 = new Property( "something:else",
6585 "improbable:research",
6588 pm.addProperty( p0 );
6589 pm.addProperty( p1 );
6590 pm.addProperty( p2 );
6591 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
6594 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
6597 if ( pm.getProperties().size() != 3 ) {
6600 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
6603 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6606 if ( pm.getProperties().size() != 3 ) {
6609 pm.removeProperty( "dimensions:diameter" );
6610 if ( pm.getProperties().size() != 2 ) {
6613 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
6616 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6620 catch ( final Exception e ) {
6621 e.printStackTrace( System.out );
6627 private static boolean testReIdMethods() {
6629 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6630 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6631 final int count = PhylogenyNode.getNodeCount();
6633 if ( p.getNode( "r" ).getId() != count ) {
6636 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6639 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6642 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6645 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6648 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6651 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6654 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6657 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6660 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6663 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6666 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6669 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6672 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6675 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6679 catch ( final Exception e ) {
6680 e.printStackTrace( System.out );
6686 private static boolean testRerooting() {
6688 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6689 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",
6690 new NHXParser() )[ 0 ];
6691 if ( !t1.isRooted() ) {
6694 t1.reRoot( t1.getNode( "D" ) );
6695 t1.reRoot( t1.getNode( "CD" ) );
6696 t1.reRoot( t1.getNode( "A" ) );
6697 t1.reRoot( t1.getNode( "B" ) );
6698 t1.reRoot( t1.getNode( "AB" ) );
6699 t1.reRoot( t1.getNode( "D" ) );
6700 t1.reRoot( t1.getNode( "C" ) );
6701 t1.reRoot( t1.getNode( "CD" ) );
6702 t1.reRoot( t1.getNode( "A" ) );
6703 t1.reRoot( t1.getNode( "B" ) );
6704 t1.reRoot( t1.getNode( "AB" ) );
6705 t1.reRoot( t1.getNode( "D" ) );
6706 t1.reRoot( t1.getNode( "D" ) );
6707 t1.reRoot( t1.getNode( "C" ) );
6708 t1.reRoot( t1.getNode( "A" ) );
6709 t1.reRoot( t1.getNode( "B" ) );
6710 t1.reRoot( t1.getNode( "AB" ) );
6711 t1.reRoot( t1.getNode( "C" ) );
6712 t1.reRoot( t1.getNode( "D" ) );
6713 t1.reRoot( t1.getNode( "CD" ) );
6714 t1.reRoot( t1.getNode( "D" ) );
6715 t1.reRoot( t1.getNode( "A" ) );
6716 t1.reRoot( t1.getNode( "B" ) );
6717 t1.reRoot( t1.getNode( "AB" ) );
6718 t1.reRoot( t1.getNode( "C" ) );
6719 t1.reRoot( t1.getNode( "D" ) );
6720 t1.reRoot( t1.getNode( "CD" ) );
6721 t1.reRoot( t1.getNode( "D" ) );
6722 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6725 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6728 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6731 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6734 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6737 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6740 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",
6741 new NHXParser() )[ 0 ];
6742 t2.reRoot( t2.getNode( "A" ) );
6743 t2.reRoot( t2.getNode( "D" ) );
6744 t2.reRoot( t2.getNode( "ABC" ) );
6745 t2.reRoot( t2.getNode( "A" ) );
6746 t2.reRoot( t2.getNode( "B" ) );
6747 t2.reRoot( t2.getNode( "D" ) );
6748 t2.reRoot( t2.getNode( "C" ) );
6749 t2.reRoot( t2.getNode( "ABC" ) );
6750 t2.reRoot( t2.getNode( "A" ) );
6751 t2.reRoot( t2.getNode( "B" ) );
6752 t2.reRoot( t2.getNode( "AB" ) );
6753 t2.reRoot( t2.getNode( "AB" ) );
6754 t2.reRoot( t2.getNode( "D" ) );
6755 t2.reRoot( t2.getNode( "C" ) );
6756 t2.reRoot( t2.getNode( "B" ) );
6757 t2.reRoot( t2.getNode( "AB" ) );
6758 t2.reRoot( t2.getNode( "D" ) );
6759 t2.reRoot( t2.getNode( "D" ) );
6760 t2.reRoot( t2.getNode( "ABC" ) );
6761 t2.reRoot( t2.getNode( "A" ) );
6762 t2.reRoot( t2.getNode( "B" ) );
6763 t2.reRoot( t2.getNode( "AB" ) );
6764 t2.reRoot( t2.getNode( "D" ) );
6765 t2.reRoot( t2.getNode( "C" ) );
6766 t2.reRoot( t2.getNode( "ABC" ) );
6767 t2.reRoot( t2.getNode( "A" ) );
6768 t2.reRoot( t2.getNode( "B" ) );
6769 t2.reRoot( t2.getNode( "AB" ) );
6770 t2.reRoot( t2.getNode( "D" ) );
6771 t2.reRoot( t2.getNode( "D" ) );
6772 t2.reRoot( t2.getNode( "C" ) );
6773 t2.reRoot( t2.getNode( "A" ) );
6774 t2.reRoot( t2.getNode( "B" ) );
6775 t2.reRoot( t2.getNode( "AB" ) );
6776 t2.reRoot( t2.getNode( "C" ) );
6777 t2.reRoot( t2.getNode( "D" ) );
6778 t2.reRoot( t2.getNode( "ABC" ) );
6779 t2.reRoot( t2.getNode( "D" ) );
6780 t2.reRoot( t2.getNode( "A" ) );
6781 t2.reRoot( t2.getNode( "B" ) );
6782 t2.reRoot( t2.getNode( "AB" ) );
6783 t2.reRoot( t2.getNode( "C" ) );
6784 t2.reRoot( t2.getNode( "D" ) );
6785 t2.reRoot( t2.getNode( "ABC" ) );
6786 t2.reRoot( t2.getNode( "D" ) );
6787 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6790 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6793 t2.reRoot( t2.getNode( "ABC" ) );
6794 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6797 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6800 t2.reRoot( t2.getNode( "AB" ) );
6801 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6804 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6807 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6810 t2.reRoot( t2.getNode( "AB" ) );
6811 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6814 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6817 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6820 t2.reRoot( t2.getNode( "D" ) );
6821 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6824 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6827 t2.reRoot( t2.getNode( "ABC" ) );
6828 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6831 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6834 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6835 new NHXParser() )[ 0 ];
6836 t3.reRoot( t3.getNode( "B" ) );
6837 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6840 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6843 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6846 t3.reRoot( t3.getNode( "B" ) );
6847 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6850 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6853 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6856 t3.reRoot( t3.getRoot() );
6857 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6860 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6863 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6867 catch ( final Exception e ) {
6868 e.printStackTrace( System.out );
6874 private static boolean testSDIse() {
6876 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6877 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6878 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6879 gene1.setRooted( true );
6880 species1.setRooted( true );
6881 final SDI sdi = new SDI( gene1, species1 );
6882 if ( !gene1.getRoot().isDuplication() ) {
6885 final Phylogeny species2 = factory
6886 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6887 new NHXParser() )[ 0 ];
6888 final Phylogeny gene2 = factory
6889 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6890 new NHXParser() )[ 0 ];
6891 species2.setRooted( true );
6892 gene2.setRooted( true );
6893 final SDI sdi2 = new SDI( gene2, species2 );
6894 if ( sdi2.getDuplicationsSum() != 0 ) {
6897 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6900 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6903 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6906 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6909 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6912 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6915 final Phylogeny species3 = factory
6916 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6917 new NHXParser() )[ 0 ];
6918 final Phylogeny gene3 = factory
6919 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6920 new NHXParser() )[ 0 ];
6921 species3.setRooted( true );
6922 gene3.setRooted( true );
6923 final SDI sdi3 = new SDI( gene3, species3 );
6924 if ( sdi3.getDuplicationsSum() != 1 ) {
6927 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6930 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6933 final Phylogeny species4 = factory
6934 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6935 new NHXParser() )[ 0 ];
6936 final Phylogeny gene4 = factory
6937 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6938 new NHXParser() )[ 0 ];
6939 species4.setRooted( true );
6940 gene4.setRooted( true );
6941 final SDI sdi4 = new SDI( gene4, species4 );
6942 if ( sdi4.getDuplicationsSum() != 1 ) {
6945 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6948 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6951 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6954 if ( species4.getNumberOfExternalNodes() != 6 ) {
6957 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6960 final Phylogeny species5 = factory
6961 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6962 new NHXParser() )[ 0 ];
6963 final Phylogeny gene5 = factory
6964 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6965 new NHXParser() )[ 0 ];
6966 species5.setRooted( true );
6967 gene5.setRooted( true );
6968 final SDI sdi5 = new SDI( gene5, species5 );
6969 if ( sdi5.getDuplicationsSum() != 2 ) {
6972 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6975 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6978 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6981 if ( species5.getNumberOfExternalNodes() != 6 ) {
6984 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6987 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6988 // Conjecture for Comparing Molecular Phylogenies"
6989 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6990 final Phylogeny species6 = factory
6991 .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,"
6992 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6993 new NHXParser() )[ 0 ];
6994 final Phylogeny gene6 = factory
6995 .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,"
6996 + "((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,"
6997 + "(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;",
6998 new NHXParser() )[ 0 ];
6999 species6.setRooted( true );
7000 gene6.setRooted( true );
7001 final SDI sdi6 = new SDI( gene6, species6 );
7002 if ( sdi6.getDuplicationsSum() != 3 ) {
7005 if ( !gene6.getNode( "r" ).isDuplication() ) {
7008 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
7011 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
7014 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
7017 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
7020 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
7023 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
7026 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
7029 sdi6.computeMappingCostL();
7030 if ( sdi6.computeMappingCostL() != 17 ) {
7033 if ( species6.getNumberOfExternalNodes() != 9 ) {
7036 if ( gene6.getNumberOfExternalNodes() != 9 ) {
7039 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
7040 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
7041 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
7042 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
7043 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
7044 species7.setRooted( true );
7045 final Phylogeny gene7_1 = Test
7046 .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])" );
7047 gene7_1.setRooted( true );
7048 final SDI sdi7 = new SDI( gene7_1, species7 );
7049 if ( sdi7.getDuplicationsSum() != 0 ) {
7052 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
7055 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
7058 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
7061 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
7064 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
7067 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
7070 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
7073 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
7076 final Phylogeny gene7_2 = Test
7077 .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])" );
7078 gene7_2.setRooted( true );
7079 final SDI sdi7_2 = new SDI( gene7_2, species7 );
7080 if ( sdi7_2.getDuplicationsSum() != 1 ) {
7083 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
7086 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
7089 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
7092 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
7095 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
7098 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
7101 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
7104 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
7107 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
7111 catch ( final Exception e ) {
7117 private static boolean testSDIunrooted() {
7119 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7120 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
7121 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
7122 final Iterator<PhylogenyBranch> iter = l.iterator();
7123 PhylogenyBranch br = iter.next();
7124 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
7127 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
7131 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7134 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7138 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
7141 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
7145 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7148 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7152 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7155 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7159 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7162 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7166 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7169 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7173 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7176 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7180 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7183 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7187 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7190 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7194 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7197 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7201 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
7204 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
7208 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7211 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7215 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
7218 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
7222 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
7225 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
7228 if ( iter.hasNext() ) {
7231 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
7232 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
7233 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
7235 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7238 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7242 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7245 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7249 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7252 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7255 if ( iter1.hasNext() ) {
7258 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
7259 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
7260 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
7262 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7265 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7269 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7272 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7276 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7279 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7282 if ( iter2.hasNext() ) {
7285 final Phylogeny species0 = factory
7286 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7287 new NHXParser() )[ 0 ];
7288 final Phylogeny gene1 = factory
7289 .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])",
7290 new NHXParser() )[ 0 ];
7291 species0.setRooted( true );
7292 gene1.setRooted( true );
7293 final SDIR sdi_unrooted = new SDIR();
7294 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
7295 if ( sdi_unrooted.getCount() != 1 ) {
7298 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
7301 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
7304 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
7307 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7310 final Phylogeny gene2 = factory
7311 .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])",
7312 new NHXParser() )[ 0 ];
7313 gene2.setRooted( true );
7314 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
7315 if ( sdi_unrooted.getCount() != 1 ) {
7318 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7321 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7324 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7327 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7330 final Phylogeny species6 = factory
7331 .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,"
7332 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7333 new NHXParser() )[ 0 ];
7334 final Phylogeny gene6 = factory
7335 .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],"
7336 + "(((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],"
7337 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7338 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7339 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7340 new NHXParser() )[ 0 ];
7341 species6.setRooted( true );
7342 gene6.setRooted( true );
7343 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7344 if ( sdi_unrooted.getCount() != 1 ) {
7347 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7350 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7353 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7356 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7359 if ( !p6[ 0 ].getRoot().isDuplication() ) {
7362 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7365 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7368 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
7371 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7374 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
7377 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
7380 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7384 final Phylogeny species7 = factory
7385 .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,"
7386 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7387 new NHXParser() )[ 0 ];
7388 final Phylogeny gene7 = factory
7389 .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],"
7390 + "(((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],"
7391 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7392 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7393 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7394 new NHXParser() )[ 0 ];
7395 species7.setRooted( true );
7396 gene7.setRooted( true );
7397 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
7398 if ( sdi_unrooted.getCount() != 1 ) {
7401 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7404 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7407 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7410 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
7413 if ( !p7[ 0 ].getRoot().isDuplication() ) {
7416 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7419 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7422 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
7425 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7428 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
7431 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
7434 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7438 final Phylogeny species8 = factory
7439 .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,"
7440 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7441 new NHXParser() )[ 0 ];
7442 final Phylogeny gene8 = factory
7443 .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],"
7444 + "(((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],"
7445 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7446 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7447 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7448 new NHXParser() )[ 0 ];
7449 species8.setRooted( true );
7450 gene8.setRooted( true );
7451 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
7452 if ( sdi_unrooted.getCount() != 1 ) {
7455 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7458 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7461 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7464 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7467 if ( !p8[ 0 ].getRoot().isDuplication() ) {
7470 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7473 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7476 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
7479 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7482 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
7485 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
7488 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7493 catch ( final Exception e ) {
7494 e.printStackTrace( System.out );
7500 private static boolean testSplit() {
7502 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7503 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7504 //Archaeopteryx.createApplication( p0 );
7505 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7506 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7507 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7508 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7509 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7510 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7511 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7512 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7513 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7514 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7515 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
7516 // System.out.println( s0.toString() );
7518 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7519 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7520 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7521 if ( s0.match( query_nodes ) ) {
7524 query_nodes = new HashSet<PhylogenyNode>();
7525 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7526 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7527 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7528 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7529 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7532 if ( !s0.match( query_nodes ) ) {
7536 query_nodes = new HashSet<PhylogenyNode>();
7537 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7540 if ( !s0.match( query_nodes ) ) {
7544 query_nodes = new HashSet<PhylogenyNode>();
7545 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7549 if ( !s0.match( query_nodes ) ) {
7553 query_nodes = new HashSet<PhylogenyNode>();
7554 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7558 if ( !s0.match( query_nodes ) ) {
7562 query_nodes = new HashSet<PhylogenyNode>();
7563 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7564 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7566 if ( !s0.match( query_nodes ) ) {
7570 query_nodes = new HashSet<PhylogenyNode>();
7571 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7572 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7573 if ( !s0.match( query_nodes ) ) {
7577 query_nodes = new HashSet<PhylogenyNode>();
7578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7583 if ( !s0.match( query_nodes ) ) {
7587 query_nodes = new HashSet<PhylogenyNode>();
7588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7591 if ( !s0.match( query_nodes ) ) {
7595 query_nodes = new HashSet<PhylogenyNode>();
7596 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7600 if ( !s0.match( query_nodes ) ) {
7604 query_nodes = new HashSet<PhylogenyNode>();
7605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7607 if ( s0.match( query_nodes ) ) {
7611 query_nodes = new HashSet<PhylogenyNode>();
7612 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7616 if ( s0.match( query_nodes ) ) {
7620 query_nodes = new HashSet<PhylogenyNode>();
7621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7626 if ( s0.match( query_nodes ) ) {
7630 query_nodes = new HashSet<PhylogenyNode>();
7631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7634 if ( s0.match( query_nodes ) ) {
7638 query_nodes = new HashSet<PhylogenyNode>();
7639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7641 if ( s0.match( query_nodes ) ) {
7645 query_nodes = new HashSet<PhylogenyNode>();
7646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7648 if ( s0.match( query_nodes ) ) {
7652 query_nodes = new HashSet<PhylogenyNode>();
7653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7655 if ( s0.match( query_nodes ) ) {
7659 query_nodes = new HashSet<PhylogenyNode>();
7660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7662 if ( s0.match( query_nodes ) ) {
7666 query_nodes = new HashSet<PhylogenyNode>();
7667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7669 if ( s0.match( query_nodes ) ) {
7673 query_nodes = new HashSet<PhylogenyNode>();
7674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7676 if ( s0.match( query_nodes ) ) {
7680 query_nodes = new HashSet<PhylogenyNode>();
7681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7683 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7684 if ( s0.match( query_nodes ) ) {
7688 query_nodes = new HashSet<PhylogenyNode>();
7689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7690 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7691 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7692 if ( s0.match( query_nodes ) ) {
7696 query_nodes = new HashSet<PhylogenyNode>();
7697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7698 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7700 if ( s0.match( query_nodes ) ) {
7704 query_nodes = new HashSet<PhylogenyNode>();
7705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7707 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7708 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7709 if ( s0.match( query_nodes ) ) {
7713 // query_nodes = new HashSet<PhylogenyNode>();
7714 // query_nodes.add( new PhylogenyNode( "X" ) );
7715 // query_nodes.add( new PhylogenyNode( "Y" ) );
7716 // query_nodes.add( new PhylogenyNode( "A" ) );
7717 // query_nodes.add( new PhylogenyNode( "B" ) );
7718 // query_nodes.add( new PhylogenyNode( "C" ) );
7719 // query_nodes.add( new PhylogenyNode( "D" ) );
7720 // query_nodes.add( new PhylogenyNode( "E" ) );
7721 // query_nodes.add( new PhylogenyNode( "F" ) );
7722 // query_nodes.add( new PhylogenyNode( "G" ) );
7723 // if ( !s0.match( query_nodes ) ) {
7726 // query_nodes = new HashSet<PhylogenyNode>();
7727 // query_nodes.add( new PhylogenyNode( "X" ) );
7728 // query_nodes.add( new PhylogenyNode( "Y" ) );
7729 // query_nodes.add( new PhylogenyNode( "A" ) );
7730 // query_nodes.add( new PhylogenyNode( "B" ) );
7731 // query_nodes.add( new PhylogenyNode( "C" ) );
7732 // if ( !s0.match( query_nodes ) ) {
7736 // query_nodes = new HashSet<PhylogenyNode>();
7737 // query_nodes.add( new PhylogenyNode( "X" ) );
7738 // query_nodes.add( new PhylogenyNode( "Y" ) );
7739 // query_nodes.add( new PhylogenyNode( "D" ) );
7740 // query_nodes.add( new PhylogenyNode( "E" ) );
7741 // query_nodes.add( new PhylogenyNode( "F" ) );
7742 // query_nodes.add( new PhylogenyNode( "G" ) );
7743 // if ( !s0.match( query_nodes ) ) {
7747 // query_nodes = new HashSet<PhylogenyNode>();
7748 // query_nodes.add( new PhylogenyNode( "X" ) );
7749 // query_nodes.add( new PhylogenyNode( "Y" ) );
7750 // query_nodes.add( new PhylogenyNode( "A" ) );
7751 // query_nodes.add( new PhylogenyNode( "B" ) );
7752 // query_nodes.add( new PhylogenyNode( "C" ) );
7753 // query_nodes.add( new PhylogenyNode( "D" ) );
7754 // if ( !s0.match( query_nodes ) ) {
7758 // query_nodes = new HashSet<PhylogenyNode>();
7759 // query_nodes.add( new PhylogenyNode( "X" ) );
7760 // query_nodes.add( new PhylogenyNode( "Y" ) );
7761 // query_nodes.add( new PhylogenyNode( "E" ) );
7762 // query_nodes.add( new PhylogenyNode( "F" ) );
7763 // query_nodes.add( new PhylogenyNode( "G" ) );
7764 // if ( !s0.match( query_nodes ) ) {
7768 // query_nodes = new HashSet<PhylogenyNode>();
7769 // query_nodes.add( new PhylogenyNode( "X" ) );
7770 // query_nodes.add( new PhylogenyNode( "Y" ) );
7771 // query_nodes.add( new PhylogenyNode( "F" ) );
7772 // query_nodes.add( new PhylogenyNode( "G" ) );
7773 // if ( !s0.match( query_nodes ) ) {
7777 query_nodes = new HashSet<PhylogenyNode>();
7778 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7779 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7780 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7781 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7782 if ( s0.match( query_nodes ) ) {
7786 query_nodes = new HashSet<PhylogenyNode>();
7787 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7788 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7789 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7790 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7791 if ( s0.match( query_nodes ) ) {
7794 ///////////////////////////
7796 query_nodes = new HashSet<PhylogenyNode>();
7797 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7798 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7799 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7800 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7801 if ( s0.match( query_nodes ) ) {
7805 query_nodes = new HashSet<PhylogenyNode>();
7806 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7807 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7808 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7809 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7810 if ( s0.match( query_nodes ) ) {
7814 query_nodes = new HashSet<PhylogenyNode>();
7815 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7816 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7817 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7818 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7819 if ( s0.match( query_nodes ) ) {
7823 query_nodes = new HashSet<PhylogenyNode>();
7824 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7827 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7828 if ( s0.match( query_nodes ) ) {
7832 query_nodes = new HashSet<PhylogenyNode>();
7833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7834 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7835 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7836 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7837 if ( s0.match( query_nodes ) ) {
7841 query_nodes = new HashSet<PhylogenyNode>();
7842 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7843 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7844 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7845 if ( s0.match( query_nodes ) ) {
7849 query_nodes = new HashSet<PhylogenyNode>();
7850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7851 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7854 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7855 if ( s0.match( query_nodes ) ) {
7859 query_nodes = new HashSet<PhylogenyNode>();
7860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7863 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7864 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7865 if ( s0.match( query_nodes ) ) {
7869 query_nodes = new HashSet<PhylogenyNode>();
7870 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7873 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7874 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7875 if ( s0.match( query_nodes ) ) {
7879 query_nodes = new HashSet<PhylogenyNode>();
7880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7881 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7882 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7883 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7886 if ( s0.match( query_nodes ) ) {
7890 catch ( final Exception e ) {
7891 e.printStackTrace();
7897 private static boolean testSplitStrict() {
7899 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7900 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7901 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7902 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7903 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7904 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7905 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7906 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7907 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7908 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7909 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7910 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7911 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7912 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7913 if ( s0.match( query_nodes ) ) {
7916 query_nodes = new HashSet<PhylogenyNode>();
7917 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7918 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7924 if ( !s0.match( query_nodes ) ) {
7928 query_nodes = new HashSet<PhylogenyNode>();
7929 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7930 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7932 if ( !s0.match( query_nodes ) ) {
7936 query_nodes = new HashSet<PhylogenyNode>();
7937 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7938 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7941 if ( !s0.match( query_nodes ) ) {
7945 query_nodes = new HashSet<PhylogenyNode>();
7946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7947 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7950 if ( !s0.match( query_nodes ) ) {
7954 query_nodes = new HashSet<PhylogenyNode>();
7955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7958 if ( !s0.match( query_nodes ) ) {
7962 query_nodes = new HashSet<PhylogenyNode>();
7963 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7964 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7965 if ( !s0.match( query_nodes ) ) {
7969 query_nodes = new HashSet<PhylogenyNode>();
7970 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7971 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7975 if ( !s0.match( query_nodes ) ) {
7979 query_nodes = new HashSet<PhylogenyNode>();
7980 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7981 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7983 if ( !s0.match( query_nodes ) ) {
7987 query_nodes = new HashSet<PhylogenyNode>();
7988 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7992 if ( !s0.match( query_nodes ) ) {
7996 query_nodes = new HashSet<PhylogenyNode>();
7997 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7999 if ( s0.match( query_nodes ) ) {
8003 query_nodes = new HashSet<PhylogenyNode>();
8004 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8005 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8008 if ( s0.match( query_nodes ) ) {
8012 query_nodes = new HashSet<PhylogenyNode>();
8013 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8014 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8018 if ( s0.match( query_nodes ) ) {
8022 query_nodes = new HashSet<PhylogenyNode>();
8023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8026 if ( s0.match( query_nodes ) ) {
8030 query_nodes = new HashSet<PhylogenyNode>();
8031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8032 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8033 if ( s0.match( query_nodes ) ) {
8037 query_nodes = new HashSet<PhylogenyNode>();
8038 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8039 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8040 if ( s0.match( query_nodes ) ) {
8044 query_nodes = new HashSet<PhylogenyNode>();
8045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8047 if ( s0.match( query_nodes ) ) {
8051 query_nodes = new HashSet<PhylogenyNode>();
8052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8054 if ( s0.match( query_nodes ) ) {
8058 query_nodes = new HashSet<PhylogenyNode>();
8059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8061 if ( s0.match( query_nodes ) ) {
8065 query_nodes = new HashSet<PhylogenyNode>();
8066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8068 if ( s0.match( query_nodes ) ) {
8072 query_nodes = new HashSet<PhylogenyNode>();
8073 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8076 if ( s0.match( query_nodes ) ) {
8080 query_nodes = new HashSet<PhylogenyNode>();
8081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8084 if ( s0.match( query_nodes ) ) {
8088 query_nodes = new HashSet<PhylogenyNode>();
8089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8092 if ( s0.match( query_nodes ) ) {
8096 query_nodes = new HashSet<PhylogenyNode>();
8097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8101 if ( s0.match( query_nodes ) ) {
8105 catch ( final Exception e ) {
8106 e.printStackTrace();
8112 private static boolean testSubtreeDeletion() {
8114 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8115 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8116 t1.deleteSubtree( t1.getNode( "A" ), false );
8117 if ( t1.getNumberOfExternalNodes() != 5 ) {
8120 t1.toNewHampshireX();
8121 t1.deleteSubtree( t1.getNode( "E" ), false );
8122 if ( t1.getNumberOfExternalNodes() != 4 ) {
8125 t1.toNewHampshireX();
8126 t1.deleteSubtree( t1.getNode( "F" ), false );
8127 if ( t1.getNumberOfExternalNodes() != 3 ) {
8130 t1.toNewHampshireX();
8131 t1.deleteSubtree( t1.getNode( "D" ), false );
8132 t1.toNewHampshireX();
8133 if ( t1.getNumberOfExternalNodes() != 3 ) {
8136 t1.deleteSubtree( t1.getNode( "def" ), false );
8137 t1.toNewHampshireX();
8138 if ( t1.getNumberOfExternalNodes() != 2 ) {
8141 t1.deleteSubtree( t1.getNode( "B" ), false );
8142 t1.toNewHampshireX();
8143 if ( t1.getNumberOfExternalNodes() != 1 ) {
8146 t1.deleteSubtree( t1.getNode( "C" ), false );
8147 t1.toNewHampshireX();
8148 if ( t1.getNumberOfExternalNodes() != 1 ) {
8151 t1.deleteSubtree( t1.getNode( "abc" ), false );
8152 t1.toNewHampshireX();
8153 if ( t1.getNumberOfExternalNodes() != 1 ) {
8156 t1.deleteSubtree( t1.getNode( "r" ), false );
8157 if ( t1.getNumberOfExternalNodes() != 0 ) {
8160 if ( !t1.isEmpty() ) {
8163 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8164 t2.deleteSubtree( t2.getNode( "A" ), false );
8165 t2.toNewHampshireX();
8166 if ( t2.getNumberOfExternalNodes() != 5 ) {
8169 t2.deleteSubtree( t2.getNode( "abc" ), false );
8170 t2.toNewHampshireX();
8171 if ( t2.getNumberOfExternalNodes() != 3 ) {
8174 t2.deleteSubtree( t2.getNode( "def" ), false );
8175 t2.toNewHampshireX();
8176 if ( t2.getNumberOfExternalNodes() != 1 ) {
8180 catch ( final Exception e ) {
8181 e.printStackTrace( System.out );
8187 private static boolean testSupportCount() {
8189 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8190 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
8191 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
8192 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
8193 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
8194 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
8195 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
8197 SupportCount.count( t0_1, phylogenies_1, true, false );
8198 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
8199 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
8200 + "(((((A,B),C),D),E),((F,G),X))"
8201 + "(((((A,Y),B),C),D),((F,G),E))"
8202 + "(((((A,B),C),D),E),(F,G))"
8203 + "(((((A,B),C),D),E),(F,G))"
8204 + "(((((A,B),C),D),E),(F,G))"
8205 + "(((((A,B),C),D),E),(F,G),Z)"
8206 + "(((((A,B),C),D),E),(F,G))"
8207 + "((((((A,B),C),D),E),F),G)"
8208 + "(((((X,Y),F,G),E),((A,B),C)),D)",
8210 SupportCount.count( t0_2, phylogenies_2, true, false );
8211 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
8212 while ( it.hasNext() ) {
8213 final PhylogenyNode n = it.next();
8214 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
8218 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
8219 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
8220 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
8221 SupportCount.count( t0_3, phylogenies_3, true, false );
8222 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
8223 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
8226 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
8229 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
8232 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
8235 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
8238 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
8241 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
8244 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
8247 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
8250 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
8253 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8254 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
8255 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
8256 SupportCount.count( t0_4, phylogenies_4, true, false );
8257 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
8258 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
8261 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
8264 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
8267 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
8270 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
8273 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
8276 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
8279 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
8282 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
8285 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
8288 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8289 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8290 double d = SupportCount.compare( b1, a, true, true, true );
8291 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
8294 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8295 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8296 d = SupportCount.compare( b2, a, true, true, true );
8297 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
8300 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8301 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
8302 d = SupportCount.compare( b3, a, true, true, true );
8303 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
8306 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
8307 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
8308 d = SupportCount.compare( b4, a, true, true, false );
8309 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
8313 catch ( final Exception e ) {
8314 e.printStackTrace( System.out );
8320 private static boolean testSupportTransfer() {
8322 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8323 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)",
8324 new NHXParser() )[ 0 ];
8325 final Phylogeny p2 = factory
8326 .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 ];
8327 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8330 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8333 support_transfer.moveBranchLengthsToBootstrap( p1 );
8334 support_transfer.transferSupportValues( p1, p2 );
8335 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8338 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8341 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8344 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8347 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
8350 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
8353 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
8356 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
8360 catch ( final Exception e ) {
8361 e.printStackTrace( System.out );
8367 private static boolean testUniprotTaxonomySearch() {
8369 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
8371 if ( results.size() != 1 ) {
8374 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8377 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8380 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8383 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8386 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8390 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
8391 if ( results.size() != 1 ) {
8394 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8397 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8400 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8403 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8406 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8410 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
8411 if ( results.size() != 1 ) {
8414 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8417 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8420 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8423 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8426 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8430 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
8431 if ( results.size() != 1 ) {
8434 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8437 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8440 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8443 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8446 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8449 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
8452 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
8455 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
8456 .equals( "Nematostella vectensis" ) ) {
8457 System.out.println( results.get( 0 ).getLineage() );
8461 catch ( final IOException e ) {
8462 System.out.println();
8463 System.out.println( "the following might be due to absence internet connection:" );
8464 e.printStackTrace( System.out );
8467 catch ( final Exception e ) {
8473 private static boolean testEmblEntryRetrieval() {
8474 //The format for GenBank Accession numbers are:
8475 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
8476 //Protein: 3 letters + 5 numerals
8477 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
8478 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
8481 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
8484 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
8487 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
8490 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
8493 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
8496 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
8499 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
8502 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
8505 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
8508 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
8511 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
8514 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8520 private static boolean testUniprotEntryRetrieval() {
8521 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8524 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8527 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8530 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8533 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8536 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8539 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8542 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8545 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8548 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8551 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8554 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8557 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8561 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8562 if ( !entry.getAccession().equals( "P12345" ) ) {
8565 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8568 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8571 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8574 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8578 catch ( final IOException e ) {
8579 System.out.println();
8580 System.out.println( "the following might be due to absence internet connection:" );
8581 e.printStackTrace( System.out );
8584 catch ( final Exception e ) {
8590 private static boolean testWabiTxSearch() {
8593 result = TxSearch.searchSimple( "nematostella" );
8594 result = TxSearch.getTxId( "nematostella" );
8595 if ( !result.equals( "45350" ) ) {
8598 result = TxSearch.getTxName( "45350" );
8599 if ( !result.equals( "Nematostella" ) ) {
8602 result = TxSearch.getTxId( "nematostella vectensis" );
8603 if ( !result.equals( "45351" ) ) {
8606 result = TxSearch.getTxName( "45351" );
8607 if ( !result.equals( "Nematostella vectensis" ) ) {
8610 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8611 if ( !result.equals( "536089" ) ) {
8614 result = TxSearch.getTxName( "536089" );
8615 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8618 final List<String> queries = new ArrayList<String>();
8619 queries.add( "Campylobacter coli" );
8620 queries.add( "Escherichia coli" );
8621 queries.add( "Arabidopsis" );
8622 queries.add( "Trichoplax" );
8623 queries.add( "Samanea saman" );
8624 queries.add( "Kluyveromyces marxianus" );
8625 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8626 queries.add( "Bornavirus parrot/PDD/2008" );
8627 final List<RANKS> ranks = new ArrayList<RANKS>();
8628 ranks.add( RANKS.SUPERKINGDOM );
8629 ranks.add( RANKS.KINGDOM );
8630 ranks.add( RANKS.FAMILY );
8631 ranks.add( RANKS.GENUS );
8632 ranks.add( RANKS.TRIBE );
8633 result = TxSearch.searchLineage( queries, ranks );
8634 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8635 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8637 catch ( final Exception e ) {
8638 System.out.println();
8639 System.out.println( "the following might be due to absence internet connection:" );
8640 e.printStackTrace( System.out );
8646 private static boolean testAminoAcidSequence() {
8648 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8649 if ( aa1.getLength() != 13 ) {
8652 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8655 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8658 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8661 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8662 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8665 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8666 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8669 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8670 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8674 catch ( final Exception e ) {
8675 e.printStackTrace();
8681 private static boolean testCreateBalancedPhylogeny() {
8683 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8684 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8687 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8690 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8691 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8694 if ( p1.getNumberOfExternalNodes() != 100 ) {
8698 catch ( final Exception e ) {
8699 e.printStackTrace();
8705 private static boolean testFastaParser() {
8707 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8710 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8713 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8714 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8717 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8720 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8723 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8726 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8729 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8733 catch ( final Exception e ) {
8734 e.printStackTrace();
8740 private static boolean testGeneralMsaParser() {
8742 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8743 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8744 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8745 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8746 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8747 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8748 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8749 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8750 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8753 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8756 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8759 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8762 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8765 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8768 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8771 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8774 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8777 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8780 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8783 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8786 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8787 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8790 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8793 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8796 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8797 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8800 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8803 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8806 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8807 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8810 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8813 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8817 catch ( final Exception e ) {
8818 e.printStackTrace();
8824 private static boolean testMafft( final String path ) {
8826 final List<String> opts = new ArrayList<String>();
8827 opts.add( "--maxiterate" );
8829 opts.add( "--localpair" );
8830 opts.add( "--quiet" );
8832 final MsaInferrer mafft = Mafft.createInstance( path );
8833 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8834 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8837 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8841 catch ( final Exception e ) {
8842 e.printStackTrace( System.out );
8848 private static boolean testNextNodeWithCollapsing() {
8850 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8852 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8853 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8854 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8855 t0.getNode( "cd" ).setCollapse( true );
8856 t0.getNode( "cde" ).setCollapse( true );
8857 n = t0.getFirstExternalNode();
8858 while ( n != null ) {
8860 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8862 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8865 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8868 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8871 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8874 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8877 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8881 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8882 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8883 t1.getNode( "ab" ).setCollapse( true );
8884 t1.getNode( "cd" ).setCollapse( true );
8885 t1.getNode( "cde" ).setCollapse( true );
8886 n = t1.getNode( "ab" );
8887 ext = new ArrayList<PhylogenyNode>();
8888 while ( n != null ) {
8890 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8892 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8895 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8898 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8901 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8904 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8910 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8911 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8912 t2.getNode( "ab" ).setCollapse( true );
8913 t2.getNode( "cd" ).setCollapse( true );
8914 t2.getNode( "cde" ).setCollapse( true );
8915 t2.getNode( "c" ).setCollapse( true );
8916 t2.getNode( "d" ).setCollapse( true );
8917 t2.getNode( "e" ).setCollapse( true );
8918 t2.getNode( "gh" ).setCollapse( true );
8919 n = t2.getNode( "ab" );
8920 ext = new ArrayList<PhylogenyNode>();
8921 while ( n != null ) {
8923 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8925 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8928 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8931 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8934 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8940 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8941 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8942 t3.getNode( "ab" ).setCollapse( true );
8943 t3.getNode( "cd" ).setCollapse( true );
8944 t3.getNode( "cde" ).setCollapse( true );
8945 t3.getNode( "c" ).setCollapse( true );
8946 t3.getNode( "d" ).setCollapse( true );
8947 t3.getNode( "e" ).setCollapse( true );
8948 t3.getNode( "gh" ).setCollapse( true );
8949 t3.getNode( "fgh" ).setCollapse( true );
8950 n = t3.getNode( "ab" );
8951 ext = new ArrayList<PhylogenyNode>();
8952 while ( n != null ) {
8954 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8956 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8959 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8962 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8968 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8969 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8970 t4.getNode( "ab" ).setCollapse( true );
8971 t4.getNode( "cd" ).setCollapse( true );
8972 t4.getNode( "cde" ).setCollapse( true );
8973 t4.getNode( "c" ).setCollapse( true );
8974 t4.getNode( "d" ).setCollapse( true );
8975 t4.getNode( "e" ).setCollapse( true );
8976 t4.getNode( "gh" ).setCollapse( true );
8977 t4.getNode( "fgh" ).setCollapse( true );
8978 t4.getNode( "abcdefgh" ).setCollapse( true );
8979 n = t4.getNode( "abcdefgh" );
8980 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8985 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8986 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8988 n = t5.getFirstExternalNode();
8989 while ( n != null ) {
8991 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8993 if ( ext.size() != 8 ) {
8996 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8999 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9002 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9005 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9008 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9011 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9014 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
9017 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
9022 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9023 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
9025 t6.getNode( "ab" ).setCollapse( true );
9026 n = t6.getNode( "ab" );
9027 while ( n != null ) {
9029 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9031 if ( ext.size() != 7 ) {
9034 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9037 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9040 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9043 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9046 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9049 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9052 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9057 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9058 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
9060 t7.getNode( "cd" ).setCollapse( true );
9061 n = t7.getNode( "a" );
9062 while ( n != null ) {
9064 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9066 if ( ext.size() != 7 ) {
9069 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9072 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9075 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9078 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9081 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9084 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9087 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9092 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9093 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
9095 t8.getNode( "cd" ).setCollapse( true );
9096 t8.getNode( "c" ).setCollapse( true );
9097 t8.getNode( "d" ).setCollapse( true );
9098 n = t8.getNode( "a" );
9099 while ( n != null ) {
9101 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9103 if ( ext.size() != 7 ) {
9106 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9109 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9112 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9113 System.out.println( "2 fail" );
9116 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9119 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9122 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9125 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9130 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9131 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
9133 t9.getNode( "gh" ).setCollapse( true );
9134 n = t9.getNode( "a" );
9135 while ( n != null ) {
9137 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9139 if ( ext.size() != 7 ) {
9142 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9145 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9148 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9151 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9154 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9157 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9160 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9165 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9166 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
9168 t10.getNode( "gh" ).setCollapse( true );
9169 t10.getNode( "g" ).setCollapse( true );
9170 t10.getNode( "h" ).setCollapse( true );
9171 n = t10.getNode( "a" );
9172 while ( n != null ) {
9174 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9176 if ( ext.size() != 7 ) {
9179 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9182 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9185 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9188 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9191 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9194 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9197 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9202 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9203 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
9205 t11.getNode( "gh" ).setCollapse( true );
9206 t11.getNode( "fgh" ).setCollapse( true );
9207 n = t11.getNode( "a" );
9208 while ( n != null ) {
9210 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9212 if ( ext.size() != 6 ) {
9215 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9218 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9221 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9224 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9227 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9230 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9235 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9236 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
9238 t12.getNode( "gh" ).setCollapse( true );
9239 t12.getNode( "fgh" ).setCollapse( true );
9240 t12.getNode( "g" ).setCollapse( true );
9241 t12.getNode( "h" ).setCollapse( true );
9242 t12.getNode( "f" ).setCollapse( true );
9243 n = t12.getNode( "a" );
9244 while ( n != null ) {
9246 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9248 if ( ext.size() != 6 ) {
9251 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9254 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9257 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9260 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9263 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9266 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9271 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9272 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
9274 t13.getNode( "ab" ).setCollapse( true );
9275 t13.getNode( "b" ).setCollapse( true );
9276 t13.getNode( "fgh" ).setCollapse( true );
9277 t13.getNode( "gh" ).setCollapse( true );
9278 n = t13.getNode( "ab" );
9279 while ( n != null ) {
9281 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9283 if ( ext.size() != 5 ) {
9286 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9289 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9292 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9295 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9298 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9303 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
9304 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
9306 t14.getNode( "ab" ).setCollapse( true );
9307 t14.getNode( "a" ).setCollapse( true );
9308 t14.getNode( "fgh" ).setCollapse( true );
9309 t14.getNode( "gh" ).setCollapse( true );
9310 n = t14.getNode( "ab" );
9311 while ( n != null ) {
9313 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9315 if ( ext.size() != 5 ) {
9318 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9321 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9324 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9327 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9330 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9335 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" );
9336 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9338 t15.getNode( "ab" ).setCollapse( true );
9339 t15.getNode( "a" ).setCollapse( true );
9340 t15.getNode( "fgh" ).setCollapse( true );
9341 t15.getNode( "gh" ).setCollapse( true );
9342 n = t15.getNode( "ab" );
9343 while ( n != null ) {
9345 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9347 if ( ext.size() != 6 ) {
9350 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9353 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9356 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9359 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9362 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
9365 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9370 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" );
9371 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
9373 t16.getNode( "ab" ).setCollapse( true );
9374 t16.getNode( "a" ).setCollapse( true );
9375 t16.getNode( "fgh" ).setCollapse( true );
9376 t16.getNode( "gh" ).setCollapse( true );
9377 t16.getNode( "cd" ).setCollapse( true );
9378 t16.getNode( "cde" ).setCollapse( true );
9379 t16.getNode( "d" ).setCollapse( true );
9380 t16.getNode( "x" ).setCollapse( true );
9381 n = t16.getNode( "ab" );
9382 while ( n != null ) {
9384 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9386 if ( ext.size() != 4 ) {
9389 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9392 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9395 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
9398 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
9402 catch ( final Exception e ) {
9403 e.printStackTrace( System.out );
9409 private static boolean testMsaQualityMethod() {
9411 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
9412 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
9413 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
9414 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
9415 final List<Sequence> l = new ArrayList<Sequence>();
9420 final Msa msa = BasicMsa.createInstance( l );
9421 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
9424 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
9427 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
9430 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
9434 catch ( final Exception e ) {
9435 e.printStackTrace( System.out );
9441 private static boolean testSequenceIdParsing() {
9443 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
9444 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9445 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9447 System.out.println( "value =" + id.getValue() );
9448 System.out.println( "provider=" + id.getProvider() );
9453 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
9454 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9455 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9457 System.out.println( "value =" + id.getValue() );
9458 System.out.println( "provider=" + id.getProvider() );
9463 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
9464 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9465 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9467 System.out.println( "value =" + id.getValue() );
9468 System.out.println( "provider=" + id.getProvider() );
9473 id = SequenceIdParser.parse( "gb_AAA96518_1" );
9474 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9475 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
9477 System.out.println( "value =" + id.getValue() );
9478 System.out.println( "provider=" + id.getProvider() );
9483 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
9484 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9485 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
9487 System.out.println( "value =" + id.getValue() );
9488 System.out.println( "provider=" + id.getProvider() );
9493 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
9494 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9495 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
9497 System.out.println( "value =" + id.getValue() );
9498 System.out.println( "provider=" + id.getProvider() );
9503 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9504 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9505 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
9507 System.out.println( "value =" + id.getValue() );
9508 System.out.println( "provider=" + id.getProvider() );
9513 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9514 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9515 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9517 System.out.println( "value =" + id.getValue() );
9518 System.out.println( "provider=" + id.getProvider() );
9523 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9524 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9525 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9527 System.out.println( "value =" + id.getValue() );
9528 System.out.println( "provider=" + id.getProvider() );
9533 id = SequenceIdParser.parse( "P4A123" );
9534 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9535 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9537 System.out.println( "value =" + id.getValue() );
9538 System.out.println( "provider=" + id.getProvider() );
9543 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
9544 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9545 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9547 System.out.println( "value =" + id.getValue() );
9548 System.out.println( "provider=" + id.getProvider() );
9553 id = SequenceIdParser.parse( "XP_12345" );
9555 System.out.println( "value =" + id.getValue() );
9556 System.out.println( "provider=" + id.getProvider() );
9559 // lcl_91970_unknown_
9561 catch ( final Exception e ) {
9562 e.printStackTrace( System.out );