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.nhx.NHXParser2;
56 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
57 import org.forester.io.parsers.tol.TolParser;
58 import org.forester.io.parsers.util.ParserUtils;
59 import org.forester.io.writers.PhylogenyWriter;
60 import org.forester.msa.BasicMsa;
61 import org.forester.msa.Mafft;
62 import org.forester.msa.Msa;
63 import org.forester.msa.MsaInferrer;
64 import org.forester.msa.MsaMethods;
65 import org.forester.pccx.TestPccx;
66 import org.forester.phylogeny.Phylogeny;
67 import org.forester.phylogeny.PhylogenyBranch;
68 import org.forester.phylogeny.PhylogenyMethods;
69 import org.forester.phylogeny.PhylogenyNode;
70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
71 import org.forester.phylogeny.data.BinaryCharacters;
72 import org.forester.phylogeny.data.BranchWidth;
73 import org.forester.phylogeny.data.Confidence;
74 import org.forester.phylogeny.data.Distribution;
75 import org.forester.phylogeny.data.DomainArchitecture;
76 import org.forester.phylogeny.data.Event;
77 import org.forester.phylogeny.data.Identifier;
78 import org.forester.phylogeny.data.PhylogenyData;
79 import org.forester.phylogeny.data.PhylogenyDataUtil;
80 import org.forester.phylogeny.data.Polygon;
81 import org.forester.phylogeny.data.PropertiesMap;
82 import org.forester.phylogeny.data.Property;
83 import org.forester.phylogeny.data.Property.AppliesTo;
84 import org.forester.phylogeny.data.ProteinDomain;
85 import org.forester.phylogeny.data.Taxonomy;
86 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
87 import org.forester.phylogeny.factories.PhylogenyFactory;
88 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
89 import org.forester.protein.Protein;
90 import org.forester.rio.TestRIO;
91 import org.forester.sdi.SDI;
92 import org.forester.sdi.SDIR;
93 import org.forester.sdi.TestGSDI;
94 import org.forester.sequence.BasicSequence;
95 import org.forester.sequence.Sequence;
96 import org.forester.surfacing.TestSurfacing;
97 import org.forester.tools.ConfidenceAssessor;
98 import org.forester.tools.SupportCount;
99 import org.forester.tools.TreeSplitMatrix;
100 import org.forester.util.AsciiHistogram;
101 import org.forester.util.BasicDescriptiveStatistics;
102 import org.forester.util.BasicTable;
103 import org.forester.util.BasicTableParser;
104 import org.forester.util.DescriptiveStatistics;
105 import org.forester.util.ForesterConstants;
106 import org.forester.util.ForesterUtil;
107 import org.forester.util.GeneralTable;
108 import org.forester.util.SequenceIdParser;
109 import org.forester.ws.seqdb.SequenceDatabaseEntry;
110 import org.forester.ws.seqdb.SequenceDbWsTools;
111 import org.forester.ws.seqdb.UniProtTaxonomy;
112 import org.forester.ws.wabi.TxSearch;
113 import org.forester.ws.wabi.TxSearch.RANKS;
114 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
115 import org.forester.ws.wabi.TxSearch.TAX_RANK;
117 @SuppressWarnings( "unused")
118 public final class Test {
120 private final static double ZERO_DIFF = 1.0E-9;
121 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
122 + ForesterUtil.getFileSeparator() + "test_data"
123 + ForesterUtil.getFileSeparator();
124 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
125 + ForesterUtil.getFileSeparator() + "resources"
126 + ForesterUtil.getFileSeparator();
127 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
128 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
129 + ForesterConstants.PHYLO_XML_VERSION + "/"
130 + ForesterConstants.PHYLO_XML_XSD;
131 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
132 + ForesterConstants.PHYLO_XML_VERSION + "/"
133 + ForesterConstants.PHYLO_XML_XSD;
135 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
136 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
140 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
141 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
144 public static boolean isEqual( final double a, final double b ) {
145 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
148 public static void main( final String[] args ) {
149 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
150 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
152 Locale.setDefault( Locale.US );
153 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
156 System.out.print( "[Test if directory with files for testing exists/is readable: " );
157 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
158 System.out.println( "OK.]" );
161 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
162 System.out.println( "Testing aborted." );
165 System.out.print( "[Test if resources directory exists/is readable: " );
166 if ( testDir( PATH_TO_RESOURCES ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
171 System.out.println( "Testing aborted." );
174 final long start_time = new Date().getTime();
175 System.out.print( "Sequence id parsing: " );
176 if ( testSequenceIdParsing() ) {
177 System.out.println( "OK." );
181 System.out.println( "failed." );
184 System.out.print( "Hmmscan output parser: " );
185 if ( testHmmscanOutputParser() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Basic node methods: " );
194 if ( Test.testBasicNodeMethods() ) {
195 System.out.println( "OK." );
199 System.out.println( "failed." );
202 System.out.print( "Taxonomy code extraction: " );
203 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
204 System.out.println( "OK." );
208 System.out.println( "failed." );
211 System.out.print( "Taxonomy extraction (general): " );
212 if ( Test.testTaxonomyExtraction() ) {
213 System.out.println( "OK." );
217 System.out.println( "failed." );
220 System.out.print( "Basic node construction and parsing of NHX (node level): " );
221 if ( Test.testNHXNodeParsing() ) {
222 System.out.println( "OK." );
226 System.out.println( "failed." );
229 System.out.print( "NH parsing: " );
230 if ( Test.testNHParsing() ) {
231 System.out.println( "OK." );
235 System.out.println( "failed." );
238 System.out.print( "Conversion to NHX (node level): " );
239 if ( Test.testNHXconversion() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "NHX parsing: " );
248 if ( Test.testNHXParsing() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "NHX parsing with quotes: " );
257 if ( Test.testNHXParsingQuotes() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "NHX parsing (MrBayes): " );
266 if ( Test.testNHXParsingMB() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "NHX parsing iterating: " );
275 if ( Test.testNHParsingIter() ) {
276 System.out.println( "OK." );
280 System.out.println( "failed." );
283 System.out.print( "Nexus characters parsing: " );
284 if ( Test.testNexusCharactersParsing() ) {
285 System.out.println( "OK." );
289 System.out.println( "failed." );
292 System.out.print( "Nexus tree parsing: " );
293 if ( Test.testNexusTreeParsing() ) {
294 System.out.println( "OK." );
298 System.out.println( "failed." );
301 System.out.print( "Nexus tree parsing (translating): " );
302 if ( Test.testNexusTreeParsingTranslating() ) {
303 System.out.println( "OK." );
307 System.out.println( "failed." );
310 System.out.print( "Nexus matrix parsing: " );
311 if ( Test.testNexusMatrixParsing() ) {
312 System.out.println( "OK." );
316 System.out.println( "failed." );
319 System.out.print( "Basic phyloXML parsing: " );
320 if ( Test.testBasicPhyloXMLparsing() ) {
321 System.out.println( "OK." );
325 System.out.println( "failed." );
328 System.out.print( "Basic phyloXML parsing (validating against schema): " );
329 if ( testBasicPhyloXMLparsingValidating() ) {
330 System.out.println( "OK." );
334 System.out.println( "failed." );
337 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
338 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
339 System.out.println( "OK." );
343 System.out.println( "failed." );
346 System.out.print( "phyloXML Distribution Element: " );
347 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
348 System.out.println( "OK." );
352 System.out.println( "failed." );
355 System.out.print( "Tol XML parsing: " );
356 if ( Test.testBasicTolXMLparsing() ) {
357 System.out.println( "OK." );
361 System.out.println( "failed." );
364 System.out.print( "Copying of node data: " );
365 if ( Test.testCopyOfNodeData() ) {
366 System.out.println( "OK." );
370 System.out.println( "failed." );
373 System.out.print( "Basic tree methods: " );
374 if ( Test.testBasicTreeMethods() ) {
375 System.out.println( "OK." );
379 System.out.println( "failed." );
382 System.out.print( "Postorder Iterator: " );
383 if ( Test.testPostOrderIterator() ) {
384 System.out.println( "OK." );
388 System.out.println( "failed." );
391 System.out.print( "Preorder Iterator: " );
392 if ( Test.testPreOrderIterator() ) {
393 System.out.println( "OK." );
397 System.out.println( "failed." );
400 System.out.print( "Levelorder Iterator: " );
401 if ( Test.testLevelOrderIterator() ) {
402 System.out.println( "OK." );
406 System.out.println( "failed." );
409 System.out.print( "Re-id methods: " );
410 if ( Test.testReIdMethods() ) {
411 System.out.println( "OK." );
415 System.out.println( "failed." );
418 System.out.print( "Methods on last external nodes: " );
419 if ( Test.testLastExternalNodeMethods() ) {
420 System.out.println( "OK." );
424 System.out.println( "failed." );
427 System.out.print( "Methods on external nodes: " );
428 if ( Test.testExternalNodeRelatedMethods() ) {
429 System.out.println( "OK." );
433 System.out.println( "failed." );
436 System.out.print( "Deletion of external nodes: " );
437 if ( Test.testDeletionOfExternalNodes() ) {
438 System.out.println( "OK." );
442 System.out.println( "failed." );
445 System.out.print( "Subtree deletion: " );
446 if ( Test.testSubtreeDeletion() ) {
447 System.out.println( "OK." );
451 System.out.println( "failed." );
454 System.out.print( "Phylogeny branch: " );
455 if ( Test.testPhylogenyBranch() ) {
456 System.out.println( "OK." );
460 System.out.println( "failed." );
463 System.out.print( "Rerooting: " );
464 if ( Test.testRerooting() ) {
465 System.out.println( "OK." );
469 System.out.println( "failed." );
472 System.out.print( "Mipoint rooting: " );
473 if ( Test.testMidpointrooting() ) {
474 System.out.println( "OK." );
478 System.out.println( "failed." );
481 System.out.print( "Node removal: " );
482 if ( Test.testNodeRemoval() ) {
483 System.out.println( "OK." );
487 System.out.println( "failed." );
490 System.out.print( "Support count: " );
491 if ( Test.testSupportCount() ) {
492 System.out.println( "OK." );
496 System.out.println( "failed." );
499 System.out.print( "Support transfer: " );
500 if ( Test.testSupportTransfer() ) {
501 System.out.println( "OK." );
505 System.out.println( "failed." );
508 System.out.print( "Finding of LCA: " );
509 if ( Test.testGetLCA() ) {
510 System.out.println( "OK." );
514 System.out.println( "failed." );
517 System.out.print( "Finding of LCA 2: " );
518 if ( Test.testGetLCA2() ) {
519 System.out.println( "OK." );
523 System.out.println( "failed." );
526 System.out.print( "Calculation of distance between nodes: " );
527 if ( Test.testGetDistance() ) {
528 System.out.println( "OK." );
532 System.out.println( "failed." );
535 System.out.print( "Descriptive statistics: " );
536 if ( Test.testDescriptiveStatistics() ) {
537 System.out.println( "OK." );
541 System.out.println( "failed." );
544 System.out.print( "Data objects and methods: " );
545 if ( Test.testDataObjects() ) {
546 System.out.println( "OK." );
550 System.out.println( "failed." );
553 System.out.print( "Properties map: " );
554 if ( Test.testPropertiesMap() ) {
555 System.out.println( "OK." );
559 System.out.println( "failed." );
562 System.out.print( "SDIse: " );
563 if ( Test.testSDIse() ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "SDIunrooted: " );
572 if ( Test.testSDIunrooted() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "GSDI: " );
581 if ( TestGSDI.test() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "RIO: " );
590 if ( TestRIO.test() ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Phylogeny reconstruction:" );
599 System.out.println();
600 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
601 System.out.println( "OK." );
605 System.out.println( "failed." );
608 System.out.print( "Analysis of domain architectures: " );
609 System.out.println();
610 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
611 System.out.println( "OK." );
615 System.out.println( "failed." );
618 System.out.print( "GO: " );
619 System.out.println();
620 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
621 System.out.println( "OK." );
625 System.out.println( "failed." );
628 System.out.print( "Modeling tools: " );
629 if ( TestPccx.test() ) {
630 System.out.println( "OK." );
634 System.out.println( "failed." );
637 System.out.print( "Split Matrix strict: " );
638 if ( Test.testSplitStrict() ) {
639 System.out.println( "OK." );
643 System.out.println( "failed." );
646 System.out.print( "Split Matrix: " );
647 if ( Test.testSplit() ) {
648 System.out.println( "OK." );
652 System.out.println( "failed." );
655 System.out.print( "Confidence Assessor: " );
656 if ( Test.testConfidenceAssessor() ) {
657 System.out.println( "OK." );
661 System.out.println( "failed." );
664 System.out.print( "Basic table: " );
665 if ( Test.testBasicTable() ) {
666 System.out.println( "OK." );
670 System.out.println( "failed." );
673 System.out.print( "General table: " );
674 if ( Test.testGeneralTable() ) {
675 System.out.println( "OK." );
679 System.out.println( "failed." );
682 System.out.print( "Amino acid sequence: " );
683 if ( Test.testAminoAcidSequence() ) {
684 System.out.println( "OK." );
688 System.out.println( "failed." );
691 System.out.print( "General MSA parser: " );
692 if ( Test.testGeneralMsaParser() ) {
693 System.out.println( "OK." );
697 System.out.println( "failed." );
700 System.out.print( "Fasta parser for msa: " );
701 if ( Test.testFastaParser() ) {
702 System.out.println( "OK." );
706 System.out.println( "failed." );
709 System.out.print( "Creation of balanced phylogeny: " );
710 if ( Test.testCreateBalancedPhylogeny() ) {
711 System.out.println( "OK." );
715 System.out.println( "failed." );
718 System.out.print( "EMBL Entry Retrieval: " );
719 if ( Test.testEmblEntryRetrieval() ) {
720 System.out.println( "OK." );
724 System.out.println( "failed." );
727 System.out.print( "Uniprot Entry Retrieval: " );
728 if ( Test.testUniprotEntryRetrieval() ) {
729 System.out.println( "OK." );
733 System.out.println( "failed." );
736 System.out.print( "Uniprot Taxonomy Search: " );
737 if ( Test.testUniprotTaxonomySearch() ) {
738 System.out.println( "OK." );
742 System.out.println( "failed." );
747 final String os = ForesterUtil.OS_NAME.toLowerCase();
748 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
749 path = "/usr/local/bin/mafft";
751 else if ( os.indexOf( "win" ) >= 0 ) {
752 path = "C:\\Program Files\\mafft-win\\mafft.bat";
755 path = "/home/czmasek/bin/mafft";
757 if ( !MsaInferrer.isInstalled( path ) ) {
760 if ( !MsaInferrer.isInstalled( path ) ) {
761 path = "/usr/local/bin/mafft";
763 if ( MsaInferrer.isInstalled( path ) ) {
764 System.out.print( "MAFFT (external program): " );
765 if ( Test.testMafft( path ) ) {
766 System.out.println( "OK." );
770 System.out.println( "failed [will not count towards failed tests]" );
774 System.out.print( "Next nodes with collapsed: " );
775 if ( Test.testNextNodeWithCollapsing() ) {
776 System.out.println( "OK." );
780 System.out.println( "failed." );
783 System.out.print( "Simple MSA quality: " );
784 if ( Test.testMsaQualityMethod() ) {
785 System.out.println( "OK." );
789 System.out.println( "failed." );
792 System.out.println();
793 final Runtime rt = java.lang.Runtime.getRuntime();
794 final long free_memory = rt.freeMemory() / 1000000;
795 final long total_memory = rt.totalMemory() / 1000000;
796 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
797 + free_memory + "MB, total memory: " + total_memory + "MB)" );
798 System.out.println();
799 System.out.println( "Successful tests: " + succeeded );
800 System.out.println( "Failed tests: " + failed );
801 System.out.println();
803 System.out.println( "OK." );
806 System.out.println( "Not OK." );
810 private static boolean testExtractTaxonomyCodeFromNodeName() {
812 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
815 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
818 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
821 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
822 .equals( "MOUSE" ) ) {
825 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
826 .equals( "MOUSE" ) ) {
829 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
830 .equals( "MOUSE" ) ) {
833 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
836 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
839 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
843 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
847 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
851 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
854 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
857 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
860 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
864 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
865 .equals( "MOUSE" ) ) {
868 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
869 .equals( "MOUSE" ) ) {
873 catch ( final Exception e ) {
874 e.printStackTrace( System.out );
880 private static boolean testBasicNodeMethods() {
882 if ( PhylogenyNode.getNodeCount() != 0 ) {
885 final PhylogenyNode n1 = new PhylogenyNode();
886 final PhylogenyNode n2 = PhylogenyNode
887 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
888 final PhylogenyNode n3 = PhylogenyNode
889 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
890 final PhylogenyNode n4 = PhylogenyNode
891 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
892 if ( n1.isHasAssignedEvent() ) {
895 if ( PhylogenyNode.getNodeCount() != 4 ) {
898 if ( n3.getIndicator() != 0 ) {
901 if ( n3.getNumberOfExternalNodes() != 1 ) {
904 if ( !n3.isExternal() ) {
907 if ( !n3.isRoot() ) {
910 if ( !n4.getName().equals( "n4" ) ) {
914 catch ( final Exception e ) {
915 e.printStackTrace( System.out );
921 private static boolean testBasicPhyloXMLparsing() {
923 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
924 final PhyloXmlParser xml_parser = new PhyloXmlParser();
925 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
927 if ( xml_parser.getErrorCount() > 0 ) {
928 System.out.println( xml_parser.getErrorMessages().toString() );
931 if ( phylogenies_0.length != 4 ) {
934 final Phylogeny t1 = phylogenies_0[ 0 ];
935 final Phylogeny t2 = phylogenies_0[ 1 ];
936 final Phylogeny t3 = phylogenies_0[ 2 ];
937 final Phylogeny t4 = phylogenies_0[ 3 ];
938 if ( t1.getNumberOfExternalNodes() != 1 ) {
941 if ( !t1.isRooted() ) {
944 if ( t1.isRerootable() ) {
947 if ( !t1.getType().equals( "gene_tree" ) ) {
950 if ( t2.getNumberOfExternalNodes() != 2 ) {
953 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
956 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
959 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
962 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
965 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
968 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
971 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
972 .startsWith( "actgtgggggt" ) ) {
975 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
976 .startsWith( "ctgtgatgcat" ) ) {
979 if ( t3.getNumberOfExternalNodes() != 4 ) {
982 if ( !t1.getName().equals( "t1" ) ) {
985 if ( !t2.getName().equals( "t2" ) ) {
988 if ( !t3.getName().equals( "t3" ) ) {
991 if ( !t4.getName().equals( "t4" ) ) {
994 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
997 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1000 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1003 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1004 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1007 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1010 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1013 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1016 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1017 .equals( "apoptosis" ) ) {
1020 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1021 .equals( "GO:0006915" ) ) {
1024 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1025 .equals( "UniProtKB" ) ) {
1028 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1029 .equals( "experimental" ) ) {
1032 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1033 .equals( "function" ) ) {
1036 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1037 .getValue() != 1 ) {
1040 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1041 .getType().equals( "ml" ) ) {
1044 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1045 .equals( "apoptosis" ) ) {
1048 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1049 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1052 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1053 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1056 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1057 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1060 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1061 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1064 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1065 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1068 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1069 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1072 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1073 .equals( "GO:0005829" ) ) {
1076 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1077 .equals( "intracellular organelle" ) ) {
1080 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1083 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1084 .equals( "UniProt link" ) ) ) {
1087 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1091 catch ( final Exception e ) {
1092 e.printStackTrace( System.out );
1098 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1100 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1101 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1102 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1103 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1106 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1108 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1110 if ( xml_parser.getErrorCount() > 0 ) {
1111 System.out.println( xml_parser.getErrorMessages().toString() );
1114 if ( phylogenies_0.length != 4 ) {
1117 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1118 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1119 if ( phylogenies_t1.length != 1 ) {
1122 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1123 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1126 if ( !t1_rt.isRooted() ) {
1129 if ( t1_rt.isRerootable() ) {
1132 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1135 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1136 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1137 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1138 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1141 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1144 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1147 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1150 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1151 .startsWith( "actgtgggggt" ) ) {
1154 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1155 .startsWith( "ctgtgatgcat" ) ) {
1158 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1159 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1160 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1161 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1162 if ( phylogenies_1.length != 1 ) {
1165 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1166 if ( !t3_rt.getName().equals( "t3" ) ) {
1169 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1172 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1175 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1178 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1181 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1182 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1185 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1188 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1191 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1192 .equals( "UniProtKB" ) ) {
1195 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1196 .equals( "apoptosis" ) ) {
1199 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1200 .equals( "GO:0006915" ) ) {
1203 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1204 .equals( "UniProtKB" ) ) {
1207 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1208 .equals( "experimental" ) ) {
1211 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1212 .equals( "function" ) ) {
1215 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1216 .getValue() != 1 ) {
1219 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1220 .getType().equals( "ml" ) ) {
1223 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1224 .equals( "apoptosis" ) ) {
1227 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1228 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1232 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1236 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1240 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1243 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1244 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1248 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1252 .equals( "GO:0005829" ) ) {
1255 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1256 .equals( "intracellular organelle" ) ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1262 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1263 .equals( "UniProt link" ) ) ) {
1266 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1269 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1272 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1273 .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." ) ) ) {
1276 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1279 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1282 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1285 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1288 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1289 .equals( "ncbi" ) ) {
1292 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1295 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1296 .getName().equals( "B" ) ) {
1299 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1300 .getFrom() != 21 ) {
1303 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1306 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1307 .getLength() != 24 ) {
1310 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1311 .getConfidence() != 2144 ) {
1314 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1315 .equals( "pfam" ) ) {
1318 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1321 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1324 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1327 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1330 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1331 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1334 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1337 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1340 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1343 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1346 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1349 if ( taxbb.getSynonyms().size() != 2 ) {
1352 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1355 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1358 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1361 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1364 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1367 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1368 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1372 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1375 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1378 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1381 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1384 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1387 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1390 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1394 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1397 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1398 .equalsIgnoreCase( "435" ) ) {
1401 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1404 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1405 .equalsIgnoreCase( "443.7" ) ) {
1408 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1411 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1414 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1415 .equalsIgnoreCase( "433" ) ) {
1419 catch ( final Exception e ) {
1420 e.printStackTrace( System.out );
1426 private static boolean testBasicPhyloXMLparsingValidating() {
1428 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1429 PhyloXmlParser xml_parser = null;
1431 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1433 catch ( final Exception e ) {
1434 // Do nothing -- means were not running from jar.
1436 if ( xml_parser == null ) {
1437 xml_parser = new PhyloXmlParser();
1438 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1439 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1442 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1445 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1447 if ( xml_parser.getErrorCount() > 0 ) {
1448 System.out.println( xml_parser.getErrorMessages().toString() );
1451 if ( phylogenies_0.length != 4 ) {
1454 final Phylogeny t1 = phylogenies_0[ 0 ];
1455 final Phylogeny t2 = phylogenies_0[ 1 ];
1456 final Phylogeny t3 = phylogenies_0[ 2 ];
1457 final Phylogeny t4 = phylogenies_0[ 3 ];
1458 if ( !t1.getName().equals( "t1" ) ) {
1461 if ( !t2.getName().equals( "t2" ) ) {
1464 if ( !t3.getName().equals( "t3" ) ) {
1467 if ( !t4.getName().equals( "t4" ) ) {
1470 if ( t1.getNumberOfExternalNodes() != 1 ) {
1473 if ( t2.getNumberOfExternalNodes() != 2 ) {
1476 if ( t3.getNumberOfExternalNodes() != 4 ) {
1479 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1480 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1481 if ( xml_parser.getErrorCount() > 0 ) {
1482 System.out.println( "errors:" );
1483 System.out.println( xml_parser.getErrorMessages().toString() );
1486 if ( phylogenies_1.length != 4 ) {
1489 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1491 if ( xml_parser.getErrorCount() > 0 ) {
1492 System.out.println( "errors:" );
1493 System.out.println( xml_parser.getErrorMessages().toString() );
1496 if ( phylogenies_2.length != 1 ) {
1499 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1502 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1504 if ( xml_parser.getErrorCount() > 0 ) {
1505 System.out.println( xml_parser.getErrorMessages().toString() );
1508 if ( phylogenies_3.length != 2 ) {
1511 final Phylogeny a = phylogenies_3[ 0 ];
1512 if ( !a.getName().equals( "tree 4" ) ) {
1515 if ( a.getNumberOfExternalNodes() != 3 ) {
1518 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1521 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1524 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1526 if ( xml_parser.getErrorCount() > 0 ) {
1527 System.out.println( xml_parser.getErrorMessages().toString() );
1530 if ( phylogenies_4.length != 1 ) {
1533 final Phylogeny s = phylogenies_4[ 0 ];
1534 if ( s.getNumberOfExternalNodes() != 6 ) {
1537 s.getNode( "first" );
1539 s.getNode( "\"<a'b&c'd\">\"" );
1540 s.getNode( "'''\"" );
1541 s.getNode( "\"\"\"" );
1542 s.getNode( "dick & doof" );
1544 catch ( final Exception e ) {
1545 e.printStackTrace( System.out );
1551 private static boolean testBasicTable() {
1553 final BasicTable<String> t0 = new BasicTable<String>();
1554 if ( t0.getNumberOfColumns() != 0 ) {
1557 if ( t0.getNumberOfRows() != 0 ) {
1560 t0.setValue( 3, 2, "23" );
1561 t0.setValue( 10, 1, "error" );
1562 t0.setValue( 10, 1, "110" );
1563 t0.setValue( 9, 1, "19" );
1564 t0.setValue( 1, 10, "101" );
1565 t0.setValue( 10, 10, "1010" );
1566 t0.setValue( 100, 10, "10100" );
1567 t0.setValue( 0, 0, "00" );
1568 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1571 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1574 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1577 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1580 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1583 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1586 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1589 if ( t0.getNumberOfColumns() != 101 ) {
1592 if ( t0.getNumberOfRows() != 11 ) {
1595 if ( t0.getValueAsString( 49, 4 ) != null ) {
1598 final String l = ForesterUtil.getLineSeparator();
1599 final StringBuffer source = new StringBuffer();
1600 source.append( "" + l );
1601 source.append( "# 1 1 1 1 1 1 1 1" + l );
1602 source.append( " 00 01 02 03" + l );
1603 source.append( " 10 11 12 13 " + l );
1604 source.append( "20 21 22 23 " + l );
1605 source.append( " 30 31 32 33" + l );
1606 source.append( "40 41 42 43" + l );
1607 source.append( " # 1 1 1 1 1 " + l );
1608 source.append( "50 51 52 53 54" + l );
1609 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1610 if ( t1.getNumberOfColumns() != 5 ) {
1613 if ( t1.getNumberOfRows() != 6 ) {
1616 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1619 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1622 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1625 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1628 final StringBuffer source1 = new StringBuffer();
1629 source1.append( "" + l );
1630 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1631 source1.append( " 00; 01 ;02;03" + l );
1632 source1.append( " 10; 11; 12; 13 " + l );
1633 source1.append( "20; 21; 22; 23 " + l );
1634 source1.append( " 30; 31; 32; 33" + l );
1635 source1.append( "40;41;42;43" + l );
1636 source1.append( " # 1 1 1 1 1 " + l );
1637 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1638 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1639 if ( t2.getNumberOfColumns() != 5 ) {
1642 if ( t2.getNumberOfRows() != 6 ) {
1645 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1648 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1651 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1654 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1657 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1660 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1663 final StringBuffer source2 = new StringBuffer();
1664 source2.append( "" + l );
1665 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1666 source2.append( " 00; 01 ;02;03" + l );
1667 source2.append( " 10; 11; 12; 13 " + l );
1668 source2.append( "20; 21; 22; 23 " + l );
1669 source2.append( " " + l );
1670 source2.append( " 30; 31; 32; 33" + l );
1671 source2.append( "40;41;42;43" + l );
1672 source2.append( " comment: 1 1 1 1 1 " + l );
1673 source2.append( ";;;50 ; 52; 53;;54 " + l );
1674 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1680 if ( tl.size() != 2 ) {
1683 final BasicTable<String> t3 = tl.get( 0 );
1684 final BasicTable<String> t4 = tl.get( 1 );
1685 if ( t3.getNumberOfColumns() != 4 ) {
1688 if ( t3.getNumberOfRows() != 3 ) {
1691 if ( t4.getNumberOfColumns() != 4 ) {
1694 if ( t4.getNumberOfRows() != 3 ) {
1697 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1700 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1704 catch ( final Exception e ) {
1705 e.printStackTrace( System.out );
1711 private static boolean testBasicTolXMLparsing() {
1713 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1714 final TolParser parser = new TolParser();
1715 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1716 if ( parser.getErrorCount() > 0 ) {
1717 System.out.println( parser.getErrorMessages().toString() );
1720 if ( phylogenies_0.length != 1 ) {
1723 final Phylogeny t1 = phylogenies_0[ 0 ];
1724 if ( t1.getNumberOfExternalNodes() != 5 ) {
1727 if ( !t1.isRooted() ) {
1730 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1733 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1736 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1739 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1742 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1743 if ( parser.getErrorCount() > 0 ) {
1744 System.out.println( parser.getErrorMessages().toString() );
1747 if ( phylogenies_1.length != 1 ) {
1750 final Phylogeny t2 = phylogenies_1[ 0 ];
1751 if ( t2.getNumberOfExternalNodes() != 664 ) {
1754 if ( !t2.isRooted() ) {
1757 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1760 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1763 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1766 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1769 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1772 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1773 .equals( "Aquifex" ) ) {
1776 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1777 if ( parser.getErrorCount() > 0 ) {
1778 System.out.println( parser.getErrorMessages().toString() );
1781 if ( phylogenies_2.length != 1 ) {
1784 final Phylogeny t3 = phylogenies_2[ 0 ];
1785 if ( t3.getNumberOfExternalNodes() != 184 ) {
1788 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1791 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1794 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1797 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1798 if ( parser.getErrorCount() > 0 ) {
1799 System.out.println( parser.getErrorMessages().toString() );
1802 if ( phylogenies_3.length != 1 ) {
1805 final Phylogeny t4 = phylogenies_3[ 0 ];
1806 if ( t4.getNumberOfExternalNodes() != 1 ) {
1809 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1812 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1815 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1818 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1819 if ( parser.getErrorCount() > 0 ) {
1820 System.out.println( parser.getErrorMessages().toString() );
1823 if ( phylogenies_4.length != 1 ) {
1826 final Phylogeny t5 = phylogenies_4[ 0 ];
1827 if ( t5.getNumberOfExternalNodes() != 13 ) {
1830 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1833 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1836 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1840 catch ( final Exception e ) {
1841 e.printStackTrace( System.out );
1847 private static boolean testBasicTreeMethods() {
1849 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1850 final Phylogeny t1 = factory.create();
1851 if ( !t1.isEmpty() ) {
1854 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1855 if ( t2.getNumberOfExternalNodes() != 4 ) {
1858 if ( t2.getHeight() != 8.5 ) {
1861 if ( !t2.isCompletelyBinary() ) {
1864 if ( t2.isEmpty() ) {
1867 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1868 if ( t3.getNumberOfExternalNodes() != 5 ) {
1871 if ( t3.getHeight() != 11 ) {
1874 if ( t3.isCompletelyBinary() ) {
1877 final PhylogenyNode n = t3.getNode( "ABC" );
1878 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 ];
1879 if ( t4.getNumberOfExternalNodes() != 9 ) {
1882 if ( t4.getHeight() != 11 ) {
1885 if ( t4.isCompletelyBinary() ) {
1888 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)" );
1889 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1890 if ( t5.getNumberOfExternalNodes() != 8 ) {
1893 if ( t5.getHeight() != 15 ) {
1896 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)" );
1897 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1898 if ( t6.getHeight() != 15 ) {
1901 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)" );
1902 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1903 if ( t7.getHeight() != 15 ) {
1906 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)" );
1907 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1908 if ( t8.getNumberOfExternalNodes() != 10 ) {
1911 if ( t8.getHeight() != 15 ) {
1914 final char[] a9 = new char[] {};
1915 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1916 if ( t9.getHeight() != 0 ) {
1919 final char[] a10 = new char[] { 'a', ':', '6' };
1920 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1921 if ( t10.getHeight() != 6 ) {
1925 catch ( final Exception e ) {
1926 e.printStackTrace( System.out );
1932 private static boolean testConfidenceAssessor() {
1934 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1935 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1936 final Phylogeny[] ev0 = factory
1937 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1939 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1940 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1943 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1946 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1947 final Phylogeny[] ev1 = factory
1948 .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)));",
1950 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1951 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1954 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1957 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1958 final Phylogeny[] ev_b = factory
1959 .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",
1961 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1962 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1965 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1969 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1970 final Phylogeny[] ev1x = factory
1971 .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)));",
1973 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1974 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1977 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1980 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1981 final Phylogeny[] ev_bx = factory
1982 .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",
1984 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1985 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1988 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1992 final Phylogeny[] t2 = factory
1993 .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);",
1995 final Phylogeny[] ev2 = factory
1996 .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);",
1998 for( final Phylogeny target : t2 ) {
1999 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2002 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2003 new NHXParser() )[ 0 ];
2004 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2005 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2006 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2009 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2012 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2016 catch ( final Exception e ) {
2017 e.printStackTrace();
2023 private static boolean testCopyOfNodeData() {
2025 final PhylogenyNode n1 = PhylogenyNode
2026 .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]" );
2027 final PhylogenyNode n2 = n1.copyNodeData();
2028 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2032 catch ( final Exception e ) {
2033 e.printStackTrace();
2039 private static boolean testDataObjects() {
2041 final Confidence s0 = new Confidence();
2042 final Confidence s1 = new Confidence();
2043 if ( !s0.isEqual( s1 ) ) {
2046 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2047 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2048 if ( s2.isEqual( s1 ) ) {
2051 if ( !s2.isEqual( s3 ) ) {
2054 final Confidence s4 = ( Confidence ) s3.copy();
2055 if ( !s4.isEqual( s3 ) ) {
2062 final Taxonomy t1 = new Taxonomy();
2063 final Taxonomy t2 = new Taxonomy();
2064 final Taxonomy t3 = new Taxonomy();
2065 final Taxonomy t4 = new Taxonomy();
2066 final Taxonomy t5 = new Taxonomy();
2067 t1.setIdentifier( new Identifier( "ecoli" ) );
2068 t1.setTaxonomyCode( "ECOLI" );
2069 t1.setScientificName( "E. coli" );
2070 t1.setCommonName( "coli" );
2071 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2072 if ( !t1.isEqual( t0 ) ) {
2075 t2.setIdentifier( new Identifier( "ecoli" ) );
2076 t2.setTaxonomyCode( "OTHER" );
2077 t2.setScientificName( "what" );
2078 t2.setCommonName( "something" );
2079 if ( !t1.isEqual( t2 ) ) {
2082 t2.setIdentifier( new Identifier( "nemve" ) );
2083 if ( t1.isEqual( t2 ) ) {
2086 t1.setIdentifier( null );
2087 t3.setTaxonomyCode( "ECOLI" );
2088 t3.setScientificName( "what" );
2089 t3.setCommonName( "something" );
2090 if ( !t1.isEqual( t3 ) ) {
2093 t1.setIdentifier( null );
2094 t1.setTaxonomyCode( "" );
2095 t4.setScientificName( "E. ColI" );
2096 t4.setCommonName( "something" );
2097 if ( !t1.isEqual( t4 ) ) {
2100 t4.setScientificName( "B. subtilis" );
2101 t4.setCommonName( "something" );
2102 if ( t1.isEqual( t4 ) ) {
2105 t1.setIdentifier( null );
2106 t1.setTaxonomyCode( "" );
2107 t1.setScientificName( "" );
2108 t5.setCommonName( "COLI" );
2109 if ( !t1.isEqual( t5 ) ) {
2112 t5.setCommonName( "vibrio" );
2113 if ( t1.isEqual( t5 ) ) {
2118 final Identifier id0 = new Identifier( "123", "pfam" );
2119 final Identifier id1 = ( Identifier ) id0.copy();
2120 if ( !id1.isEqual( id1 ) ) {
2123 if ( !id1.isEqual( id0 ) ) {
2126 if ( !id0.isEqual( id1 ) ) {
2133 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2134 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2135 if ( !pd1.isEqual( pd1 ) ) {
2138 if ( !pd1.isEqual( pd0 ) ) {
2143 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2144 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2145 if ( !pd3.isEqual( pd3 ) ) {
2148 if ( !pd2.isEqual( pd3 ) ) {
2151 if ( !pd0.isEqual( pd3 ) ) {
2156 // DomainArchitecture
2157 // ------------------
2158 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2159 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2160 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2161 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2162 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2163 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2168 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2169 if ( ds0.getNumberOfDomains() != 4 ) {
2172 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2173 if ( !ds0.isEqual( ds0 ) ) {
2176 if ( !ds0.isEqual( ds1 ) ) {
2179 if ( ds1.getNumberOfDomains() != 4 ) {
2182 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2187 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2188 if ( ds0.isEqual( ds2 ) ) {
2194 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2195 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2196 System.out.println( ds3.toNHX() );
2199 if ( ds3.getNumberOfDomains() != 3 ) {
2204 final Event e1 = new Event( Event.EventType.fusion );
2205 if ( e1.isDuplication() ) {
2208 if ( !e1.isFusion() ) {
2211 if ( !e1.asText().toString().equals( "fusion" ) ) {
2214 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2217 final Event e11 = new Event( Event.EventType.fusion );
2218 if ( !e11.isEqual( e1 ) ) {
2221 if ( !e11.toNHX().toString().equals( "" ) ) {
2224 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2225 if ( e2.isDuplication() ) {
2228 if ( !e2.isSpeciationOrDuplication() ) {
2231 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2234 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2237 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2240 if ( e11.isEqual( e2 ) ) {
2243 final Event e2c = ( Event ) e2.copy();
2244 if ( !e2c.isEqual( e2 ) ) {
2247 Event e3 = new Event( 1, 2, 3 );
2248 if ( e3.isDuplication() ) {
2251 if ( e3.isSpeciation() ) {
2254 if ( e3.isGeneLoss() ) {
2257 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2260 final Event e3c = ( Event ) e3.copy();
2261 final Event e3cc = ( Event ) e3c.copy();
2262 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2266 if ( !e3c.isEqual( e3cc ) ) {
2269 Event e4 = new Event( 1, 2, 3 );
2270 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2273 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2276 final Event e4c = ( Event ) e4.copy();
2278 final Event e4cc = ( Event ) e4c.copy();
2279 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2282 if ( !e4c.isEqual( e4cc ) ) {
2285 final Event e5 = new Event();
2286 if ( !e5.isUnassigned() ) {
2289 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2292 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2295 final Event e6 = new Event( 1, 0, 0 );
2296 if ( !e6.asText().toString().equals( "duplication" ) ) {
2299 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2302 final Event e7 = new Event( 0, 1, 0 );
2303 if ( !e7.asText().toString().equals( "speciation" ) ) {
2306 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2309 final Event e8 = new Event( 0, 0, 1 );
2310 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2313 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2317 catch ( final Exception e ) {
2318 e.printStackTrace( System.out );
2324 private static boolean testDeletionOfExternalNodes() {
2326 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2327 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2328 final PhylogenyWriter w = new PhylogenyWriter();
2329 if ( t0.isEmpty() ) {
2332 if ( t0.getNumberOfExternalNodes() != 1 ) {
2335 t0.deleteSubtree( t0.getNode( "A" ), false );
2336 if ( t0.getNumberOfExternalNodes() != 0 ) {
2339 if ( !t0.isEmpty() ) {
2342 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2343 if ( t1.getNumberOfExternalNodes() != 2 ) {
2346 t1.deleteSubtree( t1.getNode( "A" ), false );
2347 if ( t1.getNumberOfExternalNodes() != 1 ) {
2350 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2353 t1.deleteSubtree( t1.getNode( "B" ), false );
2354 if ( t1.getNumberOfExternalNodes() != 1 ) {
2357 t1.deleteSubtree( t1.getNode( "r" ), false );
2358 if ( !t1.isEmpty() ) {
2361 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2362 if ( t2.getNumberOfExternalNodes() != 3 ) {
2365 t2.deleteSubtree( t2.getNode( "B" ), false );
2366 if ( t2.getNumberOfExternalNodes() != 2 ) {
2369 t2.toNewHampshireX();
2370 PhylogenyNode n = t2.getNode( "A" );
2371 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2374 t2.deleteSubtree( t2.getNode( "A" ), false );
2375 if ( t2.getNumberOfExternalNodes() != 2 ) {
2378 t2.deleteSubtree( t2.getNode( "C" ), true );
2379 if ( t2.getNumberOfExternalNodes() != 1 ) {
2382 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2383 if ( t3.getNumberOfExternalNodes() != 4 ) {
2386 t3.deleteSubtree( t3.getNode( "B" ), true );
2387 if ( t3.getNumberOfExternalNodes() != 3 ) {
2390 n = t3.getNode( "A" );
2391 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2394 n = n.getNextExternalNode();
2395 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2398 t3.deleteSubtree( t3.getNode( "A" ), true );
2399 if ( t3.getNumberOfExternalNodes() != 2 ) {
2402 n = t3.getNode( "C" );
2403 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2406 t3.deleteSubtree( t3.getNode( "C" ), true );
2407 if ( t3.getNumberOfExternalNodes() != 1 ) {
2410 t3.deleteSubtree( t3.getNode( "D" ), true );
2411 if ( t3.getNumberOfExternalNodes() != 0 ) {
2414 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2415 if ( t4.getNumberOfExternalNodes() != 6 ) {
2418 t4.deleteSubtree( t4.getNode( "B2" ), true );
2419 if ( t4.getNumberOfExternalNodes() != 5 ) {
2422 String s = w.toNewHampshire( t4, false, true ).toString();
2423 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2426 t4.deleteSubtree( t4.getNode( "B11" ), true );
2427 if ( t4.getNumberOfExternalNodes() != 4 ) {
2430 t4.deleteSubtree( t4.getNode( "C" ), true );
2431 if ( t4.getNumberOfExternalNodes() != 3 ) {
2434 n = t4.getNode( "A" );
2435 n = n.getNextExternalNode();
2436 if ( !n.getName().equals( "B12" ) ) {
2439 n = n.getNextExternalNode();
2440 if ( !n.getName().equals( "D" ) ) {
2443 s = w.toNewHampshire( t4, false, true ).toString();
2444 if ( !s.equals( "((A,B12),D);" ) ) {
2447 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2448 t5.deleteSubtree( t5.getNode( "A" ), true );
2449 if ( t5.getNumberOfExternalNodes() != 5 ) {
2452 s = w.toNewHampshire( t5, false, true ).toString();
2453 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2456 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2457 t6.deleteSubtree( t6.getNode( "B11" ), true );
2458 if ( t6.getNumberOfExternalNodes() != 5 ) {
2461 s = w.toNewHampshire( t6, false, false ).toString();
2462 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2465 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2466 t7.deleteSubtree( t7.getNode( "B12" ), true );
2467 if ( t7.getNumberOfExternalNodes() != 5 ) {
2470 s = w.toNewHampshire( t7, false, true ).toString();
2471 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2474 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2475 t8.deleteSubtree( t8.getNode( "B2" ), true );
2476 if ( t8.getNumberOfExternalNodes() != 5 ) {
2479 s = w.toNewHampshire( t8, false, false ).toString();
2480 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2483 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2484 t9.deleteSubtree( t9.getNode( "C" ), true );
2485 if ( t9.getNumberOfExternalNodes() != 5 ) {
2488 s = w.toNewHampshire( t9, false, true ).toString();
2489 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2492 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2493 t10.deleteSubtree( t10.getNode( "D" ), true );
2494 if ( t10.getNumberOfExternalNodes() != 5 ) {
2497 s = w.toNewHampshire( t10, false, true ).toString();
2498 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2501 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2502 t11.deleteSubtree( t11.getNode( "A" ), true );
2503 if ( t11.getNumberOfExternalNodes() != 2 ) {
2506 s = w.toNewHampshire( t11, false, true ).toString();
2507 if ( !s.equals( "(B,C);" ) ) {
2510 t11.deleteSubtree( t11.getNode( "C" ), true );
2511 if ( t11.getNumberOfExternalNodes() != 1 ) {
2514 s = w.toNewHampshire( t11, false, false ).toString();
2515 if ( !s.equals( "B;" ) ) {
2518 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2519 t12.deleteSubtree( t12.getNode( "B2" ), true );
2520 if ( t12.getNumberOfExternalNodes() != 8 ) {
2523 s = w.toNewHampshire( t12, false, true ).toString();
2524 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2527 t12.deleteSubtree( t12.getNode( "B3" ), true );
2528 if ( t12.getNumberOfExternalNodes() != 7 ) {
2531 s = w.toNewHampshire( t12, false, true ).toString();
2532 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2535 t12.deleteSubtree( t12.getNode( "C3" ), true );
2536 if ( t12.getNumberOfExternalNodes() != 6 ) {
2539 s = w.toNewHampshire( t12, false, true ).toString();
2540 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2543 t12.deleteSubtree( t12.getNode( "A1" ), true );
2544 if ( t12.getNumberOfExternalNodes() != 5 ) {
2547 s = w.toNewHampshire( t12, false, true ).toString();
2548 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2551 t12.deleteSubtree( t12.getNode( "B1" ), true );
2552 if ( t12.getNumberOfExternalNodes() != 4 ) {
2555 s = w.toNewHampshire( t12, false, true ).toString();
2556 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2559 t12.deleteSubtree( t12.getNode( "A3" ), true );
2560 if ( t12.getNumberOfExternalNodes() != 3 ) {
2563 s = w.toNewHampshire( t12, false, true ).toString();
2564 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2567 t12.deleteSubtree( t12.getNode( "A2" ), true );
2568 if ( t12.getNumberOfExternalNodes() != 2 ) {
2571 s = w.toNewHampshire( t12, false, true ).toString();
2572 if ( !s.equals( "(C1,C2);" ) ) {
2575 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2576 t13.deleteSubtree( t13.getNode( "D" ), true );
2577 if ( t13.getNumberOfExternalNodes() != 4 ) {
2580 s = w.toNewHampshire( t13, false, true ).toString();
2581 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2584 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2585 t14.deleteSubtree( t14.getNode( "E" ), true );
2586 if ( t14.getNumberOfExternalNodes() != 5 ) {
2589 s = w.toNewHampshire( t14, false, true ).toString();
2590 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2593 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2594 t15.deleteSubtree( t15.getNode( "B2" ), true );
2595 if ( t15.getNumberOfExternalNodes() != 11 ) {
2598 t15.deleteSubtree( t15.getNode( "B1" ), true );
2599 if ( t15.getNumberOfExternalNodes() != 10 ) {
2602 t15.deleteSubtree( t15.getNode( "B3" ), true );
2603 if ( t15.getNumberOfExternalNodes() != 9 ) {
2606 t15.deleteSubtree( t15.getNode( "B4" ), true );
2607 if ( t15.getNumberOfExternalNodes() != 8 ) {
2610 t15.deleteSubtree( t15.getNode( "A1" ), true );
2611 if ( t15.getNumberOfExternalNodes() != 7 ) {
2614 t15.deleteSubtree( t15.getNode( "C4" ), true );
2615 if ( t15.getNumberOfExternalNodes() != 6 ) {
2619 catch ( final Exception e ) {
2620 e.printStackTrace( System.out );
2626 private static boolean testDescriptiveStatistics() {
2628 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2629 dss1.addValue( 82 );
2630 dss1.addValue( 78 );
2631 dss1.addValue( 70 );
2632 dss1.addValue( 58 );
2633 dss1.addValue( 42 );
2634 if ( dss1.getN() != 5 ) {
2637 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2640 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2643 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2646 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2649 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2652 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2655 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2658 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2661 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2664 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2667 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2670 dss1.addValue( 123 );
2671 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2674 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2677 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2680 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2681 dss2.addValue( -1.85 );
2682 dss2.addValue( 57.5 );
2683 dss2.addValue( 92.78 );
2684 dss2.addValue( 57.78 );
2685 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2688 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2691 final double[] a = dss2.getDataAsDoubleArray();
2692 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2695 dss2.addValue( -100 );
2696 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2699 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2702 final double[] ds = new double[ 14 ];
2717 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2718 if ( bins.length != 4 ) {
2721 if ( bins[ 0 ] != 2 ) {
2724 if ( bins[ 1 ] != 3 ) {
2727 if ( bins[ 2 ] != 4 ) {
2730 if ( bins[ 3 ] != 5 ) {
2733 final double[] ds1 = new double[ 9 ];
2743 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2744 if ( bins1.length != 4 ) {
2747 if ( bins1[ 0 ] != 2 ) {
2750 if ( bins1[ 1 ] != 3 ) {
2753 if ( bins1[ 2 ] != 0 ) {
2756 if ( bins1[ 3 ] != 4 ) {
2759 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2760 if ( bins1_1.length != 3 ) {
2763 if ( bins1_1[ 0 ] != 3 ) {
2766 if ( bins1_1[ 1 ] != 2 ) {
2769 if ( bins1_1[ 2 ] != 4 ) {
2772 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2773 if ( bins1_2.length != 3 ) {
2776 if ( bins1_2[ 0 ] != 2 ) {
2779 if ( bins1_2[ 1 ] != 2 ) {
2782 if ( bins1_2[ 2 ] != 2 ) {
2785 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2799 dss3.addValue( 10 );
2800 dss3.addValue( 10 );
2801 dss3.addValue( 10 );
2802 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2803 histo.toStringBuffer( 10, '=', 40, 5 );
2804 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2806 catch ( final Exception e ) {
2807 e.printStackTrace( System.out );
2813 private static boolean testDir( final String file ) {
2815 final File f = new File( file );
2816 if ( !f.exists() ) {
2819 if ( !f.isDirectory() ) {
2822 if ( !f.canRead() ) {
2826 catch ( final Exception e ) {
2832 private static boolean testExternalNodeRelatedMethods() {
2834 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2835 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2836 PhylogenyNode n = t1.getNode( "A" );
2837 n = n.getNextExternalNode();
2838 if ( !n.getName().equals( "B" ) ) {
2841 n = n.getNextExternalNode();
2842 if ( !n.getName().equals( "C" ) ) {
2845 n = n.getNextExternalNode();
2846 if ( !n.getName().equals( "D" ) ) {
2849 n = t1.getNode( "B" );
2850 while ( !n.isLastExternalNode() ) {
2851 n = n.getNextExternalNode();
2853 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2854 n = t2.getNode( "A" );
2855 n = n.getNextExternalNode();
2856 if ( !n.getName().equals( "B" ) ) {
2859 n = n.getNextExternalNode();
2860 if ( !n.getName().equals( "C" ) ) {
2863 n = n.getNextExternalNode();
2864 if ( !n.getName().equals( "D" ) ) {
2867 n = t2.getNode( "B" );
2868 while ( !n.isLastExternalNode() ) {
2869 n = n.getNextExternalNode();
2871 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2872 n = t3.getNode( "A" );
2873 n = n.getNextExternalNode();
2874 if ( !n.getName().equals( "B" ) ) {
2877 n = n.getNextExternalNode();
2878 if ( !n.getName().equals( "C" ) ) {
2881 n = n.getNextExternalNode();
2882 if ( !n.getName().equals( "D" ) ) {
2885 n = n.getNextExternalNode();
2886 if ( !n.getName().equals( "E" ) ) {
2889 n = n.getNextExternalNode();
2890 if ( !n.getName().equals( "F" ) ) {
2893 n = n.getNextExternalNode();
2894 if ( !n.getName().equals( "G" ) ) {
2897 n = n.getNextExternalNode();
2898 if ( !n.getName().equals( "H" ) ) {
2901 n = t3.getNode( "B" );
2902 while ( !n.isLastExternalNode() ) {
2903 n = n.getNextExternalNode();
2905 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2906 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2907 final PhylogenyNode node = iter.next();
2909 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2910 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2911 final PhylogenyNode node = iter.next();
2913 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2914 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2915 if ( !iter.next().getName().equals( "A" ) ) {
2918 if ( !iter.next().getName().equals( "B" ) ) {
2921 if ( !iter.next().getName().equals( "C" ) ) {
2924 if ( !iter.next().getName().equals( "D" ) ) {
2927 if ( !iter.next().getName().equals( "E" ) ) {
2930 if ( !iter.next().getName().equals( "F" ) ) {
2933 if ( iter.hasNext() ) {
2937 catch ( final Exception e ) {
2938 e.printStackTrace( System.out );
2944 private static boolean testGeneralTable() {
2946 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2947 t0.setValue( 3, 2, "23" );
2948 t0.setValue( 10, 1, "error" );
2949 t0.setValue( 10, 1, "110" );
2950 t0.setValue( 9, 1, "19" );
2951 t0.setValue( 1, 10, "101" );
2952 t0.setValue( 10, 10, "1010" );
2953 t0.setValue( 100, 10, "10100" );
2954 t0.setValue( 0, 0, "00" );
2955 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2958 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2961 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2964 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2967 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2970 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2973 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2976 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2979 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2982 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2983 t1.setValue( "3", "2", "23" );
2984 t1.setValue( "10", "1", "error" );
2985 t1.setValue( "10", "1", "110" );
2986 t1.setValue( "9", "1", "19" );
2987 t1.setValue( "1", "10", "101" );
2988 t1.setValue( "10", "10", "1010" );
2989 t1.setValue( "100", "10", "10100" );
2990 t1.setValue( "0", "0", "00" );
2991 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2992 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2995 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2998 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3001 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3004 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3007 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3010 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3013 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3016 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3019 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3023 catch ( final Exception e ) {
3024 e.printStackTrace( System.out );
3030 private static boolean testGetDistance() {
3032 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3033 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",
3034 new NHXParser() )[ 0 ];
3035 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3038 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3041 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3044 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3047 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3050 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3053 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3056 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3059 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3062 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3065 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3068 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3071 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3074 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3077 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3080 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3083 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3086 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3089 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3092 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3095 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3098 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3101 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3104 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3107 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3110 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3113 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3116 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3119 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3122 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3125 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3128 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",
3129 new NHXParser() )[ 0 ];
3130 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3133 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3136 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3139 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3142 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3145 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3148 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3151 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3154 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3157 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3160 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3164 catch ( final Exception e ) {
3165 e.printStackTrace( System.out );
3171 private static boolean testGetLCA() {
3173 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3174 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3175 new NHXParser() )[ 0 ];
3176 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3177 if ( !A.getName().equals( "A" ) ) {
3180 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3181 if ( !gh.getName().equals( "gh" ) ) {
3184 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3185 if ( !ab.getName().equals( "ab" ) ) {
3188 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3189 if ( !ab2.getName().equals( "ab" ) ) {
3192 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3193 if ( !gh2.getName().equals( "gh" ) ) {
3196 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3197 if ( !gh3.getName().equals( "gh" ) ) {
3200 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3201 if ( !abc.getName().equals( "abc" ) ) {
3204 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3205 if ( !abc2.getName().equals( "abc" ) ) {
3208 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3209 if ( !abcd.getName().equals( "abcd" ) ) {
3212 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3213 if ( !abcd2.getName().equals( "abcd" ) ) {
3216 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3217 if ( !abcdef.getName().equals( "abcdef" ) ) {
3220 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3221 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3224 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3225 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3228 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3229 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3232 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3233 if ( !abcde.getName().equals( "abcde" ) ) {
3236 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3237 if ( !abcde2.getName().equals( "abcde" ) ) {
3240 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3241 if ( !r.getName().equals( "abcdefgh" ) ) {
3244 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3245 if ( !r2.getName().equals( "abcdefgh" ) ) {
3248 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3249 if ( !r3.getName().equals( "abcdefgh" ) ) {
3252 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3253 if ( !abcde3.getName().equals( "abcde" ) ) {
3256 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3257 if ( !abcde4.getName().equals( "abcde" ) ) {
3260 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3261 if ( !ab3.getName().equals( "ab" ) ) {
3264 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3265 if ( !ab4.getName().equals( "ab" ) ) {
3268 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3269 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3270 if ( !cd.getName().equals( "cd" ) ) {
3273 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3274 if ( !cd2.getName().equals( "cd" ) ) {
3277 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3278 if ( !cde.getName().equals( "cde" ) ) {
3281 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3282 if ( !cde2.getName().equals( "cde" ) ) {
3285 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3286 if ( !cdef.getName().equals( "cdef" ) ) {
3289 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3290 if ( !cdef2.getName().equals( "cdef" ) ) {
3293 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3294 if ( !cdef3.getName().equals( "cdef" ) ) {
3297 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3298 if ( !rt.getName().equals( "r" ) ) {
3301 final Phylogeny p3 = factory
3302 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3303 new NHXParser() )[ 0 ];
3304 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3305 if ( !bc_3.getName().equals( "bc" ) ) {
3308 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3309 if ( !ac_3.getName().equals( "abc" ) ) {
3312 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3313 if ( !ad_3.getName().equals( "abcde" ) ) {
3316 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3317 if ( !af_3.getName().equals( "abcdef" ) ) {
3320 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3321 if ( !ag_3.getName().equals( "" ) ) {
3324 if ( !ag_3.isRoot() ) {
3327 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3328 if ( !al_3.getName().equals( "" ) ) {
3331 if ( !al_3.isRoot() ) {
3334 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3335 if ( !kl_3.getName().equals( "" ) ) {
3338 if ( !kl_3.isRoot() ) {
3341 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3342 if ( !fl_3.getName().equals( "" ) ) {
3345 if ( !fl_3.isRoot() ) {
3348 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3349 if ( !gk_3.getName().equals( "ghijk" ) ) {
3352 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3353 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3354 if ( !r_4.getName().equals( "r" ) ) {
3357 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3358 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3359 if ( !r_5.getName().equals( "root" ) ) {
3362 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3363 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3364 if ( !r_6.getName().equals( "rot" ) ) {
3367 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3368 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3369 if ( !r_7.getName().equals( "rott" ) ) {
3373 catch ( final Exception e ) {
3374 e.printStackTrace( System.out );
3380 private static boolean testGetLCA2() {
3382 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3383 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3384 PhylogenyMethods.preOrderReId( p_a );
3385 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3386 p_a.getNode( "a" ) );
3387 if ( !p_a_1.getName().equals( "a" ) ) {
3390 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3391 PhylogenyMethods.preOrderReId( p_b );
3392 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3393 p_b.getNode( "a" ) );
3394 if ( !p_b_1.getName().equals( "b" ) ) {
3397 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3398 p_b.getNode( "b" ) );
3399 if ( !p_b_2.getName().equals( "b" ) ) {
3402 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3403 PhylogenyMethods.preOrderReId( p_c );
3404 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3405 p_c.getNode( "a" ) );
3406 if ( !p_c_1.getName().equals( "b" ) ) {
3409 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3410 p_c.getNode( "c" ) );
3411 if ( !p_c_2.getName().equals( "c" ) ) {
3412 System.out.println( p_c_2.getName() );
3416 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3417 p_c.getNode( "b" ) );
3418 if ( !p_c_3.getName().equals( "b" ) ) {
3421 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3422 p_c.getNode( "a" ) );
3423 if ( !p_c_4.getName().equals( "c" ) ) {
3426 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3427 new NHXParser() )[ 0 ];
3428 PhylogenyMethods.preOrderReId( p1 );
3429 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3430 p1.getNode( "A" ) );
3431 if ( !A.getName().equals( "A" ) ) {
3434 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3435 p1.getNode( "gh" ) );
3436 if ( !gh.getName().equals( "gh" ) ) {
3439 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3440 p1.getNode( "B" ) );
3441 if ( !ab.getName().equals( "ab" ) ) {
3444 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3445 p1.getNode( "A" ) );
3446 if ( !ab2.getName().equals( "ab" ) ) {
3449 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3450 p1.getNode( "G" ) );
3451 if ( !gh2.getName().equals( "gh" ) ) {
3454 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3455 p1.getNode( "H" ) );
3456 if ( !gh3.getName().equals( "gh" ) ) {
3459 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3460 p1.getNode( "A" ) );
3461 if ( !abc.getName().equals( "abc" ) ) {
3464 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3465 p1.getNode( "C" ) );
3466 if ( !abc2.getName().equals( "abc" ) ) {
3469 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3470 p1.getNode( "D" ) );
3471 if ( !abcd.getName().equals( "abcd" ) ) {
3474 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3475 p1.getNode( "A" ) );
3476 if ( !abcd2.getName().equals( "abcd" ) ) {
3479 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3480 p1.getNode( "F" ) );
3481 if ( !abcdef.getName().equals( "abcdef" ) ) {
3484 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3485 p1.getNode( "A" ) );
3486 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3489 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3490 p1.getNode( "F" ) );
3491 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3494 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3495 p1.getNode( "ab" ) );
3496 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3499 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3500 p1.getNode( "E" ) );
3501 if ( !abcde.getName().equals( "abcde" ) ) {
3504 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3505 p1.getNode( "A" ) );
3506 if ( !abcde2.getName().equals( "abcde" ) ) {
3509 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3510 p1.getNode( "abcdefgh" ) );
3511 if ( !r.getName().equals( "abcdefgh" ) ) {
3514 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3515 p1.getNode( "H" ) );
3516 if ( !r2.getName().equals( "abcdefgh" ) ) {
3519 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3520 p1.getNode( "A" ) );
3521 if ( !r3.getName().equals( "abcdefgh" ) ) {
3524 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3525 p1.getNode( "abcde" ) );
3526 if ( !abcde3.getName().equals( "abcde" ) ) {
3529 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3530 p1.getNode( "E" ) );
3531 if ( !abcde4.getName().equals( "abcde" ) ) {
3534 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3535 p1.getNode( "B" ) );
3536 if ( !ab3.getName().equals( "ab" ) ) {
3539 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3540 p1.getNode( "ab" ) );
3541 if ( !ab4.getName().equals( "ab" ) ) {
3544 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3545 PhylogenyMethods.preOrderReId( p2 );
3546 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3547 p2.getNode( "d" ) );
3548 if ( !cd.getName().equals( "cd" ) ) {
3551 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3552 p2.getNode( "c" ) );
3553 if ( !cd2.getName().equals( "cd" ) ) {
3556 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3557 p2.getNode( "e" ) );
3558 if ( !cde.getName().equals( "cde" ) ) {
3561 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3562 p2.getNode( "c" ) );
3563 if ( !cde2.getName().equals( "cde" ) ) {
3566 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3567 p2.getNode( "f" ) );
3568 if ( !cdef.getName().equals( "cdef" ) ) {
3571 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3572 p2.getNode( "f" ) );
3573 if ( !cdef2.getName().equals( "cdef" ) ) {
3576 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3577 p2.getNode( "d" ) );
3578 if ( !cdef3.getName().equals( "cdef" ) ) {
3581 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3582 p2.getNode( "a" ) );
3583 if ( !rt.getName().equals( "r" ) ) {
3586 final Phylogeny p3 = factory
3587 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3588 new NHXParser() )[ 0 ];
3589 PhylogenyMethods.preOrderReId( p3 );
3590 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3591 p3.getNode( "c" ) );
3592 if ( !bc_3.getName().equals( "bc" ) ) {
3595 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3596 p3.getNode( "c" ) );
3597 if ( !ac_3.getName().equals( "abc" ) ) {
3600 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3601 p3.getNode( "d" ) );
3602 if ( !ad_3.getName().equals( "abcde" ) ) {
3605 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3606 p3.getNode( "f" ) );
3607 if ( !af_3.getName().equals( "abcdef" ) ) {
3610 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3611 p3.getNode( "g" ) );
3612 if ( !ag_3.getName().equals( "" ) ) {
3615 if ( !ag_3.isRoot() ) {
3618 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3619 p3.getNode( "l" ) );
3620 if ( !al_3.getName().equals( "" ) ) {
3623 if ( !al_3.isRoot() ) {
3626 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3627 p3.getNode( "l" ) );
3628 if ( !kl_3.getName().equals( "" ) ) {
3631 if ( !kl_3.isRoot() ) {
3634 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3635 p3.getNode( "l" ) );
3636 if ( !fl_3.getName().equals( "" ) ) {
3639 if ( !fl_3.isRoot() ) {
3642 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3643 p3.getNode( "k" ) );
3644 if ( !gk_3.getName().equals( "ghijk" ) ) {
3647 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3648 PhylogenyMethods.preOrderReId( p4 );
3649 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3650 p4.getNode( "c" ) );
3651 if ( !r_4.getName().equals( "r" ) ) {
3654 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3655 PhylogenyMethods.preOrderReId( p5 );
3656 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3657 p5.getNode( "c" ) );
3658 if ( !r_5.getName().equals( "root" ) ) {
3661 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3662 PhylogenyMethods.preOrderReId( p6 );
3663 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3664 p6.getNode( "a" ) );
3665 if ( !r_6.getName().equals( "rot" ) ) {
3668 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3669 PhylogenyMethods.preOrderReId( p7 );
3670 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3671 p7.getNode( "e" ) );
3672 if ( !r_7.getName().equals( "rott" ) ) {
3675 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3676 p7.getNode( "a" ) );
3677 if ( !r_71.getName().equals( "rott" ) ) {
3680 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3681 p7.getNode( "rott" ) );
3682 if ( !r_72.getName().equals( "rott" ) ) {
3685 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3686 p7.getNode( "a" ) );
3687 if ( !r_73.getName().equals( "rott" ) ) {
3690 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3691 p7.getNode( "rott" ) );
3692 if ( !r_74.getName().equals( "rott" ) ) {
3695 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3696 p7.getNode( "e" ) );
3697 if ( !r_75.getName().equals( "e" ) ) {
3701 catch ( final Exception e ) {
3702 e.printStackTrace( System.out );
3708 private static boolean testHmmscanOutputParser() {
3709 final String test_dir = Test.PATH_TO_TEST_DATA;
3711 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3712 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3714 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3715 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3716 final List<Protein> proteins = parser2.parse();
3717 if ( parser2.getProteinsEncountered() != 4 ) {
3720 if ( proteins.size() != 4 ) {
3723 if ( parser2.getDomainsEncountered() != 69 ) {
3726 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3729 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3732 final Protein p1 = proteins.get( 0 );
3733 if ( p1.getNumberOfProteinDomains() != 15 ) {
3736 if ( p1.getLength() != 850 ) {
3739 final Protein p2 = proteins.get( 1 );
3740 if ( p2.getNumberOfProteinDomains() != 51 ) {
3743 if ( p2.getLength() != 1291 ) {
3746 final Protein p3 = proteins.get( 2 );
3747 if ( p3.getNumberOfProteinDomains() != 2 ) {
3750 final Protein p4 = proteins.get( 3 );
3751 if ( p4.getNumberOfProteinDomains() != 1 ) {
3754 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3757 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3760 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3763 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3766 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3769 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3772 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3775 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3778 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3782 catch ( final Exception e ) {
3783 e.printStackTrace( System.out );
3789 private static boolean testLastExternalNodeMethods() {
3791 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3792 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3793 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3794 final PhylogenyNode n1 = t0.getNode( "A" );
3795 if ( n1.isLastExternalNode() ) {
3798 final PhylogenyNode n2 = t0.getNode( "B" );
3799 if ( n2.isLastExternalNode() ) {
3802 final PhylogenyNode n3 = t0.getNode( "C" );
3803 if ( n3.isLastExternalNode() ) {
3806 final PhylogenyNode n4 = t0.getNode( "D" );
3807 if ( !n4.isLastExternalNode() ) {
3811 catch ( final Exception e ) {
3812 e.printStackTrace( System.out );
3818 private static boolean testLevelOrderIterator() {
3820 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3821 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3822 PhylogenyNodeIterator it0;
3823 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3826 for( it0.reset(); it0.hasNext(); ) {
3829 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3830 if ( !it.next().getName().equals( "r" ) ) {
3833 if ( !it.next().getName().equals( "ab" ) ) {
3836 if ( !it.next().getName().equals( "cd" ) ) {
3839 if ( !it.next().getName().equals( "A" ) ) {
3842 if ( !it.next().getName().equals( "B" ) ) {
3845 if ( !it.next().getName().equals( "C" ) ) {
3848 if ( !it.next().getName().equals( "D" ) ) {
3851 if ( it.hasNext() ) {
3854 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",
3855 new NHXParser() )[ 0 ];
3856 PhylogenyNodeIterator it2;
3857 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3860 for( it2.reset(); it2.hasNext(); ) {
3863 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3864 if ( !it3.next().getName().equals( "r" ) ) {
3867 if ( !it3.next().getName().equals( "abc" ) ) {
3870 if ( !it3.next().getName().equals( "defg" ) ) {
3873 if ( !it3.next().getName().equals( "A" ) ) {
3876 if ( !it3.next().getName().equals( "B" ) ) {
3879 if ( !it3.next().getName().equals( "C" ) ) {
3882 if ( !it3.next().getName().equals( "D" ) ) {
3885 if ( !it3.next().getName().equals( "E" ) ) {
3888 if ( !it3.next().getName().equals( "F" ) ) {
3891 if ( !it3.next().getName().equals( "G" ) ) {
3894 if ( !it3.next().getName().equals( "1" ) ) {
3897 if ( !it3.next().getName().equals( "2" ) ) {
3900 if ( !it3.next().getName().equals( "3" ) ) {
3903 if ( !it3.next().getName().equals( "4" ) ) {
3906 if ( !it3.next().getName().equals( "5" ) ) {
3909 if ( !it3.next().getName().equals( "6" ) ) {
3912 if ( !it3.next().getName().equals( "f1" ) ) {
3915 if ( !it3.next().getName().equals( "f2" ) ) {
3918 if ( !it3.next().getName().equals( "f3" ) ) {
3921 if ( !it3.next().getName().equals( "a" ) ) {
3924 if ( !it3.next().getName().equals( "b" ) ) {
3927 if ( !it3.next().getName().equals( "f21" ) ) {
3930 if ( !it3.next().getName().equals( "X" ) ) {
3933 if ( !it3.next().getName().equals( "Y" ) ) {
3936 if ( !it3.next().getName().equals( "Z" ) ) {
3939 if ( it3.hasNext() ) {
3942 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3943 PhylogenyNodeIterator it4;
3944 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3947 for( it4.reset(); it4.hasNext(); ) {
3950 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3951 if ( !it5.next().getName().equals( "r" ) ) {
3954 if ( !it5.next().getName().equals( "A" ) ) {
3957 if ( !it5.next().getName().equals( "B" ) ) {
3960 if ( !it5.next().getName().equals( "C" ) ) {
3963 if ( !it5.next().getName().equals( "D" ) ) {
3966 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3967 PhylogenyNodeIterator it6;
3968 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3971 for( it6.reset(); it6.hasNext(); ) {
3974 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3975 if ( !it7.next().getName().equals( "A" ) ) {
3978 if ( it.hasNext() ) {
3982 catch ( final Exception e ) {
3983 e.printStackTrace( System.out );
3989 private static boolean testNodeRemoval() {
3991 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3992 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3993 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
3994 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
3997 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
3998 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
3999 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4002 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4003 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4004 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4008 catch ( final Exception e ) {
4009 e.printStackTrace( System.out );
4015 private static boolean testMidpointrooting() {
4017 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4018 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4019 PhylogenyMethods.midpointRoot( t0 );
4020 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4023 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4026 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4030 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",
4031 new NHXParser() )[ 0 ];
4032 if ( !t1.isRooted() ) {
4035 PhylogenyMethods.midpointRoot( t1 );
4036 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4039 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4042 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4045 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4048 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4051 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4054 t1.reRoot( t1.getNode( "A" ) );
4055 PhylogenyMethods.midpointRoot( t1 );
4056 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4059 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4062 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4065 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4068 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4072 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4076 catch ( final Exception e ) {
4077 e.printStackTrace( System.out );
4083 private static boolean testNexusCharactersParsing() {
4085 final NexusCharactersParser parser = new NexusCharactersParser();
4086 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4088 String[] labels = parser.getCharStateLabels();
4089 if ( labels.length != 7 ) {
4092 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4095 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4098 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4101 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4104 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4107 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4110 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4113 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4115 labels = parser.getCharStateLabels();
4116 if ( labels.length != 7 ) {
4119 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4122 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4125 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4128 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4131 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4134 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4137 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4141 catch ( final Exception e ) {
4142 e.printStackTrace( System.out );
4148 private static boolean testNexusMatrixParsing() {
4150 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4151 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4153 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4154 if ( m.getNumberOfCharacters() != 9 ) {
4157 if ( m.getNumberOfIdentifiers() != 5 ) {
4160 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4163 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4166 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4169 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4172 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4175 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4178 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4181 // if ( labels.length != 7 ) {
4184 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4187 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4190 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4193 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4196 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4199 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4202 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4205 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4207 // labels = parser.getCharStateLabels();
4208 // if ( labels.length != 7 ) {
4211 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4214 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4217 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4220 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4223 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4226 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4229 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4233 catch ( final Exception e ) {
4234 e.printStackTrace( System.out );
4240 private static boolean testNexusTreeParsing() {
4242 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4243 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4244 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4245 if ( phylogenies.length != 1 ) {
4248 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4251 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4255 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4256 if ( phylogenies.length != 1 ) {
4259 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4262 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4266 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4267 if ( phylogenies.length != 1 ) {
4270 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4273 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4276 if ( phylogenies[ 0 ].isRooted() ) {
4280 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4281 if ( phylogenies.length != 18 ) {
4284 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4287 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4290 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4293 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4296 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4299 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4302 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4305 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4308 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4311 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4314 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4317 if ( phylogenies[ 8 ].isRooted() ) {
4320 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4323 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4326 if ( !phylogenies[ 9 ].isRooted() ) {
4329 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4332 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4335 if ( !phylogenies[ 10 ].isRooted() ) {
4338 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4341 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4344 if ( phylogenies[ 11 ].isRooted() ) {
4347 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4350 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4353 if ( !phylogenies[ 12 ].isRooted() ) {
4356 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4359 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4362 if ( !phylogenies[ 13 ].isRooted() ) {
4365 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4368 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4371 if ( !phylogenies[ 14 ].isRooted() ) {
4374 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4377 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4380 if ( phylogenies[ 15 ].isRooted() ) {
4383 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4386 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4389 if ( !phylogenies[ 16 ].isRooted() ) {
4392 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4395 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4398 if ( phylogenies[ 17 ].isRooted() ) {
4401 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4405 catch ( final Exception e ) {
4406 e.printStackTrace( System.out );
4412 private static boolean testNexusTreeParsingTranslating() {
4414 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4415 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4416 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4417 if ( phylogenies.length != 1 ) {
4420 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4423 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4426 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4429 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4432 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4433 .equals( "Aranaeus" ) ) {
4437 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4438 if ( phylogenies.length != 3 ) {
4441 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4444 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4447 if ( phylogenies[ 0 ].isRooted() ) {
4450 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4453 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4456 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4457 .equals( "Aranaeus" ) ) {
4460 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4463 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4466 if ( phylogenies[ 1 ].isRooted() ) {
4469 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4472 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4475 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4476 .equals( "Aranaeus" ) ) {
4479 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4482 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4485 if ( !phylogenies[ 2 ].isRooted() ) {
4488 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4491 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4494 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4495 .equals( "Aranaeus" ) ) {
4499 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4500 if ( phylogenies.length != 3 ) {
4503 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4506 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4509 if ( phylogenies[ 0 ].isRooted() ) {
4512 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4515 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4518 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4519 .equals( "Aranaeus" ) ) {
4522 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4525 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4528 if ( phylogenies[ 1 ].isRooted() ) {
4531 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4534 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4537 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4538 .equals( "Aranaeus" ) ) {
4541 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4544 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4547 if ( !phylogenies[ 2 ].isRooted() ) {
4550 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4553 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4556 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4557 .equals( "Aranaeus" ) ) {
4561 catch ( final Exception e ) {
4562 e.printStackTrace( System.out );
4568 private static boolean testNHParsing() {
4570 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4571 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser2() )[ 0 ];
4572 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4575 final NHXParser nhxp = new NHXParser();
4576 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4577 nhxp.setReplaceUnderscores( true );
4578 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4579 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4582 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4585 final Phylogeny p1b = factory
4586 .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 ",
4587 new NHXParser() )[ 0 ];
4588 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4591 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4594 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser2() )[ 0 ];
4595 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser2() )[ 0 ];
4596 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser2() )[ 0 ];
4597 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser2() )[ 0 ];
4598 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser2() );
4599 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser2() );
4600 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser2() );
4601 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser2() );
4602 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser2() );
4603 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser2() );
4604 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4605 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4606 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4608 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4611 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4614 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4617 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4620 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser2() );
4621 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser2() );
4622 final String p16_S = "((A,B),C)";
4623 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser2() );
4624 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4627 final String p17_S = "(C,(A,B))";
4628 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser2() );
4629 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4632 final String p18_S = "((A,B),(C,D))";
4633 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser2() );
4634 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4637 final String p19_S = "(((A,B),C),D)";
4638 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser2() );
4639 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4642 final String p20_S = "(A,(B,(C,D)))";
4643 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser2() );
4644 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4647 final String p21_S = "(A,(B,(C,(D,E))))";
4648 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser2() );
4649 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4652 final String p22_S = "((((A,B),C),D),E)";
4653 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser2() );
4654 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4657 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4658 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser2() );
4659 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4662 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4663 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser2() );
4664 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4667 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4668 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4669 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser2() );
4670 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4673 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4676 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4677 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4678 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4679 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4680 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4681 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4682 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4683 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4684 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser2() );
4685 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4688 final String p26_S = "(A,B)ab";
4689 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser2() );
4690 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4693 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4694 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4696 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4697 System.out.println( p27[ 0 ].toNewHampshireX() );
4701 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4702 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4703 final String p28_S3 = "(A,B)ab";
4704 final String p28_S4 = "((((A,B),C),D),;E;)";
4705 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4707 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4710 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4713 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4716 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4719 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";
4720 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4721 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4724 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";
4725 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4726 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4729 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4730 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4731 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4734 final String p33_S = "A";
4735 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4736 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4739 final String p34_S = "B;";
4740 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4741 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4744 final String p35_S = "B:0.2";
4745 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4746 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4749 final String p36_S = "(A)";
4750 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4751 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4754 final String p37_S = "((A))";
4755 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4756 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4759 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4760 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4761 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4764 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4765 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4766 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4769 final String p40_S = "(A,B,C)";
4770 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4771 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4774 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4775 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4776 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4779 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4780 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4781 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4784 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)";
4785 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4786 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4789 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)))";
4790 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4791 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4794 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4795 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4796 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4799 final String p46_S = "";
4800 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4801 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4804 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4805 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4808 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4809 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4812 final Phylogeny p49 = factory
4813 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4814 new NHXParser() )[ 0 ];
4815 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4818 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4819 if ( p50.getNode( "A" ) == null ) {
4822 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4823 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4826 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4829 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4830 .equals( "((A,B)88:2.0,C);" ) ) {
4833 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4834 if ( p51.getNode( "A(A" ) == null ) {
4837 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4838 if ( p52.getNode( "A(A" ) == null ) {
4841 final Phylogeny p53 = factory
4842 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4843 new NHXParser() )[ 0 ];
4844 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4848 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4849 if ( p54.getNode( "A" ) == null ) {
4852 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4853 .equals( "((A,B)[88],C);" ) ) {
4857 catch ( final Exception e ) {
4858 e.printStackTrace( System.out );
4864 private static boolean testNHParsingIter() {
4866 String p0_str = "(A,B);";
4867 NHXParser2 p = new NHXParser2();
4868 p.setSource( p0_str );
4869 if ( !p.hasNext() ) {
4872 Phylogeny p0 = p.next();
4873 if ( !p0.toNewHampshire().equals( p0_str ) ) {
4874 System.out.println( p0.toNewHampshire() );
4877 if ( p.hasNext() ) {
4880 if ( p.next() != null ) {
4884 String p00_str = "(A,B)root;";
4885 p.setSource( p00_str );
4886 Phylogeny p00 = p.next();
4887 if ( !p00.toNewHampshire().equals( p00_str ) ) {
4888 System.out.println( p00.toNewHampshire() );
4892 String p000_str = "A;";
4893 p.setSource( p000_str );
4894 Phylogeny p000 = p.next();
4895 if ( !p000.toNewHampshire().equals( p000_str ) ) {
4896 System.out.println( p000.toNewHampshire() );
4900 String p0000_str = "A";
4901 p.setSource( p0000_str );
4902 Phylogeny p0000 = p.next();
4903 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
4904 System.out.println( p0000.toNewHampshire() );
4908 p.setSource( "(A)" );
4909 Phylogeny p00000 = p.next();
4910 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
4911 System.out.println( p00000.toNewHampshire() );
4915 String p1_str = "(A,B)(C,D)(E,F)(G,H)";
4916 p.setSource( p1_str );
4917 if ( !p.hasNext() ) {
4920 Phylogeny p1_0 = p.next();
4921 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
4922 System.out.println( p1_0.toNewHampshire() );
4925 if ( !p.hasNext() ) {
4928 Phylogeny p1_1 = p.next();
4929 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
4930 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
4933 if ( !p.hasNext() ) {
4936 Phylogeny p1_2 = p.next();
4937 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
4938 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
4941 if ( !p.hasNext() ) {
4944 Phylogeny p1_3 = p.next();
4945 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
4946 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
4949 if ( p.hasNext() ) {
4952 if ( p.next() != null ) {
4956 String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
4957 p.setSource( p2_str );
4958 if ( !p.hasNext() ) {
4961 Phylogeny p2_0 = p.next();
4962 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
4963 System.out.println( p2_0.toNewHampshire() );
4966 if ( !p.hasNext() ) {
4969 Phylogeny p2_1 = p.next();
4970 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
4971 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
4974 if ( !p.hasNext() ) {
4977 Phylogeny p2_2 = p.next();
4978 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
4979 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
4982 if ( !p.hasNext() ) {
4985 Phylogeny p2_3 = p.next();
4986 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
4987 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
4990 if ( !p.hasNext() ) {
4993 Phylogeny p2_4 = p.next();
4994 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
4995 System.out.println( "(X) != " + p2_4.toNewHampshire() );
4998 if ( p.hasNext() ) {
5001 if ( p.next() != null ) {
5006 if ( !p.hasNext() ) {
5010 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5011 System.out.println( p2_0.toNewHampshire() );
5014 if ( !p.hasNext() ) {
5018 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5019 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5022 if ( !p.hasNext() ) {
5026 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5027 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5030 if ( !p.hasNext() ) {
5034 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5035 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5038 if ( !p.hasNext() ) {
5042 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5043 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5046 if ( p.hasNext() ) {
5049 if ( p.next() != null ) {
5053 catch ( final Exception e ) {
5054 e.printStackTrace( System.out );
5060 private static boolean testNHXconversion() {
5062 final PhylogenyNode n1 = new PhylogenyNode();
5063 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5064 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5065 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5066 final PhylogenyNode n5 = PhylogenyNode
5067 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30]" );
5068 final PhylogenyNode n6 = PhylogenyNode
5069 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0]" );
5070 if ( !n1.toNewHampshireX().equals( "" ) ) {
5073 if ( !n2.toNewHampshireX().equals( "" ) ) {
5076 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
5079 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
5082 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56:W=2.0:C=10.20.30]" ) ) {
5085 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100:W=2.0:C=0.0.0]" ) ) {
5089 catch ( final Exception e ) {
5090 e.printStackTrace( System.out );
5096 private static boolean testTaxonomyExtraction() {
5098 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5099 NHXParser.TAXONOMY_EXTRACTION.YES );
5100 if ( n0.getNodeData().isHasTaxonomy() ) {
5103 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
5104 NHXParser.TAXONOMY_EXTRACTION.YES );
5105 if ( n1.getNodeData().isHasTaxonomy() ) {
5106 System.out.println( n1.toString() );
5109 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
5110 NHXParser.TAXONOMY_EXTRACTION.YES );
5111 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5112 System.out.println( n2.toString() );
5115 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
5116 NHXParser.TAXONOMY_EXTRACTION.YES );
5117 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5118 System.out.println( n3.toString() );
5121 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
5122 NHXParser.TAXONOMY_EXTRACTION.YES );
5123 if ( n4.getNodeData().isHasTaxonomy() ) {
5124 System.out.println( n4.toString() );
5127 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
5128 NHXParser.TAXONOMY_EXTRACTION.YES );
5129 if ( n5.getNodeData().isHasTaxonomy() ) {
5130 System.out.println( n5.toString() );
5133 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
5134 NHXParser.TAXONOMY_EXTRACTION.YES );
5135 if ( n6.getNodeData().isHasTaxonomy() ) {
5136 System.out.println( n6.toString() );
5139 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
5140 NHXParser.TAXONOMY_EXTRACTION.YES );
5141 if ( n7.getNodeData().isHasTaxonomy() ) {
5142 System.out.println( n7.toString() );
5145 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
5146 NHXParser.TAXONOMY_EXTRACTION.YES );
5147 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5148 System.out.println( n8.toString() );
5151 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
5152 NHXParser.TAXONOMY_EXTRACTION.YES );
5153 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5154 System.out.println( n9.toString() );
5157 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
5158 NHXParser.TAXONOMY_EXTRACTION.YES );
5159 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
5160 System.out.println( n10.toString() );
5163 final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
5164 NHXParser.TAXONOMY_EXTRACTION.YES );
5165 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
5166 System.out.println( n11.toString() );
5169 final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
5170 NHXParser.TAXONOMY_EXTRACTION.YES );
5171 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
5172 System.out.println( n12.toString() );
5175 final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
5176 NHXParser.TAXONOMY_EXTRACTION.YES );
5177 if ( n13.getNodeData().isHasTaxonomy() ) {
5178 System.out.println( n13.toString() );
5181 final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
5182 NHXParser.TAXONOMY_EXTRACTION.YES );
5183 if ( n14.getNodeData().isHasTaxonomy() ) {
5184 System.out.println( n14.toString() );
5187 final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
5188 NHXParser.TAXONOMY_EXTRACTION.YES );
5189 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
5190 System.out.println( n15.toString() );
5193 final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
5194 NHXParser.TAXONOMY_EXTRACTION.YES );
5195 if ( n16.getNodeData().isHasTaxonomy() ) {
5196 System.out.println( n16.toString() );
5199 final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
5200 NHXParser.TAXONOMY_EXTRACTION.YES );
5201 if ( n17.getNodeData().isHasTaxonomy() ) {
5202 System.out.println( n17.toString() );
5206 catch ( final Exception e ) {
5207 e.printStackTrace( System.out );
5213 private static boolean testNHXNodeParsing() {
5215 final PhylogenyNode n1 = new PhylogenyNode();
5216 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5217 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5218 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5219 final PhylogenyNode n5 = PhylogenyNode
5220 .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]" );
5221 if ( !n3.getName().equals( "n3" ) ) {
5224 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5227 if ( n3.isDuplication() ) {
5230 if ( n3.isHasAssignedEvent() ) {
5233 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
5236 if ( !n4.getName().equals( "n4" ) ) {
5239 if ( n4.getDistanceToParent() != 0.01 ) {
5242 if ( !n5.getName().equals( "n5" ) ) {
5245 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
5248 if ( n5.getDistanceToParent() != 0.1 ) {
5251 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
5254 if ( !n5.isDuplication() ) {
5257 if ( !n5.isHasAssignedEvent() ) {
5260 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
5263 final PhylogenyNode n8 = PhylogenyNode
5264 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5265 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
5268 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
5271 final PhylogenyNode n9 = PhylogenyNode
5272 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5273 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
5276 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
5279 final PhylogenyNode n10 = PhylogenyNode
5280 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5281 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
5284 final PhylogenyNode n20 = PhylogenyNode
5285 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5286 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
5289 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
5292 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
5293 NHXParser.TAXONOMY_EXTRACTION.YES );
5294 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
5297 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
5300 final PhylogenyNode n20xx = PhylogenyNode
5301 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5302 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
5305 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
5308 final PhylogenyNode n20xxx = PhylogenyNode
5309 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5310 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
5313 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
5316 final PhylogenyNode n20xxxx = PhylogenyNode
5317 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5318 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
5321 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
5324 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
5325 NHXParser.TAXONOMY_EXTRACTION.YES );
5326 if ( !n21.getName().equals( "n21_PIG" ) ) {
5329 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
5332 final PhylogenyNode n21x = PhylogenyNode
5333 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5334 if ( !n21x.getName().equals( "n21_PIG" ) ) {
5337 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
5340 final PhylogenyNode n22 = PhylogenyNode
5341 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5342 if ( !n22.getName().equals( "n22/PIG" ) ) {
5345 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
5348 final PhylogenyNode n23 = PhylogenyNode
5349 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5350 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
5353 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
5356 final PhylogenyNode a = PhylogenyNode
5357 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5358 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
5361 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
5364 final PhylogenyNode b = PhylogenyNode
5365 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5366 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
5369 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
5372 final PhylogenyNode c = PhylogenyNode
5373 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
5374 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5375 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
5378 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
5381 final PhylogenyNode c1 = PhylogenyNode
5382 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
5383 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5384 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
5387 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
5390 final PhylogenyNode c2 = PhylogenyNode
5391 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
5392 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5393 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5396 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5399 final PhylogenyNode d = PhylogenyNode
5400 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5401 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5404 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5407 final PhylogenyNode e = PhylogenyNode
5408 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5409 if ( !e.getName().equals( "n10_RAT1" ) ) {
5412 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5415 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5416 NHXParser.TAXONOMY_EXTRACTION.YES );
5417 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5420 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5423 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5424 NHXParser.TAXONOMY_EXTRACTION.YES );
5425 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5428 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5431 final PhylogenyNode n11 = PhylogenyNode
5432 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5433 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5434 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5437 if ( n11.getDistanceToParent() != 0.4 ) {
5440 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5443 final PhylogenyNode n12 = PhylogenyNode
5444 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5445 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5446 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5449 if ( n12.getDistanceToParent() != 0.4 ) {
5452 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5455 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5456 NHXParser.TAXONOMY_EXTRACTION.YES );
5457 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5460 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5463 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5464 NHXParser.TAXONOMY_EXTRACTION.YES );
5465 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5468 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5471 if ( n1.getName().compareTo( "" ) != 0 ) {
5474 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5477 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5480 if ( n2.getName().compareTo( "" ) != 0 ) {
5483 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5486 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5489 final PhylogenyNode n00 = PhylogenyNode
5490 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1:W=2:C=0.0.0]" );
5491 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5494 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5497 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5498 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5501 final PhylogenyNode n13 = PhylogenyNode
5502 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5503 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5506 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5509 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5512 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5515 final PhylogenyNode n14 = PhylogenyNode
5516 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5517 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5520 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5523 final PhylogenyNode n15 = PhylogenyNode
5524 .createInstanceFromNhxString( "something_wicked[123]",
5525 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5526 if ( !n15.getName().equals( "something_wicked" ) ) {
5529 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5532 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5535 final PhylogenyNode n16 = PhylogenyNode
5536 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5537 if ( !n16.getName().equals( "something_wicked2" ) ) {
5540 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5543 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5546 final PhylogenyNode n17 = PhylogenyNode
5547 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5548 if ( !n17.getName().equals( "something_wicked3" ) ) {
5551 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5554 final PhylogenyNode n18 = PhylogenyNode
5555 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5556 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5559 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5562 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5565 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
5566 NHXParser.TAXONOMY_EXTRACTION.YES );
5567 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
5570 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5573 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
5574 NHXParser.TAXONOMY_EXTRACTION.YES );
5575 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
5578 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5581 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
5582 NHXParser.TAXONOMY_EXTRACTION.YES );
5583 if ( n31.getNodeData().isHasTaxonomy() ) {
5586 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5587 NHXParser.TAXONOMY_EXTRACTION.YES );
5588 if ( n32.getNodeData().isHasTaxonomy() ) {
5592 catch ( final Exception e ) {
5593 e.printStackTrace( System.out );
5599 private static boolean testNHXParsing() {
5601 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5602 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5603 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5606 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]";
5607 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5608 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5611 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]";
5612 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5613 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5616 final Phylogeny[] p3 = factory
5617 .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]",
5619 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5622 final Phylogeny[] p4 = factory
5623 .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(]",
5625 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5628 final Phylogeny[] p5 = factory
5629 .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(((]",
5631 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5634 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)";
5635 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)";
5636 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5637 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5640 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)))";
5641 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)))";
5642 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5643 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5646 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]) ))[,,, ])))))))";
5647 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5648 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5649 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5652 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5653 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5656 final Phylogeny p10 = factory
5657 .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]",
5658 new NHXParser() )[ 0 ];
5659 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5663 catch ( final Exception e ) {
5664 e.printStackTrace( System.out );
5670 private static boolean testNHXParsingQuotes() {
5672 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5673 final NHXParser p = new NHXParser();
5674 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5675 if ( phylogenies_0.length != 5 ) {
5678 final Phylogeny phy = phylogenies_0[ 4 ];
5679 if ( phy.getNumberOfExternalNodes() != 7 ) {
5682 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5685 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5688 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5689 .getScientificName().equals( "hsapiens" ) ) {
5692 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5695 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5698 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5701 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5704 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5707 final NHXParser p1p = new NHXParser();
5708 p1p.setIgnoreQuotes( true );
5709 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5710 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5713 final NHXParser p2p = new NHXParser();
5714 p1p.setIgnoreQuotes( false );
5715 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5716 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5719 final NHXParser p3p = new NHXParser();
5720 p3p.setIgnoreQuotes( false );
5721 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5722 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5725 final NHXParser p4p = new NHXParser();
5726 p4p.setIgnoreQuotes( false );
5727 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5728 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5731 final Phylogeny p10 = factory
5732 .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]",
5733 new NHXParser() )[ 0 ];
5734 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]";
5735 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5738 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5739 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5743 final Phylogeny p12 = factory
5744 .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]",
5745 new NHXParser() )[ 0 ];
5746 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]";
5747 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5750 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5751 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5754 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;";
5755 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5758 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5759 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5763 catch ( final Exception e ) {
5764 e.printStackTrace( System.out );
5770 private static boolean testNHXParsingMB() {
5772 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5773 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5774 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5775 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5776 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5777 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5778 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5779 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5780 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5781 + "7.369400000000000e-02}])", new NHXParser2() )[ 0 ];
5782 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5785 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5788 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5789 0.1100000000000000e+00 ) ) {
5792 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5795 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5798 final Phylogeny p2 = factory
5799 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5800 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5801 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5802 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5803 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5804 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5805 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5806 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5807 + "7.369400000000000e-02}])",
5808 new NHXParser2() )[ 0 ];
5809 if ( p2.getNode( "1" ) == null ) {
5812 if ( p2.getNode( "2" ) == null ) {
5816 catch ( final Exception e ) {
5817 e.printStackTrace( System.out );
5824 private static boolean testPhylogenyBranch() {
5826 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5827 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5828 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5829 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5830 if ( !a1b1.equals( a1b1 ) ) {
5833 if ( !a1b1.equals( b1a1 ) ) {
5836 if ( !b1a1.equals( a1b1 ) ) {
5839 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5840 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5841 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5842 if ( a1_b1.equals( b1_a1 ) ) {
5845 if ( a1_b1.equals( a1_b1_ ) ) {
5848 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5849 if ( !a1_b1.equals( b1_a1_ ) ) {
5852 if ( a1_b1_.equals( b1_a1_ ) ) {
5855 if ( !a1_b1_.equals( b1_a1 ) ) {
5859 catch ( final Exception e ) {
5860 e.printStackTrace( System.out );
5866 private static boolean testPhyloXMLparsingOfDistributionElement() {
5868 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5869 PhyloXmlParser xml_parser = null;
5871 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5873 catch ( final Exception e ) {
5874 // Do nothing -- means were not running from jar.
5876 if ( xml_parser == null ) {
5877 xml_parser = new PhyloXmlParser();
5878 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5879 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5882 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5885 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5887 if ( xml_parser.getErrorCount() > 0 ) {
5888 System.out.println( xml_parser.getErrorMessages().toString() );
5891 if ( phylogenies_0.length != 1 ) {
5894 final Phylogeny t1 = phylogenies_0[ 0 ];
5895 PhylogenyNode n = null;
5896 Distribution d = null;
5897 n = t1.getNode( "root node" );
5898 if ( !n.getNodeData().isHasDistribution() ) {
5901 if ( n.getNodeData().getDistributions().size() != 1 ) {
5904 d = n.getNodeData().getDistribution();
5905 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5908 if ( d.getPoints().size() != 1 ) {
5911 if ( d.getPolygons() != null ) {
5914 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5917 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5920 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5923 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5926 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5929 n = t1.getNode( "node a" );
5930 if ( !n.getNodeData().isHasDistribution() ) {
5933 if ( n.getNodeData().getDistributions().size() != 2 ) {
5936 d = n.getNodeData().getDistribution( 1 );
5937 if ( !d.getDesc().equals( "San Diego" ) ) {
5940 if ( d.getPoints().size() != 1 ) {
5943 if ( d.getPolygons() != null ) {
5946 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5949 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5952 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5955 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5958 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5961 n = t1.getNode( "node bb" );
5962 if ( !n.getNodeData().isHasDistribution() ) {
5965 if ( n.getNodeData().getDistributions().size() != 1 ) {
5968 d = n.getNodeData().getDistribution( 0 );
5969 if ( d.getPoints().size() != 3 ) {
5972 if ( d.getPolygons().size() != 2 ) {
5975 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5978 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5981 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5984 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5987 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5990 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5993 Polygon p = d.getPolygons().get( 0 );
5994 if ( p.getPoints().size() != 3 ) {
5997 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6000 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6003 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6006 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6009 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6012 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6015 p = d.getPolygons().get( 1 );
6016 if ( p.getPoints().size() != 3 ) {
6019 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6022 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6025 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6029 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
6030 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
6031 if ( rt.length != 1 ) {
6034 final Phylogeny t1_rt = rt[ 0 ];
6035 n = t1_rt.getNode( "root node" );
6036 if ( !n.getNodeData().isHasDistribution() ) {
6039 if ( n.getNodeData().getDistributions().size() != 1 ) {
6042 d = n.getNodeData().getDistribution();
6043 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6046 if ( d.getPoints().size() != 1 ) {
6049 if ( d.getPolygons() != null ) {
6052 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6055 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6058 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6061 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6064 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6067 n = t1_rt.getNode( "node a" );
6068 if ( !n.getNodeData().isHasDistribution() ) {
6071 if ( n.getNodeData().getDistributions().size() != 2 ) {
6074 d = n.getNodeData().getDistribution( 1 );
6075 if ( !d.getDesc().equals( "San Diego" ) ) {
6078 if ( d.getPoints().size() != 1 ) {
6081 if ( d.getPolygons() != null ) {
6084 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6087 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6090 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6093 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6096 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6099 n = t1_rt.getNode( "node bb" );
6100 if ( !n.getNodeData().isHasDistribution() ) {
6103 if ( n.getNodeData().getDistributions().size() != 1 ) {
6106 d = n.getNodeData().getDistribution( 0 );
6107 if ( d.getPoints().size() != 3 ) {
6110 if ( d.getPolygons().size() != 2 ) {
6113 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6116 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6119 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6122 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6125 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6128 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6131 p = d.getPolygons().get( 0 );
6132 if ( p.getPoints().size() != 3 ) {
6135 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6138 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6141 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6144 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6147 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6150 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6153 p = d.getPolygons().get( 1 );
6154 if ( p.getPoints().size() != 3 ) {
6157 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6160 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6163 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6167 catch ( final Exception e ) {
6168 e.printStackTrace( System.out );
6174 private static boolean testPostOrderIterator() {
6176 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6177 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6178 PhylogenyNodeIterator it0;
6179 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
6182 for( it0.reset(); it0.hasNext(); ) {
6185 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6186 final PhylogenyNodeIterator it = t1.iteratorPostorder();
6187 if ( !it.next().getName().equals( "A" ) ) {
6190 if ( !it.next().getName().equals( "B" ) ) {
6193 if ( !it.next().getName().equals( "ab" ) ) {
6196 if ( !it.next().getName().equals( "C" ) ) {
6199 if ( !it.next().getName().equals( "D" ) ) {
6202 if ( !it.next().getName().equals( "cd" ) ) {
6205 if ( !it.next().getName().equals( "abcd" ) ) {
6208 if ( !it.next().getName().equals( "E" ) ) {
6211 if ( !it.next().getName().equals( "F" ) ) {
6214 if ( !it.next().getName().equals( "ef" ) ) {
6217 if ( !it.next().getName().equals( "G" ) ) {
6220 if ( !it.next().getName().equals( "H" ) ) {
6223 if ( !it.next().getName().equals( "gh" ) ) {
6226 if ( !it.next().getName().equals( "efgh" ) ) {
6229 if ( !it.next().getName().equals( "r" ) ) {
6232 if ( it.hasNext() ) {
6236 catch ( final Exception e ) {
6237 e.printStackTrace( System.out );
6243 private static boolean testPreOrderIterator() {
6245 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6246 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6247 PhylogenyNodeIterator it0;
6248 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
6251 for( it0.reset(); it0.hasNext(); ) {
6254 PhylogenyNodeIterator it = t0.iteratorPreorder();
6255 if ( !it.next().getName().equals( "r" ) ) {
6258 if ( !it.next().getName().equals( "ab" ) ) {
6261 if ( !it.next().getName().equals( "A" ) ) {
6264 if ( !it.next().getName().equals( "B" ) ) {
6267 if ( !it.next().getName().equals( "cd" ) ) {
6270 if ( !it.next().getName().equals( "C" ) ) {
6273 if ( !it.next().getName().equals( "D" ) ) {
6276 if ( it.hasNext() ) {
6279 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6280 it = t1.iteratorPreorder();
6281 if ( !it.next().getName().equals( "r" ) ) {
6284 if ( !it.next().getName().equals( "abcd" ) ) {
6287 if ( !it.next().getName().equals( "ab" ) ) {
6290 if ( !it.next().getName().equals( "A" ) ) {
6293 if ( !it.next().getName().equals( "B" ) ) {
6296 if ( !it.next().getName().equals( "cd" ) ) {
6299 if ( !it.next().getName().equals( "C" ) ) {
6302 if ( !it.next().getName().equals( "D" ) ) {
6305 if ( !it.next().getName().equals( "efgh" ) ) {
6308 if ( !it.next().getName().equals( "ef" ) ) {
6311 if ( !it.next().getName().equals( "E" ) ) {
6314 if ( !it.next().getName().equals( "F" ) ) {
6317 if ( !it.next().getName().equals( "gh" ) ) {
6320 if ( !it.next().getName().equals( "G" ) ) {
6323 if ( !it.next().getName().equals( "H" ) ) {
6326 if ( it.hasNext() ) {
6330 catch ( final Exception e ) {
6331 e.printStackTrace( System.out );
6337 private static boolean testPropertiesMap() {
6339 final PropertiesMap pm = new PropertiesMap();
6340 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6341 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6342 final Property p2 = new Property( "something:else",
6344 "improbable:research",
6347 pm.addProperty( p0 );
6348 pm.addProperty( p1 );
6349 pm.addProperty( p2 );
6350 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
6353 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
6356 if ( pm.getProperties().size() != 3 ) {
6359 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
6362 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6365 if ( pm.getProperties().size() != 3 ) {
6368 pm.removeProperty( "dimensions:diameter" );
6369 if ( pm.getProperties().size() != 2 ) {
6372 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
6375 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6379 catch ( final Exception e ) {
6380 e.printStackTrace( System.out );
6386 private static boolean testReIdMethods() {
6388 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6389 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6390 final int count = PhylogenyNode.getNodeCount();
6392 if ( p.getNode( "r" ).getId() != count ) {
6395 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6398 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6401 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6404 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6407 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6410 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6413 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6416 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6419 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6422 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6425 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6428 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6431 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6434 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6438 catch ( final Exception e ) {
6439 e.printStackTrace( System.out );
6445 private static boolean testRerooting() {
6447 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6448 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",
6449 new NHXParser() )[ 0 ];
6450 if ( !t1.isRooted() ) {
6453 t1.reRoot( t1.getNode( "D" ) );
6454 t1.reRoot( t1.getNode( "CD" ) );
6455 t1.reRoot( t1.getNode( "A" ) );
6456 t1.reRoot( t1.getNode( "B" ) );
6457 t1.reRoot( t1.getNode( "AB" ) );
6458 t1.reRoot( t1.getNode( "D" ) );
6459 t1.reRoot( t1.getNode( "C" ) );
6460 t1.reRoot( t1.getNode( "CD" ) );
6461 t1.reRoot( t1.getNode( "A" ) );
6462 t1.reRoot( t1.getNode( "B" ) );
6463 t1.reRoot( t1.getNode( "AB" ) );
6464 t1.reRoot( t1.getNode( "D" ) );
6465 t1.reRoot( t1.getNode( "D" ) );
6466 t1.reRoot( t1.getNode( "C" ) );
6467 t1.reRoot( t1.getNode( "A" ) );
6468 t1.reRoot( t1.getNode( "B" ) );
6469 t1.reRoot( t1.getNode( "AB" ) );
6470 t1.reRoot( t1.getNode( "C" ) );
6471 t1.reRoot( t1.getNode( "D" ) );
6472 t1.reRoot( t1.getNode( "CD" ) );
6473 t1.reRoot( t1.getNode( "D" ) );
6474 t1.reRoot( t1.getNode( "A" ) );
6475 t1.reRoot( t1.getNode( "B" ) );
6476 t1.reRoot( t1.getNode( "AB" ) );
6477 t1.reRoot( t1.getNode( "C" ) );
6478 t1.reRoot( t1.getNode( "D" ) );
6479 t1.reRoot( t1.getNode( "CD" ) );
6480 t1.reRoot( t1.getNode( "D" ) );
6481 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6484 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6487 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6490 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6493 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6496 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6499 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",
6500 new NHXParser() )[ 0 ];
6501 t2.reRoot( t2.getNode( "A" ) );
6502 t2.reRoot( t2.getNode( "D" ) );
6503 t2.reRoot( t2.getNode( "ABC" ) );
6504 t2.reRoot( t2.getNode( "A" ) );
6505 t2.reRoot( t2.getNode( "B" ) );
6506 t2.reRoot( t2.getNode( "D" ) );
6507 t2.reRoot( t2.getNode( "C" ) );
6508 t2.reRoot( t2.getNode( "ABC" ) );
6509 t2.reRoot( t2.getNode( "A" ) );
6510 t2.reRoot( t2.getNode( "B" ) );
6511 t2.reRoot( t2.getNode( "AB" ) );
6512 t2.reRoot( t2.getNode( "AB" ) );
6513 t2.reRoot( t2.getNode( "D" ) );
6514 t2.reRoot( t2.getNode( "C" ) );
6515 t2.reRoot( t2.getNode( "B" ) );
6516 t2.reRoot( t2.getNode( "AB" ) );
6517 t2.reRoot( t2.getNode( "D" ) );
6518 t2.reRoot( t2.getNode( "D" ) );
6519 t2.reRoot( t2.getNode( "ABC" ) );
6520 t2.reRoot( t2.getNode( "A" ) );
6521 t2.reRoot( t2.getNode( "B" ) );
6522 t2.reRoot( t2.getNode( "AB" ) );
6523 t2.reRoot( t2.getNode( "D" ) );
6524 t2.reRoot( t2.getNode( "C" ) );
6525 t2.reRoot( t2.getNode( "ABC" ) );
6526 t2.reRoot( t2.getNode( "A" ) );
6527 t2.reRoot( t2.getNode( "B" ) );
6528 t2.reRoot( t2.getNode( "AB" ) );
6529 t2.reRoot( t2.getNode( "D" ) );
6530 t2.reRoot( t2.getNode( "D" ) );
6531 t2.reRoot( t2.getNode( "C" ) );
6532 t2.reRoot( t2.getNode( "A" ) );
6533 t2.reRoot( t2.getNode( "B" ) );
6534 t2.reRoot( t2.getNode( "AB" ) );
6535 t2.reRoot( t2.getNode( "C" ) );
6536 t2.reRoot( t2.getNode( "D" ) );
6537 t2.reRoot( t2.getNode( "ABC" ) );
6538 t2.reRoot( t2.getNode( "D" ) );
6539 t2.reRoot( t2.getNode( "A" ) );
6540 t2.reRoot( t2.getNode( "B" ) );
6541 t2.reRoot( t2.getNode( "AB" ) );
6542 t2.reRoot( t2.getNode( "C" ) );
6543 t2.reRoot( t2.getNode( "D" ) );
6544 t2.reRoot( t2.getNode( "ABC" ) );
6545 t2.reRoot( t2.getNode( "D" ) );
6546 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6549 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6552 t2.reRoot( t2.getNode( "ABC" ) );
6553 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6556 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6559 t2.reRoot( t2.getNode( "AB" ) );
6560 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6563 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6566 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6569 t2.reRoot( t2.getNode( "AB" ) );
6570 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6573 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6576 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6579 t2.reRoot( t2.getNode( "D" ) );
6580 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6583 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6586 t2.reRoot( t2.getNode( "ABC" ) );
6587 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6590 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6593 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6594 new NHXParser() )[ 0 ];
6595 t3.reRoot( t3.getNode( "B" ) );
6596 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6599 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6602 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6605 t3.reRoot( t3.getNode( "B" ) );
6606 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6609 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6612 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6615 t3.reRoot( t3.getRoot() );
6616 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6619 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6622 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6626 catch ( final Exception e ) {
6627 e.printStackTrace( System.out );
6633 private static boolean testSDIse() {
6635 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6636 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6637 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6638 gene1.setRooted( true );
6639 species1.setRooted( true );
6640 final SDI sdi = new SDI( gene1, species1 );
6641 if ( !gene1.getRoot().isDuplication() ) {
6644 final Phylogeny species2 = factory
6645 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6646 new NHXParser() )[ 0 ];
6647 final Phylogeny gene2 = factory
6648 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6649 new NHXParser() )[ 0 ];
6650 species2.setRooted( true );
6651 gene2.setRooted( true );
6652 final SDI sdi2 = new SDI( gene2, species2 );
6653 if ( sdi2.getDuplicationsSum() != 0 ) {
6656 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6659 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6662 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6665 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6668 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6671 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6674 final Phylogeny species3 = factory
6675 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6676 new NHXParser() )[ 0 ];
6677 final Phylogeny gene3 = factory
6678 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6679 new NHXParser() )[ 0 ];
6680 species3.setRooted( true );
6681 gene3.setRooted( true );
6682 final SDI sdi3 = new SDI( gene3, species3 );
6683 if ( sdi3.getDuplicationsSum() != 1 ) {
6686 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6689 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6692 final Phylogeny species4 = factory
6693 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6694 new NHXParser() )[ 0 ];
6695 final Phylogeny gene4 = factory
6696 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6697 new NHXParser() )[ 0 ];
6698 species4.setRooted( true );
6699 gene4.setRooted( true );
6700 final SDI sdi4 = new SDI( gene4, species4 );
6701 if ( sdi4.getDuplicationsSum() != 1 ) {
6704 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6707 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6710 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6713 if ( species4.getNumberOfExternalNodes() != 6 ) {
6716 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6719 final Phylogeny species5 = factory
6720 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6721 new NHXParser() )[ 0 ];
6722 final Phylogeny gene5 = factory
6723 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6724 new NHXParser() )[ 0 ];
6725 species5.setRooted( true );
6726 gene5.setRooted( true );
6727 final SDI sdi5 = new SDI( gene5, species5 );
6728 if ( sdi5.getDuplicationsSum() != 2 ) {
6731 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6734 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6737 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6740 if ( species5.getNumberOfExternalNodes() != 6 ) {
6743 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6746 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6747 // Conjecture for Comparing Molecular Phylogenies"
6748 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6749 final Phylogeny species6 = factory
6750 .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,"
6751 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6752 new NHXParser() )[ 0 ];
6753 final Phylogeny gene6 = factory
6754 .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,"
6755 + "((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,"
6756 + "(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;",
6757 new NHXParser() )[ 0 ];
6758 species6.setRooted( true );
6759 gene6.setRooted( true );
6760 final SDI sdi6 = new SDI( gene6, species6 );
6761 if ( sdi6.getDuplicationsSum() != 3 ) {
6764 if ( !gene6.getNode( "r" ).isDuplication() ) {
6767 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6770 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6773 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6776 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6779 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6782 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6785 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6788 sdi6.computeMappingCostL();
6789 if ( sdi6.computeMappingCostL() != 17 ) {
6792 if ( species6.getNumberOfExternalNodes() != 9 ) {
6795 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6798 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6799 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6800 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6801 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6802 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6803 species7.setRooted( true );
6804 final Phylogeny gene7_1 = Test
6805 .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])" );
6806 gene7_1.setRooted( true );
6807 final SDI sdi7 = new SDI( gene7_1, species7 );
6808 if ( sdi7.getDuplicationsSum() != 0 ) {
6811 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6814 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6817 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6820 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6823 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6826 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6829 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6832 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6835 final Phylogeny gene7_2 = Test
6836 .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])" );
6837 gene7_2.setRooted( true );
6838 final SDI sdi7_2 = new SDI( gene7_2, species7 );
6839 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6842 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6845 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6848 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6851 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6854 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6857 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6860 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6863 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6866 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6870 catch ( final Exception e ) {
6876 private static boolean testSDIunrooted() {
6878 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6879 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6880 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6881 final Iterator<PhylogenyBranch> iter = l.iterator();
6882 PhylogenyBranch br = iter.next();
6883 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6886 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6890 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6893 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6897 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6900 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6904 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6907 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6911 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6914 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6918 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6921 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6925 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6928 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6932 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6935 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6939 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6942 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6946 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6949 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6953 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6956 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6960 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6963 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6967 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6970 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6974 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6977 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6981 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6984 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6987 if ( iter.hasNext() ) {
6990 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6991 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6992 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6994 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6997 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7001 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7004 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7008 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7011 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7014 if ( iter1.hasNext() ) {
7017 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
7018 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
7019 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
7021 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7024 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7028 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7031 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7035 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7038 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7041 if ( iter2.hasNext() ) {
7044 final Phylogeny species0 = factory
7045 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7046 new NHXParser() )[ 0 ];
7047 final Phylogeny gene1 = factory
7048 .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])",
7049 new NHXParser() )[ 0 ];
7050 species0.setRooted( true );
7051 gene1.setRooted( true );
7052 final SDIR sdi_unrooted = new SDIR();
7053 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
7054 if ( sdi_unrooted.getCount() != 1 ) {
7057 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
7060 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
7063 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
7066 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7069 final Phylogeny gene2 = factory
7070 .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])",
7071 new NHXParser() )[ 0 ];
7072 gene2.setRooted( true );
7073 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
7074 if ( sdi_unrooted.getCount() != 1 ) {
7077 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7080 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7083 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7086 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7089 final Phylogeny species6 = factory
7090 .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,"
7091 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7092 new NHXParser() )[ 0 ];
7093 final Phylogeny gene6 = factory
7094 .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],"
7095 + "(((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],"
7096 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7097 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7098 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7099 new NHXParser() )[ 0 ];
7100 species6.setRooted( true );
7101 gene6.setRooted( true );
7102 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7103 if ( sdi_unrooted.getCount() != 1 ) {
7106 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7109 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7112 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7115 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7118 if ( !p6[ 0 ].getRoot().isDuplication() ) {
7121 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7124 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7127 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
7130 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7133 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
7136 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
7139 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7143 final Phylogeny species7 = factory
7144 .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,"
7145 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7146 new NHXParser() )[ 0 ];
7147 final Phylogeny gene7 = factory
7148 .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],"
7149 + "(((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],"
7150 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7151 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7152 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7153 new NHXParser() )[ 0 ];
7154 species7.setRooted( true );
7155 gene7.setRooted( true );
7156 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
7157 if ( sdi_unrooted.getCount() != 1 ) {
7160 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7163 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7166 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7169 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
7172 if ( !p7[ 0 ].getRoot().isDuplication() ) {
7175 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7178 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7181 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
7184 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7187 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
7190 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
7193 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7197 final Phylogeny species8 = factory
7198 .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,"
7199 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7200 new NHXParser() )[ 0 ];
7201 final Phylogeny gene8 = factory
7202 .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],"
7203 + "(((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],"
7204 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7205 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7206 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7207 new NHXParser() )[ 0 ];
7208 species8.setRooted( true );
7209 gene8.setRooted( true );
7210 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
7211 if ( sdi_unrooted.getCount() != 1 ) {
7214 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7217 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7220 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7223 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7226 if ( !p8[ 0 ].getRoot().isDuplication() ) {
7229 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7232 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7235 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
7238 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7241 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
7244 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
7247 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7252 catch ( final Exception e ) {
7253 e.printStackTrace( System.out );
7259 private static boolean testSplit() {
7261 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7262 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7263 //Archaeopteryx.createApplication( p0 );
7264 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7265 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7266 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7267 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7268 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7269 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7270 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7271 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7272 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7273 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7274 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
7275 // System.out.println( s0.toString() );
7277 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7278 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7279 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7280 if ( s0.match( query_nodes ) ) {
7283 query_nodes = new HashSet<PhylogenyNode>();
7284 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7285 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7287 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7288 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7289 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7290 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7291 if ( !s0.match( query_nodes ) ) {
7295 query_nodes = new HashSet<PhylogenyNode>();
7296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7297 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7298 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7299 if ( !s0.match( query_nodes ) ) {
7303 query_nodes = new HashSet<PhylogenyNode>();
7304 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7305 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7306 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7307 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7308 if ( !s0.match( query_nodes ) ) {
7312 query_nodes = new HashSet<PhylogenyNode>();
7313 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7314 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7315 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7316 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7317 if ( !s0.match( query_nodes ) ) {
7321 query_nodes = new HashSet<PhylogenyNode>();
7322 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7323 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7324 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7325 if ( !s0.match( query_nodes ) ) {
7329 query_nodes = new HashSet<PhylogenyNode>();
7330 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7332 if ( !s0.match( query_nodes ) ) {
7336 query_nodes = new HashSet<PhylogenyNode>();
7337 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7338 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7342 if ( !s0.match( query_nodes ) ) {
7346 query_nodes = new HashSet<PhylogenyNode>();
7347 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7350 if ( !s0.match( query_nodes ) ) {
7354 query_nodes = new HashSet<PhylogenyNode>();
7355 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7359 if ( !s0.match( query_nodes ) ) {
7363 query_nodes = new HashSet<PhylogenyNode>();
7364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7366 if ( s0.match( query_nodes ) ) {
7370 query_nodes = new HashSet<PhylogenyNode>();
7371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7375 if ( s0.match( query_nodes ) ) {
7379 query_nodes = new HashSet<PhylogenyNode>();
7380 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7383 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7384 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7385 if ( s0.match( query_nodes ) ) {
7389 query_nodes = new HashSet<PhylogenyNode>();
7390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7391 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7393 if ( s0.match( query_nodes ) ) {
7397 query_nodes = new HashSet<PhylogenyNode>();
7398 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7400 if ( s0.match( query_nodes ) ) {
7404 query_nodes = new HashSet<PhylogenyNode>();
7405 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7407 if ( s0.match( query_nodes ) ) {
7411 query_nodes = new HashSet<PhylogenyNode>();
7412 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7413 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7414 if ( s0.match( query_nodes ) ) {
7418 query_nodes = new HashSet<PhylogenyNode>();
7419 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7420 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7421 if ( s0.match( query_nodes ) ) {
7425 query_nodes = new HashSet<PhylogenyNode>();
7426 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7427 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7428 if ( s0.match( query_nodes ) ) {
7432 query_nodes = new HashSet<PhylogenyNode>();
7433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7434 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7435 if ( s0.match( query_nodes ) ) {
7439 query_nodes = new HashSet<PhylogenyNode>();
7440 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7441 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7442 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7443 if ( s0.match( query_nodes ) ) {
7447 query_nodes = new HashSet<PhylogenyNode>();
7448 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7449 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7450 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7451 if ( s0.match( query_nodes ) ) {
7455 query_nodes = new HashSet<PhylogenyNode>();
7456 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7457 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7458 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7459 if ( s0.match( query_nodes ) ) {
7463 query_nodes = new HashSet<PhylogenyNode>();
7464 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7465 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7466 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7467 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7468 if ( s0.match( query_nodes ) ) {
7472 // query_nodes = new HashSet<PhylogenyNode>();
7473 // query_nodes.add( new PhylogenyNode( "X" ) );
7474 // query_nodes.add( new PhylogenyNode( "Y" ) );
7475 // query_nodes.add( new PhylogenyNode( "A" ) );
7476 // query_nodes.add( new PhylogenyNode( "B" ) );
7477 // query_nodes.add( new PhylogenyNode( "C" ) );
7478 // query_nodes.add( new PhylogenyNode( "D" ) );
7479 // query_nodes.add( new PhylogenyNode( "E" ) );
7480 // query_nodes.add( new PhylogenyNode( "F" ) );
7481 // query_nodes.add( new PhylogenyNode( "G" ) );
7482 // if ( !s0.match( query_nodes ) ) {
7485 // query_nodes = new HashSet<PhylogenyNode>();
7486 // query_nodes.add( new PhylogenyNode( "X" ) );
7487 // query_nodes.add( new PhylogenyNode( "Y" ) );
7488 // query_nodes.add( new PhylogenyNode( "A" ) );
7489 // query_nodes.add( new PhylogenyNode( "B" ) );
7490 // query_nodes.add( new PhylogenyNode( "C" ) );
7491 // if ( !s0.match( query_nodes ) ) {
7495 // query_nodes = new HashSet<PhylogenyNode>();
7496 // query_nodes.add( new PhylogenyNode( "X" ) );
7497 // query_nodes.add( new PhylogenyNode( "Y" ) );
7498 // query_nodes.add( new PhylogenyNode( "D" ) );
7499 // query_nodes.add( new PhylogenyNode( "E" ) );
7500 // query_nodes.add( new PhylogenyNode( "F" ) );
7501 // query_nodes.add( new PhylogenyNode( "G" ) );
7502 // if ( !s0.match( query_nodes ) ) {
7506 // query_nodes = new HashSet<PhylogenyNode>();
7507 // query_nodes.add( new PhylogenyNode( "X" ) );
7508 // query_nodes.add( new PhylogenyNode( "Y" ) );
7509 // query_nodes.add( new PhylogenyNode( "A" ) );
7510 // query_nodes.add( new PhylogenyNode( "B" ) );
7511 // query_nodes.add( new PhylogenyNode( "C" ) );
7512 // query_nodes.add( new PhylogenyNode( "D" ) );
7513 // if ( !s0.match( query_nodes ) ) {
7517 // query_nodes = new HashSet<PhylogenyNode>();
7518 // query_nodes.add( new PhylogenyNode( "X" ) );
7519 // query_nodes.add( new PhylogenyNode( "Y" ) );
7520 // query_nodes.add( new PhylogenyNode( "E" ) );
7521 // query_nodes.add( new PhylogenyNode( "F" ) );
7522 // query_nodes.add( new PhylogenyNode( "G" ) );
7523 // if ( !s0.match( query_nodes ) ) {
7527 // query_nodes = new HashSet<PhylogenyNode>();
7528 // query_nodes.add( new PhylogenyNode( "X" ) );
7529 // query_nodes.add( new PhylogenyNode( "Y" ) );
7530 // query_nodes.add( new PhylogenyNode( "F" ) );
7531 // query_nodes.add( new PhylogenyNode( "G" ) );
7532 // if ( !s0.match( query_nodes ) ) {
7536 query_nodes = new HashSet<PhylogenyNode>();
7537 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7540 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7541 if ( s0.match( query_nodes ) ) {
7545 query_nodes = new HashSet<PhylogenyNode>();
7546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7549 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7550 if ( s0.match( query_nodes ) ) {
7553 ///////////////////////////
7555 query_nodes = new HashSet<PhylogenyNode>();
7556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7560 if ( s0.match( query_nodes ) ) {
7564 query_nodes = new HashSet<PhylogenyNode>();
7565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7569 if ( s0.match( query_nodes ) ) {
7573 query_nodes = new HashSet<PhylogenyNode>();
7574 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7575 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7578 if ( s0.match( query_nodes ) ) {
7582 query_nodes = new HashSet<PhylogenyNode>();
7583 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7584 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7587 if ( s0.match( query_nodes ) ) {
7591 query_nodes = new HashSet<PhylogenyNode>();
7592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7594 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7595 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7596 if ( s0.match( query_nodes ) ) {
7600 query_nodes = new HashSet<PhylogenyNode>();
7601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7602 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7603 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7604 if ( s0.match( query_nodes ) ) {
7608 query_nodes = new HashSet<PhylogenyNode>();
7609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7612 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7614 if ( s0.match( query_nodes ) ) {
7618 query_nodes = new HashSet<PhylogenyNode>();
7619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7624 if ( s0.match( query_nodes ) ) {
7628 query_nodes = new HashSet<PhylogenyNode>();
7629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7634 if ( s0.match( query_nodes ) ) {
7638 query_nodes = new HashSet<PhylogenyNode>();
7639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7645 if ( s0.match( query_nodes ) ) {
7649 catch ( final Exception e ) {
7650 e.printStackTrace();
7656 private static boolean testSplitStrict() {
7658 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7659 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7660 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7661 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7662 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7663 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7664 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7665 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7666 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7667 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7668 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7669 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7672 if ( s0.match( query_nodes ) ) {
7675 query_nodes = new HashSet<PhylogenyNode>();
7676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7683 if ( !s0.match( query_nodes ) ) {
7687 query_nodes = new HashSet<PhylogenyNode>();
7688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7690 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7691 if ( !s0.match( query_nodes ) ) {
7695 query_nodes = new HashSet<PhylogenyNode>();
7696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7698 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7700 if ( !s0.match( query_nodes ) ) {
7704 query_nodes = new HashSet<PhylogenyNode>();
7705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7707 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7708 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7709 if ( !s0.match( query_nodes ) ) {
7713 query_nodes = new HashSet<PhylogenyNode>();
7714 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7715 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7716 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7717 if ( !s0.match( query_nodes ) ) {
7721 query_nodes = new HashSet<PhylogenyNode>();
7722 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7724 if ( !s0.match( query_nodes ) ) {
7728 query_nodes = new HashSet<PhylogenyNode>();
7729 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7730 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7732 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7734 if ( !s0.match( query_nodes ) ) {
7738 query_nodes = new HashSet<PhylogenyNode>();
7739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7742 if ( !s0.match( query_nodes ) ) {
7746 query_nodes = new HashSet<PhylogenyNode>();
7747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7751 if ( !s0.match( query_nodes ) ) {
7755 query_nodes = new HashSet<PhylogenyNode>();
7756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7757 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7758 if ( s0.match( query_nodes ) ) {
7762 query_nodes = new HashSet<PhylogenyNode>();
7763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7766 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7767 if ( s0.match( query_nodes ) ) {
7771 query_nodes = new HashSet<PhylogenyNode>();
7772 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7773 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7774 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7775 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7776 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7777 if ( s0.match( query_nodes ) ) {
7781 query_nodes = new HashSet<PhylogenyNode>();
7782 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7783 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7784 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7785 if ( s0.match( query_nodes ) ) {
7789 query_nodes = new HashSet<PhylogenyNode>();
7790 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7791 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7792 if ( s0.match( query_nodes ) ) {
7796 query_nodes = new HashSet<PhylogenyNode>();
7797 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7798 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7799 if ( s0.match( query_nodes ) ) {
7803 query_nodes = new HashSet<PhylogenyNode>();
7804 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7805 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7806 if ( s0.match( query_nodes ) ) {
7810 query_nodes = new HashSet<PhylogenyNode>();
7811 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7813 if ( s0.match( query_nodes ) ) {
7817 query_nodes = new HashSet<PhylogenyNode>();
7818 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7819 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7820 if ( s0.match( query_nodes ) ) {
7824 query_nodes = new HashSet<PhylogenyNode>();
7825 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7827 if ( s0.match( query_nodes ) ) {
7831 query_nodes = new HashSet<PhylogenyNode>();
7832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7833 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7834 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7835 if ( s0.match( query_nodes ) ) {
7839 query_nodes = new HashSet<PhylogenyNode>();
7840 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7841 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7842 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7843 if ( s0.match( query_nodes ) ) {
7847 query_nodes = new HashSet<PhylogenyNode>();
7848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7851 if ( s0.match( query_nodes ) ) {
7855 query_nodes = new HashSet<PhylogenyNode>();
7856 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7857 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7858 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7860 if ( s0.match( query_nodes ) ) {
7864 catch ( final Exception e ) {
7865 e.printStackTrace();
7871 private static boolean testSubtreeDeletion() {
7873 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7874 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7875 t1.deleteSubtree( t1.getNode( "A" ), false );
7876 if ( t1.getNumberOfExternalNodes() != 5 ) {
7879 t1.toNewHampshireX();
7880 t1.deleteSubtree( t1.getNode( "E" ), false );
7881 if ( t1.getNumberOfExternalNodes() != 4 ) {
7884 t1.toNewHampshireX();
7885 t1.deleteSubtree( t1.getNode( "F" ), false );
7886 if ( t1.getNumberOfExternalNodes() != 3 ) {
7889 t1.toNewHampshireX();
7890 t1.deleteSubtree( t1.getNode( "D" ), false );
7891 t1.toNewHampshireX();
7892 if ( t1.getNumberOfExternalNodes() != 3 ) {
7895 t1.deleteSubtree( t1.getNode( "def" ), false );
7896 t1.toNewHampshireX();
7897 if ( t1.getNumberOfExternalNodes() != 2 ) {
7900 t1.deleteSubtree( t1.getNode( "B" ), false );
7901 t1.toNewHampshireX();
7902 if ( t1.getNumberOfExternalNodes() != 1 ) {
7905 t1.deleteSubtree( t1.getNode( "C" ), false );
7906 t1.toNewHampshireX();
7907 if ( t1.getNumberOfExternalNodes() != 1 ) {
7910 t1.deleteSubtree( t1.getNode( "abc" ), false );
7911 t1.toNewHampshireX();
7912 if ( t1.getNumberOfExternalNodes() != 1 ) {
7915 t1.deleteSubtree( t1.getNode( "r" ), false );
7916 if ( t1.getNumberOfExternalNodes() != 0 ) {
7919 if ( !t1.isEmpty() ) {
7922 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7923 t2.deleteSubtree( t2.getNode( "A" ), false );
7924 t2.toNewHampshireX();
7925 if ( t2.getNumberOfExternalNodes() != 5 ) {
7928 t2.deleteSubtree( t2.getNode( "abc" ), false );
7929 t2.toNewHampshireX();
7930 if ( t2.getNumberOfExternalNodes() != 3 ) {
7933 t2.deleteSubtree( t2.getNode( "def" ), false );
7934 t2.toNewHampshireX();
7935 if ( t2.getNumberOfExternalNodes() != 1 ) {
7939 catch ( final Exception e ) {
7940 e.printStackTrace( System.out );
7946 private static boolean testSupportCount() {
7948 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7949 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7950 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7951 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7952 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7953 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7954 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7956 SupportCount.count( t0_1, phylogenies_1, true, false );
7957 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7958 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7959 + "(((((A,B),C),D),E),((F,G),X))"
7960 + "(((((A,Y),B),C),D),((F,G),E))"
7961 + "(((((A,B),C),D),E),(F,G))"
7962 + "(((((A,B),C),D),E),(F,G))"
7963 + "(((((A,B),C),D),E),(F,G))"
7964 + "(((((A,B),C),D),E),(F,G),Z)"
7965 + "(((((A,B),C),D),E),(F,G))"
7966 + "((((((A,B),C),D),E),F),G)"
7967 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7969 SupportCount.count( t0_2, phylogenies_2, true, false );
7970 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7971 while ( it.hasNext() ) {
7972 final PhylogenyNode n = it.next();
7973 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7977 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7978 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7979 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7980 SupportCount.count( t0_3, phylogenies_3, true, false );
7981 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7982 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7985 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7988 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7991 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7994 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7997 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
8000 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
8003 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
8006 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
8009 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
8012 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8013 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
8014 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
8015 SupportCount.count( t0_4, phylogenies_4, true, false );
8016 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
8017 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
8020 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
8023 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
8026 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
8029 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
8032 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
8035 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
8038 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
8041 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
8044 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
8047 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8048 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8049 double d = SupportCount.compare( b1, a, true, true, true );
8050 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
8053 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8054 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8055 d = SupportCount.compare( b2, a, true, true, true );
8056 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
8059 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8060 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
8061 d = SupportCount.compare( b3, a, true, true, true );
8062 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
8065 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
8066 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
8067 d = SupportCount.compare( b4, a, true, true, false );
8068 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
8072 catch ( final Exception e ) {
8073 e.printStackTrace( System.out );
8079 private static boolean testSupportTransfer() {
8081 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8082 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)",
8083 new NHXParser() )[ 0 ];
8084 final Phylogeny p2 = factory
8085 .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 ];
8086 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8089 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8092 support_transfer.moveBranchLengthsToBootstrap( p1 );
8093 support_transfer.transferSupportValues( p1, p2 );
8094 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8097 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8100 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8103 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8106 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
8109 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
8112 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
8115 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
8119 catch ( final Exception e ) {
8120 e.printStackTrace( System.out );
8126 private static boolean testUniprotTaxonomySearch() {
8128 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
8130 if ( results.size() != 1 ) {
8133 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8136 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8139 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8142 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8145 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8149 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
8150 if ( results.size() != 1 ) {
8153 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8156 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8159 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8162 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8165 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8169 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
8170 if ( results.size() != 1 ) {
8173 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8176 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8179 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8182 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8185 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8189 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
8190 if ( results.size() != 1 ) {
8193 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8196 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8199 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8202 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8205 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8208 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
8211 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
8214 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
8215 .equals( "Nematostella vectensis" ) ) {
8216 System.out.println( results.get( 0 ).getLineage() );
8220 catch ( final IOException e ) {
8221 System.out.println();
8222 System.out.println( "the following might be due to absence internet connection:" );
8223 e.printStackTrace( System.out );
8226 catch ( final Exception e ) {
8232 private static boolean testEmblEntryRetrieval() {
8233 //The format for GenBank Accession numbers are:
8234 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
8235 //Protein: 3 letters + 5 numerals
8236 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
8237 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
8240 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
8243 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
8246 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
8249 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
8252 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
8255 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
8258 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
8261 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
8264 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
8267 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
8270 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
8273 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8279 private static boolean testUniprotEntryRetrieval() {
8280 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8283 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8286 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8289 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8292 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8295 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8298 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8301 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8304 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8307 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8310 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8313 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8316 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8320 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8321 if ( !entry.getAccession().equals( "P12345" ) ) {
8324 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8327 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8330 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8333 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8337 catch ( final IOException e ) {
8338 System.out.println();
8339 System.out.println( "the following might be due to absence internet connection:" );
8340 e.printStackTrace( System.out );
8343 catch ( final Exception e ) {
8349 private static boolean testWabiTxSearch() {
8352 result = TxSearch.searchSimple( "nematostella" );
8353 result = TxSearch.getTxId( "nematostella" );
8354 if ( !result.equals( "45350" ) ) {
8357 result = TxSearch.getTxName( "45350" );
8358 if ( !result.equals( "Nematostella" ) ) {
8361 result = TxSearch.getTxId( "nematostella vectensis" );
8362 if ( !result.equals( "45351" ) ) {
8365 result = TxSearch.getTxName( "45351" );
8366 if ( !result.equals( "Nematostella vectensis" ) ) {
8369 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8370 if ( !result.equals( "536089" ) ) {
8373 result = TxSearch.getTxName( "536089" );
8374 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8377 final List<String> queries = new ArrayList<String>();
8378 queries.add( "Campylobacter coli" );
8379 queries.add( "Escherichia coli" );
8380 queries.add( "Arabidopsis" );
8381 queries.add( "Trichoplax" );
8382 queries.add( "Samanea saman" );
8383 queries.add( "Kluyveromyces marxianus" );
8384 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8385 queries.add( "Bornavirus parrot/PDD/2008" );
8386 final List<RANKS> ranks = new ArrayList<RANKS>();
8387 ranks.add( RANKS.SUPERKINGDOM );
8388 ranks.add( RANKS.KINGDOM );
8389 ranks.add( RANKS.FAMILY );
8390 ranks.add( RANKS.GENUS );
8391 ranks.add( RANKS.TRIBE );
8392 result = TxSearch.searchLineage( queries, ranks );
8393 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8394 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8396 catch ( final Exception e ) {
8397 System.out.println();
8398 System.out.println( "the following might be due to absence internet connection:" );
8399 e.printStackTrace( System.out );
8405 private static boolean testAminoAcidSequence() {
8407 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8408 if ( aa1.getLength() != 13 ) {
8411 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8414 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8417 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8420 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8421 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8424 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8425 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8428 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8429 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8433 catch ( final Exception e ) {
8434 e.printStackTrace();
8440 private static boolean testCreateBalancedPhylogeny() {
8442 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8443 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8446 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8449 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8450 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8453 if ( p1.getNumberOfExternalNodes() != 100 ) {
8457 catch ( final Exception e ) {
8458 e.printStackTrace();
8464 private static boolean testFastaParser() {
8466 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8469 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8472 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8473 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8476 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8479 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8482 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8485 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8488 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8492 catch ( final Exception e ) {
8493 e.printStackTrace();
8499 private static boolean testGeneralMsaParser() {
8501 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8502 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8503 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8504 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8505 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8506 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8507 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8508 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8509 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8512 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8515 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8518 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8521 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8524 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8527 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8530 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8533 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8536 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8539 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8542 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8545 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8546 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8549 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8552 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8555 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8556 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8559 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8562 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8565 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8566 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8569 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8572 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8576 catch ( final Exception e ) {
8577 e.printStackTrace();
8583 private static boolean testMafft( final String path ) {
8585 final List<String> opts = new ArrayList<String>();
8586 opts.add( "--maxiterate" );
8588 opts.add( "--localpair" );
8589 opts.add( "--quiet" );
8591 final MsaInferrer mafft = Mafft.createInstance( path );
8592 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8593 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8596 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8600 catch ( final Exception e ) {
8601 e.printStackTrace( System.out );
8607 private static boolean testNextNodeWithCollapsing() {
8609 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8611 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8612 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8613 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8614 t0.getNode( "cd" ).setCollapse( true );
8615 t0.getNode( "cde" ).setCollapse( true );
8616 n = t0.getFirstExternalNode();
8617 while ( n != null ) {
8619 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8621 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8624 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8627 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8630 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8633 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8636 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8640 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8641 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8642 t1.getNode( "ab" ).setCollapse( true );
8643 t1.getNode( "cd" ).setCollapse( true );
8644 t1.getNode( "cde" ).setCollapse( true );
8645 n = t1.getNode( "ab" );
8646 ext = new ArrayList<PhylogenyNode>();
8647 while ( n != null ) {
8649 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8651 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8654 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8657 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8660 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8663 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8669 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8670 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8671 t2.getNode( "ab" ).setCollapse( true );
8672 t2.getNode( "cd" ).setCollapse( true );
8673 t2.getNode( "cde" ).setCollapse( true );
8674 t2.getNode( "c" ).setCollapse( true );
8675 t2.getNode( "d" ).setCollapse( true );
8676 t2.getNode( "e" ).setCollapse( true );
8677 t2.getNode( "gh" ).setCollapse( true );
8678 n = t2.getNode( "ab" );
8679 ext = new ArrayList<PhylogenyNode>();
8680 while ( n != null ) {
8682 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8684 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8687 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8690 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8693 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8699 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8700 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8701 t3.getNode( "ab" ).setCollapse( true );
8702 t3.getNode( "cd" ).setCollapse( true );
8703 t3.getNode( "cde" ).setCollapse( true );
8704 t3.getNode( "c" ).setCollapse( true );
8705 t3.getNode( "d" ).setCollapse( true );
8706 t3.getNode( "e" ).setCollapse( true );
8707 t3.getNode( "gh" ).setCollapse( true );
8708 t3.getNode( "fgh" ).setCollapse( true );
8709 n = t3.getNode( "ab" );
8710 ext = new ArrayList<PhylogenyNode>();
8711 while ( n != null ) {
8713 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8715 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8718 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8721 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8727 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8728 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8729 t4.getNode( "ab" ).setCollapse( true );
8730 t4.getNode( "cd" ).setCollapse( true );
8731 t4.getNode( "cde" ).setCollapse( true );
8732 t4.getNode( "c" ).setCollapse( true );
8733 t4.getNode( "d" ).setCollapse( true );
8734 t4.getNode( "e" ).setCollapse( true );
8735 t4.getNode( "gh" ).setCollapse( true );
8736 t4.getNode( "fgh" ).setCollapse( true );
8737 t4.getNode( "abcdefgh" ).setCollapse( true );
8738 n = t4.getNode( "abcdefgh" );
8739 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8744 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8745 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8747 n = t5.getFirstExternalNode();
8748 while ( n != null ) {
8750 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8752 if ( ext.size() != 8 ) {
8755 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8758 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8761 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8764 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8767 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8770 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8773 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8776 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8781 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8782 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8784 t6.getNode( "ab" ).setCollapse( true );
8785 n = t6.getNode( "ab" );
8786 while ( n != null ) {
8788 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8790 if ( ext.size() != 7 ) {
8793 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8796 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8799 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8802 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8805 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8808 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8811 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8816 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8817 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8819 t7.getNode( "cd" ).setCollapse( true );
8820 n = t7.getNode( "a" );
8821 while ( n != null ) {
8823 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8825 if ( ext.size() != 7 ) {
8828 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8831 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8834 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8837 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8840 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8843 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8846 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8851 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8852 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8854 t8.getNode( "cd" ).setCollapse( true );
8855 t8.getNode( "c" ).setCollapse( true );
8856 t8.getNode( "d" ).setCollapse( true );
8857 n = t8.getNode( "a" );
8858 while ( n != null ) {
8860 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8862 if ( ext.size() != 7 ) {
8865 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8868 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8871 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8872 System.out.println( "2 fail" );
8875 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8878 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8881 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8884 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8889 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8890 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8892 t9.getNode( "gh" ).setCollapse( true );
8893 n = t9.getNode( "a" );
8894 while ( n != null ) {
8896 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8898 if ( ext.size() != 7 ) {
8901 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8904 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8907 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8910 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8913 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8916 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8919 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8924 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8925 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8927 t10.getNode( "gh" ).setCollapse( true );
8928 t10.getNode( "g" ).setCollapse( true );
8929 t10.getNode( "h" ).setCollapse( true );
8930 n = t10.getNode( "a" );
8931 while ( n != null ) {
8933 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8935 if ( ext.size() != 7 ) {
8938 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8941 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8944 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8947 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8950 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8953 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8956 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8961 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8962 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8964 t11.getNode( "gh" ).setCollapse( true );
8965 t11.getNode( "fgh" ).setCollapse( true );
8966 n = t11.getNode( "a" );
8967 while ( n != null ) {
8969 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8971 if ( ext.size() != 6 ) {
8974 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8977 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8980 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8983 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8986 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8989 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8994 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8995 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8997 t12.getNode( "gh" ).setCollapse( true );
8998 t12.getNode( "fgh" ).setCollapse( true );
8999 t12.getNode( "g" ).setCollapse( true );
9000 t12.getNode( "h" ).setCollapse( true );
9001 t12.getNode( "f" ).setCollapse( true );
9002 n = t12.getNode( "a" );
9003 while ( n != null ) {
9005 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9007 if ( ext.size() != 6 ) {
9010 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9013 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9016 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9019 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9022 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9025 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9030 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9031 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
9033 t13.getNode( "ab" ).setCollapse( true );
9034 t13.getNode( "b" ).setCollapse( true );
9035 t13.getNode( "fgh" ).setCollapse( true );
9036 t13.getNode( "gh" ).setCollapse( true );
9037 n = t13.getNode( "ab" );
9038 while ( n != null ) {
9040 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9042 if ( ext.size() != 5 ) {
9045 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9048 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9051 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9054 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9057 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9062 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
9063 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
9065 t14.getNode( "ab" ).setCollapse( true );
9066 t14.getNode( "a" ).setCollapse( true );
9067 t14.getNode( "fgh" ).setCollapse( true );
9068 t14.getNode( "gh" ).setCollapse( true );
9069 n = t14.getNode( "ab" );
9070 while ( n != null ) {
9072 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9074 if ( ext.size() != 5 ) {
9077 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9080 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9083 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9086 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9089 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9094 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" );
9095 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9097 t15.getNode( "ab" ).setCollapse( true );
9098 t15.getNode( "a" ).setCollapse( true );
9099 t15.getNode( "fgh" ).setCollapse( true );
9100 t15.getNode( "gh" ).setCollapse( true );
9101 n = t15.getNode( "ab" );
9102 while ( n != null ) {
9104 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9106 if ( ext.size() != 6 ) {
9109 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9112 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9115 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9118 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9121 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
9124 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9129 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" );
9130 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
9132 t16.getNode( "ab" ).setCollapse( true );
9133 t16.getNode( "a" ).setCollapse( true );
9134 t16.getNode( "fgh" ).setCollapse( true );
9135 t16.getNode( "gh" ).setCollapse( true );
9136 t16.getNode( "cd" ).setCollapse( true );
9137 t16.getNode( "cde" ).setCollapse( true );
9138 t16.getNode( "d" ).setCollapse( true );
9139 t16.getNode( "x" ).setCollapse( true );
9140 n = t16.getNode( "ab" );
9141 while ( n != null ) {
9143 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9145 if ( ext.size() != 4 ) {
9148 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9151 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9154 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
9157 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
9161 catch ( final Exception e ) {
9162 e.printStackTrace( System.out );
9168 private static boolean testMsaQualityMethod() {
9170 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
9171 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
9172 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
9173 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
9174 final List<Sequence> l = new ArrayList<Sequence>();
9179 final Msa msa = BasicMsa.createInstance( l );
9180 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
9183 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
9186 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
9189 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
9193 catch ( final Exception e ) {
9194 e.printStackTrace( System.out );
9200 private static boolean testSequenceIdParsing() {
9202 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
9203 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9204 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9206 System.out.println( "value =" + id.getValue() );
9207 System.out.println( "provider=" + id.getProvider() );
9212 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
9213 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9214 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9216 System.out.println( "value =" + id.getValue() );
9217 System.out.println( "provider=" + id.getProvider() );
9222 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
9223 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9224 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9226 System.out.println( "value =" + id.getValue() );
9227 System.out.println( "provider=" + id.getProvider() );
9232 id = SequenceIdParser.parse( "gb_AAA96518_1" );
9233 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9234 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
9236 System.out.println( "value =" + id.getValue() );
9237 System.out.println( "provider=" + id.getProvider() );
9242 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
9243 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9244 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
9246 System.out.println( "value =" + id.getValue() );
9247 System.out.println( "provider=" + id.getProvider() );
9252 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
9253 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9254 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
9256 System.out.println( "value =" + id.getValue() );
9257 System.out.println( "provider=" + id.getProvider() );
9262 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9263 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9264 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
9266 System.out.println( "value =" + id.getValue() );
9267 System.out.println( "provider=" + id.getProvider() );
9272 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9273 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9274 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9276 System.out.println( "value =" + id.getValue() );
9277 System.out.println( "provider=" + id.getProvider() );
9282 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9283 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9284 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9286 System.out.println( "value =" + id.getValue() );
9287 System.out.println( "provider=" + id.getProvider() );
9292 id = SequenceIdParser.parse( "P4A123" );
9293 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9294 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9296 System.out.println( "value =" + id.getValue() );
9297 System.out.println( "provider=" + id.getProvider() );
9302 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
9303 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9304 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9306 System.out.println( "value =" + id.getValue() );
9307 System.out.println( "provider=" + id.getProvider() );
9312 id = SequenceIdParser.parse( "XP_12345" );
9314 System.out.println( "value =" + id.getValue() );
9315 System.out.println( "provider=" + id.getProvider() );
9318 // lcl_91970_unknown_
9320 catch ( final Exception e ) {
9321 e.printStackTrace( System.out );