2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
56 import org.forester.io.parsers.tol.TolParser;
57 import org.forester.io.parsers.util.ParserUtils;
58 import org.forester.io.writers.PhylogenyWriter;
59 import org.forester.msa.BasicMsa;
60 import org.forester.msa.Mafft;
61 import org.forester.msa.Msa;
62 import org.forester.msa.MsaInferrer;
63 import org.forester.msa.MsaMethods;
64 import org.forester.pccx.TestPccx;
65 import org.forester.phylogeny.Phylogeny;
66 import org.forester.phylogeny.PhylogenyBranch;
67 import org.forester.phylogeny.PhylogenyMethods;
68 import org.forester.phylogeny.PhylogenyNode;
69 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
70 import org.forester.phylogeny.data.BinaryCharacters;
71 import org.forester.phylogeny.data.BranchWidth;
72 import org.forester.phylogeny.data.Confidence;
73 import org.forester.phylogeny.data.Distribution;
74 import org.forester.phylogeny.data.DomainArchitecture;
75 import org.forester.phylogeny.data.Event;
76 import org.forester.phylogeny.data.Identifier;
77 import org.forester.phylogeny.data.PhylogenyData;
78 import org.forester.phylogeny.data.PhylogenyDataUtil;
79 import org.forester.phylogeny.data.Polygon;
80 import org.forester.phylogeny.data.PropertiesMap;
81 import org.forester.phylogeny.data.Property;
82 import org.forester.phylogeny.data.Property.AppliesTo;
83 import org.forester.phylogeny.data.ProteinDomain;
84 import org.forester.phylogeny.data.Taxonomy;
85 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
86 import org.forester.phylogeny.factories.PhylogenyFactory;
87 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
88 import org.forester.protein.Protein;
89 import org.forester.rio.TestRIO;
90 import org.forester.sdi.SDI;
91 import org.forester.sdi.SDIR;
92 import org.forester.sdi.TestGSDI;
93 import org.forester.sequence.BasicSequence;
94 import org.forester.sequence.Sequence;
95 import org.forester.surfacing.TestSurfacing;
96 import org.forester.tools.ConfidenceAssessor;
97 import org.forester.tools.SupportCount;
98 import org.forester.tools.TreeSplitMatrix;
99 import org.forester.util.AsciiHistogram;
100 import org.forester.util.BasicDescriptiveStatistics;
101 import org.forester.util.BasicTable;
102 import org.forester.util.BasicTableParser;
103 import org.forester.util.DescriptiveStatistics;
104 import org.forester.util.ForesterConstants;
105 import org.forester.util.ForesterUtil;
106 import org.forester.util.GeneralTable;
107 import org.forester.util.SequenceIdParser;
108 import org.forester.ws.seqdb.SequenceDatabaseEntry;
109 import org.forester.ws.seqdb.SequenceDbWsTools;
110 import org.forester.ws.seqdb.UniProtTaxonomy;
111 import org.forester.ws.wabi.TxSearch;
112 import org.forester.ws.wabi.TxSearch.RANKS;
113 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
114 import org.forester.ws.wabi.TxSearch.TAX_RANK;
116 @SuppressWarnings( "unused")
117 public final class Test {
119 private final static double ZERO_DIFF = 1.0E-9;
120 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "test_data"
122 + ForesterUtil.getFileSeparator();
123 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "resources"
125 + ForesterUtil.getFileSeparator();
126 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
127 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
130 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
134 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
135 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
139 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
140 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
143 public static boolean isEqual( final double a, final double b ) {
144 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
147 public static void main( final String[] args ) {
148 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
149 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
151 Locale.setDefault( Locale.US );
152 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
155 System.out.print( "[Test if directory with files for testing exists/is readable: " );
156 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
157 System.out.println( "OK.]" );
160 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
161 System.out.println( "Testing aborted." );
164 System.out.print( "[Test if resources directory exists/is readable: " );
165 if ( testDir( PATH_TO_RESOURCES ) ) {
166 System.out.println( "OK.]" );
169 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
170 System.out.println( "Testing aborted." );
173 final long start_time = new Date().getTime();
174 System.out.print( "Sequence id parsing: " );
175 if ( testSequenceIdParsing() ) {
176 System.out.println( "OK." );
180 System.out.println( "failed." );
183 System.out.print( "Hmmscan output parser: " );
184 if ( testHmmscanOutputParser() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node methods: " );
193 if ( Test.testBasicNodeMethods() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "Taxonomy code extraction: " );
202 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "Taxonomy extraction (general): " );
211 if ( Test.testTaxonomyExtraction() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "Basic node construction and parsing of NHX (node level): " );
220 if ( Test.testNHXNodeParsing() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NHX parsing iterating: " );
229 if ( Test.testNHParsingIter() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "NH parsing: " );
238 if ( Test.testNHParsing() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "Conversion to NHX (node level): " );
247 if ( Test.testNHXconversion() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "NHX parsing: " );
256 if ( Test.testNHXParsing() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "NHX parsing with quotes: " );
265 if ( Test.testNHXParsingQuotes() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "NHX parsing (MrBayes): " );
274 if ( Test.testNHXParsingMB() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Nexus characters parsing: " );
283 if ( Test.testNexusCharactersParsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Nexus tree parsing iterating: " );
292 if ( Test.testNexusTreeParsingIterating() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Nexus tree parsing: " );
301 if ( Test.testNexusTreeParsing() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "Nexus tree parsing (translating): " );
310 if ( Test.testNexusTreeParsingTranslating() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "Nexus matrix parsing: " );
319 if ( Test.testNexusMatrixParsing() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Basic phyloXML parsing: " );
328 if ( Test.testBasicPhyloXMLparsing() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "Basic phyloXML parsing (validating against schema): " );
337 if ( testBasicPhyloXMLparsingValidating() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
346 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "phyloXML Distribution Element: " );
355 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Tol XML parsing: " );
364 if ( Test.testBasicTolXMLparsing() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Copying of node data: " );
373 if ( Test.testCopyOfNodeData() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Basic tree methods: " );
382 if ( Test.testBasicTreeMethods() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Postorder Iterator: " );
391 if ( Test.testPostOrderIterator() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Preorder Iterator: " );
400 if ( Test.testPreOrderIterator() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Levelorder Iterator: " );
409 if ( Test.testLevelOrderIterator() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Re-id methods: " );
418 if ( Test.testReIdMethods() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Methods on last external nodes: " );
427 if ( Test.testLastExternalNodeMethods() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Methods on external nodes: " );
436 if ( Test.testExternalNodeRelatedMethods() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Deletion of external nodes: " );
445 if ( Test.testDeletionOfExternalNodes() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Subtree deletion: " );
454 if ( Test.testSubtreeDeletion() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Phylogeny branch: " );
463 if ( Test.testPhylogenyBranch() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Rerooting: " );
472 if ( Test.testRerooting() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "Mipoint rooting: " );
481 if ( Test.testMidpointrooting() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "Node removal: " );
490 if ( Test.testNodeRemoval() ) {
491 System.out.println( "OK." );
495 System.out.println( "failed." );
498 System.out.print( "Support count: " );
499 if ( Test.testSupportCount() ) {
500 System.out.println( "OK." );
504 System.out.println( "failed." );
507 System.out.print( "Support transfer: " );
508 if ( Test.testSupportTransfer() ) {
509 System.out.println( "OK." );
513 System.out.println( "failed." );
516 System.out.print( "Finding of LCA: " );
517 if ( Test.testGetLCA() ) {
518 System.out.println( "OK." );
522 System.out.println( "failed." );
525 System.out.print( "Finding of LCA 2: " );
526 if ( Test.testGetLCA2() ) {
527 System.out.println( "OK." );
531 System.out.println( "failed." );
534 System.out.print( "Calculation of distance between nodes: " );
535 if ( Test.testGetDistance() ) {
536 System.out.println( "OK." );
540 System.out.println( "failed." );
543 System.out.print( "Descriptive statistics: " );
544 if ( Test.testDescriptiveStatistics() ) {
545 System.out.println( "OK." );
549 System.out.println( "failed." );
552 System.out.print( "Data objects and methods: " );
553 if ( Test.testDataObjects() ) {
554 System.out.println( "OK." );
558 System.out.println( "failed." );
561 System.out.print( "Properties map: " );
562 if ( Test.testPropertiesMap() ) {
563 System.out.println( "OK." );
567 System.out.println( "failed." );
570 System.out.print( "SDIse: " );
571 if ( Test.testSDIse() ) {
572 System.out.println( "OK." );
576 System.out.println( "failed." );
579 System.out.print( "SDIunrooted: " );
580 if ( Test.testSDIunrooted() ) {
581 System.out.println( "OK." );
585 System.out.println( "failed." );
588 System.out.print( "GSDI: " );
589 if ( TestGSDI.test() ) {
590 System.out.println( "OK." );
594 System.out.println( "failed." );
597 System.out.print( "RIO: " );
598 if ( TestRIO.test() ) {
599 System.out.println( "OK." );
603 System.out.println( "failed." );
606 System.out.print( "Phylogeny reconstruction:" );
607 System.out.println();
608 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
609 System.out.println( "OK." );
613 System.out.println( "failed." );
616 System.out.print( "Analysis of domain architectures: " );
617 System.out.println();
618 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
619 System.out.println( "OK." );
623 System.out.println( "failed." );
626 System.out.print( "GO: " );
627 System.out.println();
628 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
629 System.out.println( "OK." );
633 System.out.println( "failed." );
636 System.out.print( "Modeling tools: " );
637 if ( TestPccx.test() ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "Split Matrix strict: " );
646 if ( Test.testSplitStrict() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "Split Matrix: " );
655 if ( Test.testSplit() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "Confidence Assessor: " );
664 if ( Test.testConfidenceAssessor() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "Basic table: " );
673 if ( Test.testBasicTable() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "General table: " );
682 if ( Test.testGeneralTable() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
690 System.out.print( "Amino acid sequence: " );
691 if ( Test.testAminoAcidSequence() ) {
692 System.out.println( "OK." );
696 System.out.println( "failed." );
699 System.out.print( "General MSA parser: " );
700 if ( Test.testGeneralMsaParser() ) {
701 System.out.println( "OK." );
705 System.out.println( "failed." );
708 System.out.print( "Fasta parser for msa: " );
709 if ( Test.testFastaParser() ) {
710 System.out.println( "OK." );
714 System.out.println( "failed." );
717 System.out.print( "Creation of balanced phylogeny: " );
718 if ( Test.testCreateBalancedPhylogeny() ) {
719 System.out.println( "OK." );
723 System.out.println( "failed." );
726 System.out.print( "EMBL Entry Retrieval: " );
727 if ( Test.testEmblEntryRetrieval() ) {
728 System.out.println( "OK." );
732 System.out.println( "failed." );
735 System.out.print( "Uniprot Entry Retrieval: " );
736 if ( Test.testUniprotEntryRetrieval() ) {
737 System.out.println( "OK." );
741 System.out.println( "failed." );
744 System.out.print( "Uniprot Taxonomy Search: " );
745 if ( Test.testUniprotTaxonomySearch() ) {
746 System.out.println( "OK." );
750 System.out.println( "failed." );
755 final String os = ForesterUtil.OS_NAME.toLowerCase();
756 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
757 path = "/usr/local/bin/mafft";
759 else if ( os.indexOf( "win" ) >= 0 ) {
760 path = "C:\\Program Files\\mafft-win\\mafft.bat";
763 path = "/home/czmasek/bin/mafft";
765 if ( !MsaInferrer.isInstalled( path ) ) {
768 if ( !MsaInferrer.isInstalled( path ) ) {
769 path = "/usr/local/bin/mafft";
771 if ( MsaInferrer.isInstalled( path ) ) {
772 System.out.print( "MAFFT (external program): " );
773 if ( Test.testMafft( path ) ) {
774 System.out.println( "OK." );
778 System.out.println( "failed [will not count towards failed tests]" );
782 System.out.print( "Next nodes with collapsed: " );
783 if ( Test.testNextNodeWithCollapsing() ) {
784 System.out.println( "OK." );
788 System.out.println( "failed." );
791 System.out.print( "Simple MSA quality: " );
792 if ( Test.testMsaQualityMethod() ) {
793 System.out.println( "OK." );
797 System.out.println( "failed." );
800 System.out.println();
801 final Runtime rt = java.lang.Runtime.getRuntime();
802 final long free_memory = rt.freeMemory() / 1000000;
803 final long total_memory = rt.totalMemory() / 1000000;
804 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
805 + free_memory + "MB, total memory: " + total_memory + "MB)" );
806 System.out.println();
807 System.out.println( "Successful tests: " + succeeded );
808 System.out.println( "Failed tests: " + failed );
809 System.out.println();
811 System.out.println( "OK." );
814 System.out.println( "Not OK." );
818 private static boolean testExtractTaxonomyCodeFromNodeName() {
820 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
823 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
826 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
829 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
830 .equals( "MOUSE" ) ) {
833 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
834 .equals( "MOUSE" ) ) {
837 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
838 .equals( "MOUSE" ) ) {
841 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
844 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
847 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
851 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
855 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
859 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
862 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
865 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
868 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
872 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
873 .equals( "MOUSE" ) ) {
876 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
877 .equals( "MOUSE" ) ) {
881 catch ( final Exception e ) {
882 e.printStackTrace( System.out );
888 private static boolean testBasicNodeMethods() {
890 if ( PhylogenyNode.getNodeCount() != 0 ) {
893 final PhylogenyNode n1 = new PhylogenyNode();
894 final PhylogenyNode n2 = PhylogenyNode
895 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
896 final PhylogenyNode n3 = PhylogenyNode
897 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
898 final PhylogenyNode n4 = PhylogenyNode
899 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
900 if ( n1.isHasAssignedEvent() ) {
903 if ( PhylogenyNode.getNodeCount() != 4 ) {
906 if ( n3.getIndicator() != 0 ) {
909 if ( n3.getNumberOfExternalNodes() != 1 ) {
912 if ( !n3.isExternal() ) {
915 if ( !n3.isRoot() ) {
918 if ( !n4.getName().equals( "n4" ) ) {
922 catch ( final Exception e ) {
923 e.printStackTrace( System.out );
929 private static boolean testBasicPhyloXMLparsing() {
931 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
932 final PhyloXmlParser xml_parser = new PhyloXmlParser();
933 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
935 if ( xml_parser.getErrorCount() > 0 ) {
936 System.out.println( xml_parser.getErrorMessages().toString() );
939 if ( phylogenies_0.length != 4 ) {
942 final Phylogeny t1 = phylogenies_0[ 0 ];
943 final Phylogeny t2 = phylogenies_0[ 1 ];
944 final Phylogeny t3 = phylogenies_0[ 2 ];
945 final Phylogeny t4 = phylogenies_0[ 3 ];
946 if ( t1.getNumberOfExternalNodes() != 1 ) {
949 if ( !t1.isRooted() ) {
952 if ( t1.isRerootable() ) {
955 if ( !t1.getType().equals( "gene_tree" ) ) {
958 if ( t2.getNumberOfExternalNodes() != 2 ) {
961 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
964 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
967 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
970 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
973 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
976 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
979 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
980 .startsWith( "actgtgggggt" ) ) {
983 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
984 .startsWith( "ctgtgatgcat" ) ) {
987 if ( t3.getNumberOfExternalNodes() != 4 ) {
990 if ( !t1.getName().equals( "t1" ) ) {
993 if ( !t2.getName().equals( "t2" ) ) {
996 if ( !t3.getName().equals( "t3" ) ) {
999 if ( !t4.getName().equals( "t4" ) ) {
1002 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1005 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1008 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1011 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1012 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1015 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1018 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1021 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1024 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1025 .equals( "apoptosis" ) ) {
1028 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1029 .equals( "GO:0006915" ) ) {
1032 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1033 .equals( "UniProtKB" ) ) {
1036 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1037 .equals( "experimental" ) ) {
1040 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1041 .equals( "function" ) ) {
1044 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1045 .getValue() != 1 ) {
1048 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1049 .getType().equals( "ml" ) ) {
1052 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1053 .equals( "apoptosis" ) ) {
1056 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1057 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1060 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1061 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1064 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1065 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1068 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1069 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1072 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1073 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1076 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1077 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1080 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1081 .equals( "GO:0005829" ) ) {
1084 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1085 .equals( "intracellular organelle" ) ) {
1088 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1091 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1092 .equals( "UniProt link" ) ) ) {
1095 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1099 catch ( final Exception e ) {
1100 e.printStackTrace( System.out );
1106 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1108 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1109 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1110 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1111 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1114 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1116 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1118 if ( xml_parser.getErrorCount() > 0 ) {
1119 System.out.println( xml_parser.getErrorMessages().toString() );
1122 if ( phylogenies_0.length != 4 ) {
1125 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1126 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1127 if ( phylogenies_t1.length != 1 ) {
1130 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1131 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1134 if ( !t1_rt.isRooted() ) {
1137 if ( t1_rt.isRerootable() ) {
1140 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1143 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1144 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1145 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1146 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1149 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1152 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1155 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1158 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1159 .startsWith( "actgtgggggt" ) ) {
1162 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1163 .startsWith( "ctgtgatgcat" ) ) {
1166 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1167 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1168 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1169 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1170 if ( phylogenies_1.length != 1 ) {
1173 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1174 if ( !t3_rt.getName().equals( "t3" ) ) {
1177 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1180 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1183 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1186 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1189 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1190 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1193 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1196 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1199 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1200 .equals( "UniProtKB" ) ) {
1203 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1204 .equals( "apoptosis" ) ) {
1207 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1208 .equals( "GO:0006915" ) ) {
1211 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1212 .equals( "UniProtKB" ) ) {
1215 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1216 .equals( "experimental" ) ) {
1219 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1220 .equals( "function" ) ) {
1223 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1224 .getValue() != 1 ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1228 .getType().equals( "ml" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1232 .equals( "apoptosis" ) ) {
1235 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1236 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1240 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1243 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1244 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1248 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1252 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1255 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1256 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1260 .equals( "GO:0005829" ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1264 .equals( "intracellular organelle" ) ) {
1267 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1270 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1271 .equals( "UniProt link" ) ) ) {
1274 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1277 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1280 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1281 .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." ) ) ) {
1284 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1287 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1290 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1293 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1296 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1297 .equals( "ncbi" ) ) {
1300 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1303 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1304 .getName().equals( "B" ) ) {
1307 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1308 .getFrom() != 21 ) {
1311 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1314 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1315 .getLength() != 24 ) {
1318 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1319 .getConfidence() != 2144 ) {
1322 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1323 .equals( "pfam" ) ) {
1326 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1329 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1332 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1335 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1338 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1339 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1342 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1345 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1348 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1351 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1354 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1357 if ( taxbb.getSynonyms().size() != 2 ) {
1360 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1363 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1366 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1369 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1372 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1375 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1376 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1380 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1383 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1386 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1389 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1392 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1395 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1398 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1402 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1405 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1406 .equalsIgnoreCase( "435" ) ) {
1409 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1412 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1413 .equalsIgnoreCase( "443.7" ) ) {
1416 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1419 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1422 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1423 .equalsIgnoreCase( "433" ) ) {
1427 catch ( final Exception e ) {
1428 e.printStackTrace( System.out );
1434 private static boolean testBasicPhyloXMLparsingValidating() {
1436 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1437 PhyloXmlParser xml_parser = null;
1439 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1441 catch ( final Exception e ) {
1442 // Do nothing -- means were not running from jar.
1444 if ( xml_parser == null ) {
1445 xml_parser = new PhyloXmlParser();
1446 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1447 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1450 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1453 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1455 if ( xml_parser.getErrorCount() > 0 ) {
1456 System.out.println( xml_parser.getErrorMessages().toString() );
1459 if ( phylogenies_0.length != 4 ) {
1462 final Phylogeny t1 = phylogenies_0[ 0 ];
1463 final Phylogeny t2 = phylogenies_0[ 1 ];
1464 final Phylogeny t3 = phylogenies_0[ 2 ];
1465 final Phylogeny t4 = phylogenies_0[ 3 ];
1466 if ( !t1.getName().equals( "t1" ) ) {
1469 if ( !t2.getName().equals( "t2" ) ) {
1472 if ( !t3.getName().equals( "t3" ) ) {
1475 if ( !t4.getName().equals( "t4" ) ) {
1478 if ( t1.getNumberOfExternalNodes() != 1 ) {
1481 if ( t2.getNumberOfExternalNodes() != 2 ) {
1484 if ( t3.getNumberOfExternalNodes() != 4 ) {
1487 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1488 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1489 if ( xml_parser.getErrorCount() > 0 ) {
1490 System.out.println( "errors:" );
1491 System.out.println( xml_parser.getErrorMessages().toString() );
1494 if ( phylogenies_1.length != 4 ) {
1497 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1499 if ( xml_parser.getErrorCount() > 0 ) {
1500 System.out.println( "errors:" );
1501 System.out.println( xml_parser.getErrorMessages().toString() );
1504 if ( phylogenies_2.length != 1 ) {
1507 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1510 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1512 if ( xml_parser.getErrorCount() > 0 ) {
1513 System.out.println( xml_parser.getErrorMessages().toString() );
1516 if ( phylogenies_3.length != 2 ) {
1519 final Phylogeny a = phylogenies_3[ 0 ];
1520 if ( !a.getName().equals( "tree 4" ) ) {
1523 if ( a.getNumberOfExternalNodes() != 3 ) {
1526 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1529 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1532 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1534 if ( xml_parser.getErrorCount() > 0 ) {
1535 System.out.println( xml_parser.getErrorMessages().toString() );
1538 if ( phylogenies_4.length != 1 ) {
1541 final Phylogeny s = phylogenies_4[ 0 ];
1542 if ( s.getNumberOfExternalNodes() != 6 ) {
1545 s.getNode( "first" );
1547 s.getNode( "\"<a'b&c'd\">\"" );
1548 s.getNode( "'''\"" );
1549 s.getNode( "\"\"\"" );
1550 s.getNode( "dick & doof" );
1552 catch ( final Exception e ) {
1553 e.printStackTrace( System.out );
1559 private static boolean testBasicTable() {
1561 final BasicTable<String> t0 = new BasicTable<String>();
1562 if ( t0.getNumberOfColumns() != 0 ) {
1565 if ( t0.getNumberOfRows() != 0 ) {
1568 t0.setValue( 3, 2, "23" );
1569 t0.setValue( 10, 1, "error" );
1570 t0.setValue( 10, 1, "110" );
1571 t0.setValue( 9, 1, "19" );
1572 t0.setValue( 1, 10, "101" );
1573 t0.setValue( 10, 10, "1010" );
1574 t0.setValue( 100, 10, "10100" );
1575 t0.setValue( 0, 0, "00" );
1576 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1579 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1582 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1585 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1588 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1591 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1594 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1597 if ( t0.getNumberOfColumns() != 101 ) {
1600 if ( t0.getNumberOfRows() != 11 ) {
1603 if ( t0.getValueAsString( 49, 4 ) != null ) {
1606 final String l = ForesterUtil.getLineSeparator();
1607 final StringBuffer source = new StringBuffer();
1608 source.append( "" + l );
1609 source.append( "# 1 1 1 1 1 1 1 1" + l );
1610 source.append( " 00 01 02 03" + l );
1611 source.append( " 10 11 12 13 " + l );
1612 source.append( "20 21 22 23 " + l );
1613 source.append( " 30 31 32 33" + l );
1614 source.append( "40 41 42 43" + l );
1615 source.append( " # 1 1 1 1 1 " + l );
1616 source.append( "50 51 52 53 54" + l );
1617 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1618 if ( t1.getNumberOfColumns() != 5 ) {
1621 if ( t1.getNumberOfRows() != 6 ) {
1624 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1627 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1630 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1633 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1636 final StringBuffer source1 = new StringBuffer();
1637 source1.append( "" + l );
1638 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1639 source1.append( " 00; 01 ;02;03" + l );
1640 source1.append( " 10; 11; 12; 13 " + l );
1641 source1.append( "20; 21; 22; 23 " + l );
1642 source1.append( " 30; 31; 32; 33" + l );
1643 source1.append( "40;41;42;43" + l );
1644 source1.append( " # 1 1 1 1 1 " + l );
1645 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1646 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1647 if ( t2.getNumberOfColumns() != 5 ) {
1650 if ( t2.getNumberOfRows() != 6 ) {
1653 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1656 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1659 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1662 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1665 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1668 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1671 final StringBuffer source2 = new StringBuffer();
1672 source2.append( "" + l );
1673 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1674 source2.append( " 00; 01 ;02;03" + l );
1675 source2.append( " 10; 11; 12; 13 " + l );
1676 source2.append( "20; 21; 22; 23 " + l );
1677 source2.append( " " + l );
1678 source2.append( " 30; 31; 32; 33" + l );
1679 source2.append( "40;41;42;43" + l );
1680 source2.append( " comment: 1 1 1 1 1 " + l );
1681 source2.append( ";;;50 ; 52; 53;;54 " + l );
1682 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1688 if ( tl.size() != 2 ) {
1691 final BasicTable<String> t3 = tl.get( 0 );
1692 final BasicTable<String> t4 = tl.get( 1 );
1693 if ( t3.getNumberOfColumns() != 4 ) {
1696 if ( t3.getNumberOfRows() != 3 ) {
1699 if ( t4.getNumberOfColumns() != 4 ) {
1702 if ( t4.getNumberOfRows() != 3 ) {
1705 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1708 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1712 catch ( final Exception e ) {
1713 e.printStackTrace( System.out );
1719 private static boolean testBasicTolXMLparsing() {
1721 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1722 final TolParser parser = new TolParser();
1723 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1724 if ( parser.getErrorCount() > 0 ) {
1725 System.out.println( parser.getErrorMessages().toString() );
1728 if ( phylogenies_0.length != 1 ) {
1731 final Phylogeny t1 = phylogenies_0[ 0 ];
1732 if ( t1.getNumberOfExternalNodes() != 5 ) {
1735 if ( !t1.isRooted() ) {
1738 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1741 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1744 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1747 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1750 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1751 if ( parser.getErrorCount() > 0 ) {
1752 System.out.println( parser.getErrorMessages().toString() );
1755 if ( phylogenies_1.length != 1 ) {
1758 final Phylogeny t2 = phylogenies_1[ 0 ];
1759 if ( t2.getNumberOfExternalNodes() != 664 ) {
1762 if ( !t2.isRooted() ) {
1765 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1768 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1771 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1774 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1777 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1780 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1781 .equals( "Aquifex" ) ) {
1784 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1785 if ( parser.getErrorCount() > 0 ) {
1786 System.out.println( parser.getErrorMessages().toString() );
1789 if ( phylogenies_2.length != 1 ) {
1792 final Phylogeny t3 = phylogenies_2[ 0 ];
1793 if ( t3.getNumberOfExternalNodes() != 184 ) {
1796 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1799 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1802 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1805 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1806 if ( parser.getErrorCount() > 0 ) {
1807 System.out.println( parser.getErrorMessages().toString() );
1810 if ( phylogenies_3.length != 1 ) {
1813 final Phylogeny t4 = phylogenies_3[ 0 ];
1814 if ( t4.getNumberOfExternalNodes() != 1 ) {
1817 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1820 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1823 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1826 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1827 if ( parser.getErrorCount() > 0 ) {
1828 System.out.println( parser.getErrorMessages().toString() );
1831 if ( phylogenies_4.length != 1 ) {
1834 final Phylogeny t5 = phylogenies_4[ 0 ];
1835 if ( t5.getNumberOfExternalNodes() != 13 ) {
1838 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1841 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1844 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1848 catch ( final Exception e ) {
1849 e.printStackTrace( System.out );
1855 private static boolean testBasicTreeMethods() {
1857 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1858 final Phylogeny t1 = factory.create();
1859 if ( !t1.isEmpty() ) {
1862 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1863 if ( t2.getNumberOfExternalNodes() != 4 ) {
1866 if ( t2.getHeight() != 8.5 ) {
1869 if ( !t2.isCompletelyBinary() ) {
1872 if ( t2.isEmpty() ) {
1875 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1876 if ( t3.getNumberOfExternalNodes() != 5 ) {
1879 if ( t3.getHeight() != 11 ) {
1882 if ( t3.isCompletelyBinary() ) {
1885 final PhylogenyNode n = t3.getNode( "ABC" );
1886 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 ];
1887 if ( t4.getNumberOfExternalNodes() != 9 ) {
1890 if ( t4.getHeight() != 11 ) {
1893 if ( t4.isCompletelyBinary() ) {
1896 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)" );
1897 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1898 if ( t5.getNumberOfExternalNodes() != 8 ) {
1901 if ( t5.getHeight() != 15 ) {
1904 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)" );
1905 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1906 if ( t6.getHeight() != 15 ) {
1909 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)" );
1910 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1911 if ( t7.getHeight() != 15 ) {
1914 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)" );
1915 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1916 if ( t8.getNumberOfExternalNodes() != 10 ) {
1919 if ( t8.getHeight() != 15 ) {
1922 final char[] a9 = new char[] { 'a' };
1923 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1924 if ( t9.getHeight() != 0 ) {
1927 final char[] a10 = new char[] { 'a', ':', '6' };
1928 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1929 if ( t10.getHeight() != 6 ) {
1933 catch ( final Exception e ) {
1934 e.printStackTrace( System.out );
1940 private static boolean testConfidenceAssessor() {
1942 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1943 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1944 final Phylogeny[] ev0 = factory
1945 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1947 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1948 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1951 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1954 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1955 final Phylogeny[] ev1 = factory
1956 .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)));",
1958 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1959 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1962 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1965 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1966 final Phylogeny[] ev_b = factory
1967 .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",
1969 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1970 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1973 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1977 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1978 final Phylogeny[] ev1x = factory
1979 .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)));",
1981 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1982 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1985 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1988 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1989 final Phylogeny[] ev_bx = factory
1990 .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",
1992 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1993 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1996 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2000 final Phylogeny[] t2 = factory
2001 .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);",
2003 final Phylogeny[] ev2 = factory
2004 .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);",
2006 for( final Phylogeny target : t2 ) {
2007 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2010 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2011 new NHXParser() )[ 0 ];
2012 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2013 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2014 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2017 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2020 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2024 catch ( final Exception e ) {
2025 e.printStackTrace();
2031 private static boolean testCopyOfNodeData() {
2033 final PhylogenyNode n1 = PhylogenyNode
2034 .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]" );
2035 final PhylogenyNode n2 = n1.copyNodeData();
2036 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2040 catch ( final Exception e ) {
2041 e.printStackTrace();
2047 private static boolean testDataObjects() {
2049 final Confidence s0 = new Confidence();
2050 final Confidence s1 = new Confidence();
2051 if ( !s0.isEqual( s1 ) ) {
2054 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2055 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2056 if ( s2.isEqual( s1 ) ) {
2059 if ( !s2.isEqual( s3 ) ) {
2062 final Confidence s4 = ( Confidence ) s3.copy();
2063 if ( !s4.isEqual( s3 ) ) {
2070 final Taxonomy t1 = new Taxonomy();
2071 final Taxonomy t2 = new Taxonomy();
2072 final Taxonomy t3 = new Taxonomy();
2073 final Taxonomy t4 = new Taxonomy();
2074 final Taxonomy t5 = new Taxonomy();
2075 t1.setIdentifier( new Identifier( "ecoli" ) );
2076 t1.setTaxonomyCode( "ECOLI" );
2077 t1.setScientificName( "E. coli" );
2078 t1.setCommonName( "coli" );
2079 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2080 if ( !t1.isEqual( t0 ) ) {
2083 t2.setIdentifier( new Identifier( "ecoli" ) );
2084 t2.setTaxonomyCode( "OTHER" );
2085 t2.setScientificName( "what" );
2086 t2.setCommonName( "something" );
2087 if ( !t1.isEqual( t2 ) ) {
2090 t2.setIdentifier( new Identifier( "nemve" ) );
2091 if ( t1.isEqual( t2 ) ) {
2094 t1.setIdentifier( null );
2095 t3.setTaxonomyCode( "ECOLI" );
2096 t3.setScientificName( "what" );
2097 t3.setCommonName( "something" );
2098 if ( !t1.isEqual( t3 ) ) {
2101 t1.setIdentifier( null );
2102 t1.setTaxonomyCode( "" );
2103 t4.setScientificName( "E. ColI" );
2104 t4.setCommonName( "something" );
2105 if ( !t1.isEqual( t4 ) ) {
2108 t4.setScientificName( "B. subtilis" );
2109 t4.setCommonName( "something" );
2110 if ( t1.isEqual( t4 ) ) {
2113 t1.setIdentifier( null );
2114 t1.setTaxonomyCode( "" );
2115 t1.setScientificName( "" );
2116 t5.setCommonName( "COLI" );
2117 if ( !t1.isEqual( t5 ) ) {
2120 t5.setCommonName( "vibrio" );
2121 if ( t1.isEqual( t5 ) ) {
2126 final Identifier id0 = new Identifier( "123", "pfam" );
2127 final Identifier id1 = ( Identifier ) id0.copy();
2128 if ( !id1.isEqual( id1 ) ) {
2131 if ( !id1.isEqual( id0 ) ) {
2134 if ( !id0.isEqual( id1 ) ) {
2141 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2142 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2143 if ( !pd1.isEqual( pd1 ) ) {
2146 if ( !pd1.isEqual( pd0 ) ) {
2151 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2152 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2153 if ( !pd3.isEqual( pd3 ) ) {
2156 if ( !pd2.isEqual( pd3 ) ) {
2159 if ( !pd0.isEqual( pd3 ) ) {
2164 // DomainArchitecture
2165 // ------------------
2166 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2167 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2168 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2169 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2170 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2171 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2176 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2177 if ( ds0.getNumberOfDomains() != 4 ) {
2180 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2181 if ( !ds0.isEqual( ds0 ) ) {
2184 if ( !ds0.isEqual( ds1 ) ) {
2187 if ( ds1.getNumberOfDomains() != 4 ) {
2190 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2195 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2196 if ( ds0.isEqual( ds2 ) ) {
2202 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2203 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2204 System.out.println( ds3.toNHX() );
2207 if ( ds3.getNumberOfDomains() != 3 ) {
2212 final Event e1 = new Event( Event.EventType.fusion );
2213 if ( e1.isDuplication() ) {
2216 if ( !e1.isFusion() ) {
2219 if ( !e1.asText().toString().equals( "fusion" ) ) {
2222 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2225 final Event e11 = new Event( Event.EventType.fusion );
2226 if ( !e11.isEqual( e1 ) ) {
2229 if ( !e11.toNHX().toString().equals( "" ) ) {
2232 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2233 if ( e2.isDuplication() ) {
2236 if ( !e2.isSpeciationOrDuplication() ) {
2239 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2242 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2245 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2248 if ( e11.isEqual( e2 ) ) {
2251 final Event e2c = ( Event ) e2.copy();
2252 if ( !e2c.isEqual( e2 ) ) {
2255 Event e3 = new Event( 1, 2, 3 );
2256 if ( e3.isDuplication() ) {
2259 if ( e3.isSpeciation() ) {
2262 if ( e3.isGeneLoss() ) {
2265 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2268 final Event e3c = ( Event ) e3.copy();
2269 final Event e3cc = ( Event ) e3c.copy();
2270 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2274 if ( !e3c.isEqual( e3cc ) ) {
2277 Event e4 = new Event( 1, 2, 3 );
2278 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2281 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2284 final Event e4c = ( Event ) e4.copy();
2286 final Event e4cc = ( Event ) e4c.copy();
2287 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2290 if ( !e4c.isEqual( e4cc ) ) {
2293 final Event e5 = new Event();
2294 if ( !e5.isUnassigned() ) {
2297 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2300 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2303 final Event e6 = new Event( 1, 0, 0 );
2304 if ( !e6.asText().toString().equals( "duplication" ) ) {
2307 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2310 final Event e7 = new Event( 0, 1, 0 );
2311 if ( !e7.asText().toString().equals( "speciation" ) ) {
2314 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2317 final Event e8 = new Event( 0, 0, 1 );
2318 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2321 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2325 catch ( final Exception e ) {
2326 e.printStackTrace( System.out );
2332 private static boolean testDeletionOfExternalNodes() {
2334 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2335 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2336 final PhylogenyWriter w = new PhylogenyWriter();
2337 if ( t0.isEmpty() ) {
2340 if ( t0.getNumberOfExternalNodes() != 1 ) {
2343 t0.deleteSubtree( t0.getNode( "A" ), false );
2344 if ( t0.getNumberOfExternalNodes() != 0 ) {
2347 if ( !t0.isEmpty() ) {
2350 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2351 if ( t1.getNumberOfExternalNodes() != 2 ) {
2354 t1.deleteSubtree( t1.getNode( "A" ), false );
2355 if ( t1.getNumberOfExternalNodes() != 1 ) {
2358 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2361 t1.deleteSubtree( t1.getNode( "B" ), false );
2362 if ( t1.getNumberOfExternalNodes() != 1 ) {
2365 t1.deleteSubtree( t1.getNode( "r" ), false );
2366 if ( !t1.isEmpty() ) {
2369 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2370 if ( t2.getNumberOfExternalNodes() != 3 ) {
2373 t2.deleteSubtree( t2.getNode( "B" ), false );
2374 if ( t2.getNumberOfExternalNodes() != 2 ) {
2377 t2.toNewHampshireX();
2378 PhylogenyNode n = t2.getNode( "A" );
2379 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2382 t2.deleteSubtree( t2.getNode( "A" ), false );
2383 if ( t2.getNumberOfExternalNodes() != 2 ) {
2386 t2.deleteSubtree( t2.getNode( "C" ), true );
2387 if ( t2.getNumberOfExternalNodes() != 1 ) {
2390 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2391 if ( t3.getNumberOfExternalNodes() != 4 ) {
2394 t3.deleteSubtree( t3.getNode( "B" ), true );
2395 if ( t3.getNumberOfExternalNodes() != 3 ) {
2398 n = t3.getNode( "A" );
2399 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2402 n = n.getNextExternalNode();
2403 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2406 t3.deleteSubtree( t3.getNode( "A" ), true );
2407 if ( t3.getNumberOfExternalNodes() != 2 ) {
2410 n = t3.getNode( "C" );
2411 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2414 t3.deleteSubtree( t3.getNode( "C" ), true );
2415 if ( t3.getNumberOfExternalNodes() != 1 ) {
2418 t3.deleteSubtree( t3.getNode( "D" ), true );
2419 if ( t3.getNumberOfExternalNodes() != 0 ) {
2422 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2423 if ( t4.getNumberOfExternalNodes() != 6 ) {
2426 t4.deleteSubtree( t4.getNode( "B2" ), true );
2427 if ( t4.getNumberOfExternalNodes() != 5 ) {
2430 String s = w.toNewHampshire( t4, false, true ).toString();
2431 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2434 t4.deleteSubtree( t4.getNode( "B11" ), true );
2435 if ( t4.getNumberOfExternalNodes() != 4 ) {
2438 t4.deleteSubtree( t4.getNode( "C" ), true );
2439 if ( t4.getNumberOfExternalNodes() != 3 ) {
2442 n = t4.getNode( "A" );
2443 n = n.getNextExternalNode();
2444 if ( !n.getName().equals( "B12" ) ) {
2447 n = n.getNextExternalNode();
2448 if ( !n.getName().equals( "D" ) ) {
2451 s = w.toNewHampshire( t4, false, true ).toString();
2452 if ( !s.equals( "((A,B12),D);" ) ) {
2455 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2456 t5.deleteSubtree( t5.getNode( "A" ), true );
2457 if ( t5.getNumberOfExternalNodes() != 5 ) {
2460 s = w.toNewHampshire( t5, false, true ).toString();
2461 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2464 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2465 t6.deleteSubtree( t6.getNode( "B11" ), true );
2466 if ( t6.getNumberOfExternalNodes() != 5 ) {
2469 s = w.toNewHampshire( t6, false, false ).toString();
2470 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2473 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2474 t7.deleteSubtree( t7.getNode( "B12" ), true );
2475 if ( t7.getNumberOfExternalNodes() != 5 ) {
2478 s = w.toNewHampshire( t7, false, true ).toString();
2479 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2482 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2483 t8.deleteSubtree( t8.getNode( "B2" ), true );
2484 if ( t8.getNumberOfExternalNodes() != 5 ) {
2487 s = w.toNewHampshire( t8, false, false ).toString();
2488 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2491 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2492 t9.deleteSubtree( t9.getNode( "C" ), true );
2493 if ( t9.getNumberOfExternalNodes() != 5 ) {
2496 s = w.toNewHampshire( t9, false, true ).toString();
2497 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2500 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2501 t10.deleteSubtree( t10.getNode( "D" ), true );
2502 if ( t10.getNumberOfExternalNodes() != 5 ) {
2505 s = w.toNewHampshire( t10, false, true ).toString();
2506 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2509 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2510 t11.deleteSubtree( t11.getNode( "A" ), true );
2511 if ( t11.getNumberOfExternalNodes() != 2 ) {
2514 s = w.toNewHampshire( t11, false, true ).toString();
2515 if ( !s.equals( "(B,C);" ) ) {
2518 t11.deleteSubtree( t11.getNode( "C" ), true );
2519 if ( t11.getNumberOfExternalNodes() != 1 ) {
2522 s = w.toNewHampshire( t11, false, false ).toString();
2523 if ( !s.equals( "B;" ) ) {
2526 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2527 t12.deleteSubtree( t12.getNode( "B2" ), true );
2528 if ( t12.getNumberOfExternalNodes() != 8 ) {
2531 s = w.toNewHampshire( t12, false, true ).toString();
2532 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2535 t12.deleteSubtree( t12.getNode( "B3" ), true );
2536 if ( t12.getNumberOfExternalNodes() != 7 ) {
2539 s = w.toNewHampshire( t12, false, true ).toString();
2540 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2543 t12.deleteSubtree( t12.getNode( "C3" ), true );
2544 if ( t12.getNumberOfExternalNodes() != 6 ) {
2547 s = w.toNewHampshire( t12, false, true ).toString();
2548 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2551 t12.deleteSubtree( t12.getNode( "A1" ), true );
2552 if ( t12.getNumberOfExternalNodes() != 5 ) {
2555 s = w.toNewHampshire( t12, false, true ).toString();
2556 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2559 t12.deleteSubtree( t12.getNode( "B1" ), true );
2560 if ( t12.getNumberOfExternalNodes() != 4 ) {
2563 s = w.toNewHampshire( t12, false, true ).toString();
2564 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2567 t12.deleteSubtree( t12.getNode( "A3" ), true );
2568 if ( t12.getNumberOfExternalNodes() != 3 ) {
2571 s = w.toNewHampshire( t12, false, true ).toString();
2572 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2575 t12.deleteSubtree( t12.getNode( "A2" ), true );
2576 if ( t12.getNumberOfExternalNodes() != 2 ) {
2579 s = w.toNewHampshire( t12, false, true ).toString();
2580 if ( !s.equals( "(C1,C2);" ) ) {
2583 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2584 t13.deleteSubtree( t13.getNode( "D" ), true );
2585 if ( t13.getNumberOfExternalNodes() != 4 ) {
2588 s = w.toNewHampshire( t13, false, true ).toString();
2589 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2592 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2593 t14.deleteSubtree( t14.getNode( "E" ), true );
2594 if ( t14.getNumberOfExternalNodes() != 5 ) {
2597 s = w.toNewHampshire( t14, false, true ).toString();
2598 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2601 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2602 t15.deleteSubtree( t15.getNode( "B2" ), true );
2603 if ( t15.getNumberOfExternalNodes() != 11 ) {
2606 t15.deleteSubtree( t15.getNode( "B1" ), true );
2607 if ( t15.getNumberOfExternalNodes() != 10 ) {
2610 t15.deleteSubtree( t15.getNode( "B3" ), true );
2611 if ( t15.getNumberOfExternalNodes() != 9 ) {
2614 t15.deleteSubtree( t15.getNode( "B4" ), true );
2615 if ( t15.getNumberOfExternalNodes() != 8 ) {
2618 t15.deleteSubtree( t15.getNode( "A1" ), true );
2619 if ( t15.getNumberOfExternalNodes() != 7 ) {
2622 t15.deleteSubtree( t15.getNode( "C4" ), true );
2623 if ( t15.getNumberOfExternalNodes() != 6 ) {
2627 catch ( final Exception e ) {
2628 e.printStackTrace( System.out );
2634 private static boolean testDescriptiveStatistics() {
2636 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2637 dss1.addValue( 82 );
2638 dss1.addValue( 78 );
2639 dss1.addValue( 70 );
2640 dss1.addValue( 58 );
2641 dss1.addValue( 42 );
2642 if ( dss1.getN() != 5 ) {
2645 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2648 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2651 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2654 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2657 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2660 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2663 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2666 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2669 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2672 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2675 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2678 dss1.addValue( 123 );
2679 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2682 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2685 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2688 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2689 dss2.addValue( -1.85 );
2690 dss2.addValue( 57.5 );
2691 dss2.addValue( 92.78 );
2692 dss2.addValue( 57.78 );
2693 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2696 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2699 final double[] a = dss2.getDataAsDoubleArray();
2700 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2703 dss2.addValue( -100 );
2704 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2707 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2710 final double[] ds = new double[ 14 ];
2725 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2726 if ( bins.length != 4 ) {
2729 if ( bins[ 0 ] != 2 ) {
2732 if ( bins[ 1 ] != 3 ) {
2735 if ( bins[ 2 ] != 4 ) {
2738 if ( bins[ 3 ] != 5 ) {
2741 final double[] ds1 = new double[ 9 ];
2751 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2752 if ( bins1.length != 4 ) {
2755 if ( bins1[ 0 ] != 2 ) {
2758 if ( bins1[ 1 ] != 3 ) {
2761 if ( bins1[ 2 ] != 0 ) {
2764 if ( bins1[ 3 ] != 4 ) {
2767 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2768 if ( bins1_1.length != 3 ) {
2771 if ( bins1_1[ 0 ] != 3 ) {
2774 if ( bins1_1[ 1 ] != 2 ) {
2777 if ( bins1_1[ 2 ] != 4 ) {
2780 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2781 if ( bins1_2.length != 3 ) {
2784 if ( bins1_2[ 0 ] != 2 ) {
2787 if ( bins1_2[ 1 ] != 2 ) {
2790 if ( bins1_2[ 2 ] != 2 ) {
2793 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2807 dss3.addValue( 10 );
2808 dss3.addValue( 10 );
2809 dss3.addValue( 10 );
2810 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2811 histo.toStringBuffer( 10, '=', 40, 5 );
2812 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2814 catch ( final Exception e ) {
2815 e.printStackTrace( System.out );
2821 private static boolean testDir( final String file ) {
2823 final File f = new File( file );
2824 if ( !f.exists() ) {
2827 if ( !f.isDirectory() ) {
2830 if ( !f.canRead() ) {
2834 catch ( final Exception e ) {
2840 private static boolean testExternalNodeRelatedMethods() {
2842 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2843 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2844 PhylogenyNode n = t1.getNode( "A" );
2845 n = n.getNextExternalNode();
2846 if ( !n.getName().equals( "B" ) ) {
2849 n = n.getNextExternalNode();
2850 if ( !n.getName().equals( "C" ) ) {
2853 n = n.getNextExternalNode();
2854 if ( !n.getName().equals( "D" ) ) {
2857 n = t1.getNode( "B" );
2858 while ( !n.isLastExternalNode() ) {
2859 n = n.getNextExternalNode();
2861 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2862 n = t2.getNode( "A" );
2863 n = n.getNextExternalNode();
2864 if ( !n.getName().equals( "B" ) ) {
2867 n = n.getNextExternalNode();
2868 if ( !n.getName().equals( "C" ) ) {
2871 n = n.getNextExternalNode();
2872 if ( !n.getName().equals( "D" ) ) {
2875 n = t2.getNode( "B" );
2876 while ( !n.isLastExternalNode() ) {
2877 n = n.getNextExternalNode();
2879 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2880 n = t3.getNode( "A" );
2881 n = n.getNextExternalNode();
2882 if ( !n.getName().equals( "B" ) ) {
2885 n = n.getNextExternalNode();
2886 if ( !n.getName().equals( "C" ) ) {
2889 n = n.getNextExternalNode();
2890 if ( !n.getName().equals( "D" ) ) {
2893 n = n.getNextExternalNode();
2894 if ( !n.getName().equals( "E" ) ) {
2897 n = n.getNextExternalNode();
2898 if ( !n.getName().equals( "F" ) ) {
2901 n = n.getNextExternalNode();
2902 if ( !n.getName().equals( "G" ) ) {
2905 n = n.getNextExternalNode();
2906 if ( !n.getName().equals( "H" ) ) {
2909 n = t3.getNode( "B" );
2910 while ( !n.isLastExternalNode() ) {
2911 n = n.getNextExternalNode();
2913 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2914 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2915 final PhylogenyNode node = iter.next();
2917 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2918 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2919 final PhylogenyNode node = iter.next();
2921 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2922 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2923 if ( !iter.next().getName().equals( "A" ) ) {
2926 if ( !iter.next().getName().equals( "B" ) ) {
2929 if ( !iter.next().getName().equals( "C" ) ) {
2932 if ( !iter.next().getName().equals( "D" ) ) {
2935 if ( !iter.next().getName().equals( "E" ) ) {
2938 if ( !iter.next().getName().equals( "F" ) ) {
2941 if ( iter.hasNext() ) {
2945 catch ( final Exception e ) {
2946 e.printStackTrace( System.out );
2952 private static boolean testGeneralTable() {
2954 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2955 t0.setValue( 3, 2, "23" );
2956 t0.setValue( 10, 1, "error" );
2957 t0.setValue( 10, 1, "110" );
2958 t0.setValue( 9, 1, "19" );
2959 t0.setValue( 1, 10, "101" );
2960 t0.setValue( 10, 10, "1010" );
2961 t0.setValue( 100, 10, "10100" );
2962 t0.setValue( 0, 0, "00" );
2963 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2966 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2969 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2972 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2975 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2978 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2981 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2984 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2987 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2990 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2991 t1.setValue( "3", "2", "23" );
2992 t1.setValue( "10", "1", "error" );
2993 t1.setValue( "10", "1", "110" );
2994 t1.setValue( "9", "1", "19" );
2995 t1.setValue( "1", "10", "101" );
2996 t1.setValue( "10", "10", "1010" );
2997 t1.setValue( "100", "10", "10100" );
2998 t1.setValue( "0", "0", "00" );
2999 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3000 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3003 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3006 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3009 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3012 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3015 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3018 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3021 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3024 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3027 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3031 catch ( final Exception e ) {
3032 e.printStackTrace( System.out );
3038 private static boolean testGetDistance() {
3040 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3041 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",
3042 new NHXParser() )[ 0 ];
3043 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3046 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3049 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3052 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3055 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3058 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3061 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3064 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3067 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3070 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3073 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3076 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3079 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3082 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3085 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3088 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3091 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3094 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3097 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3100 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3103 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3106 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3109 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3112 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3115 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3118 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3121 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3124 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3127 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3130 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3133 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3136 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",
3137 new NHXParser() )[ 0 ];
3138 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3141 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3144 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3147 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3150 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3153 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3156 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3159 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3162 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3165 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3168 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3172 catch ( final Exception e ) {
3173 e.printStackTrace( System.out );
3179 private static boolean testGetLCA() {
3181 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3182 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3183 new NHXParser() )[ 0 ];
3184 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3185 if ( !A.getName().equals( "A" ) ) {
3188 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3189 if ( !gh.getName().equals( "gh" ) ) {
3192 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3193 if ( !ab.getName().equals( "ab" ) ) {
3196 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3197 if ( !ab2.getName().equals( "ab" ) ) {
3200 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3201 if ( !gh2.getName().equals( "gh" ) ) {
3204 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3205 if ( !gh3.getName().equals( "gh" ) ) {
3208 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3209 if ( !abc.getName().equals( "abc" ) ) {
3212 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3213 if ( !abc2.getName().equals( "abc" ) ) {
3216 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3217 if ( !abcd.getName().equals( "abcd" ) ) {
3220 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3221 if ( !abcd2.getName().equals( "abcd" ) ) {
3224 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3225 if ( !abcdef.getName().equals( "abcdef" ) ) {
3228 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3229 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3232 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3233 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3236 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3237 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3240 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3241 if ( !abcde.getName().equals( "abcde" ) ) {
3244 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3245 if ( !abcde2.getName().equals( "abcde" ) ) {
3248 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3249 if ( !r.getName().equals( "abcdefgh" ) ) {
3252 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3253 if ( !r2.getName().equals( "abcdefgh" ) ) {
3256 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3257 if ( !r3.getName().equals( "abcdefgh" ) ) {
3260 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3261 if ( !abcde3.getName().equals( "abcde" ) ) {
3264 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3265 if ( !abcde4.getName().equals( "abcde" ) ) {
3268 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3269 if ( !ab3.getName().equals( "ab" ) ) {
3272 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3273 if ( !ab4.getName().equals( "ab" ) ) {
3276 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3277 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3278 if ( !cd.getName().equals( "cd" ) ) {
3281 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3282 if ( !cd2.getName().equals( "cd" ) ) {
3285 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3286 if ( !cde.getName().equals( "cde" ) ) {
3289 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3290 if ( !cde2.getName().equals( "cde" ) ) {
3293 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3294 if ( !cdef.getName().equals( "cdef" ) ) {
3297 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3298 if ( !cdef2.getName().equals( "cdef" ) ) {
3301 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3302 if ( !cdef3.getName().equals( "cdef" ) ) {
3305 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3306 if ( !rt.getName().equals( "r" ) ) {
3309 final Phylogeny p3 = factory
3310 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3311 new NHXParser() )[ 0 ];
3312 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3313 if ( !bc_3.getName().equals( "bc" ) ) {
3316 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3317 if ( !ac_3.getName().equals( "abc" ) ) {
3320 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3321 if ( !ad_3.getName().equals( "abcde" ) ) {
3324 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3325 if ( !af_3.getName().equals( "abcdef" ) ) {
3328 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3329 if ( !ag_3.getName().equals( "" ) ) {
3332 if ( !ag_3.isRoot() ) {
3335 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3336 if ( !al_3.getName().equals( "" ) ) {
3339 if ( !al_3.isRoot() ) {
3342 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3343 if ( !kl_3.getName().equals( "" ) ) {
3346 if ( !kl_3.isRoot() ) {
3349 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3350 if ( !fl_3.getName().equals( "" ) ) {
3353 if ( !fl_3.isRoot() ) {
3356 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3357 if ( !gk_3.getName().equals( "ghijk" ) ) {
3360 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3361 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3362 if ( !r_4.getName().equals( "r" ) ) {
3365 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3366 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3367 if ( !r_5.getName().equals( "root" ) ) {
3370 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3371 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3372 if ( !r_6.getName().equals( "rot" ) ) {
3375 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3376 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3377 if ( !r_7.getName().equals( "rott" ) ) {
3381 catch ( final Exception e ) {
3382 e.printStackTrace( System.out );
3388 private static boolean testGetLCA2() {
3390 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3391 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3392 PhylogenyMethods.preOrderReId( p_a );
3393 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3394 p_a.getNode( "a" ) );
3395 if ( !p_a_1.getName().equals( "a" ) ) {
3398 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3399 PhylogenyMethods.preOrderReId( p_b );
3400 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3401 p_b.getNode( "a" ) );
3402 if ( !p_b_1.getName().equals( "b" ) ) {
3405 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3406 p_b.getNode( "b" ) );
3407 if ( !p_b_2.getName().equals( "b" ) ) {
3410 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3411 PhylogenyMethods.preOrderReId( p_c );
3412 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3413 p_c.getNode( "a" ) );
3414 if ( !p_c_1.getName().equals( "b" ) ) {
3417 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3418 p_c.getNode( "c" ) );
3419 if ( !p_c_2.getName().equals( "c" ) ) {
3420 System.out.println( p_c_2.getName() );
3424 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3425 p_c.getNode( "b" ) );
3426 if ( !p_c_3.getName().equals( "b" ) ) {
3429 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3430 p_c.getNode( "a" ) );
3431 if ( !p_c_4.getName().equals( "c" ) ) {
3434 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3435 new NHXParser() )[ 0 ];
3436 PhylogenyMethods.preOrderReId( p1 );
3437 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3438 p1.getNode( "A" ) );
3439 if ( !A.getName().equals( "A" ) ) {
3442 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3443 p1.getNode( "gh" ) );
3444 if ( !gh.getName().equals( "gh" ) ) {
3447 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3448 p1.getNode( "B" ) );
3449 if ( !ab.getName().equals( "ab" ) ) {
3452 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3453 p1.getNode( "A" ) );
3454 if ( !ab2.getName().equals( "ab" ) ) {
3457 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3458 p1.getNode( "G" ) );
3459 if ( !gh2.getName().equals( "gh" ) ) {
3462 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3463 p1.getNode( "H" ) );
3464 if ( !gh3.getName().equals( "gh" ) ) {
3467 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3468 p1.getNode( "A" ) );
3469 if ( !abc.getName().equals( "abc" ) ) {
3472 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3473 p1.getNode( "C" ) );
3474 if ( !abc2.getName().equals( "abc" ) ) {
3477 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3478 p1.getNode( "D" ) );
3479 if ( !abcd.getName().equals( "abcd" ) ) {
3482 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3483 p1.getNode( "A" ) );
3484 if ( !abcd2.getName().equals( "abcd" ) ) {
3487 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3488 p1.getNode( "F" ) );
3489 if ( !abcdef.getName().equals( "abcdef" ) ) {
3492 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3493 p1.getNode( "A" ) );
3494 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3497 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3498 p1.getNode( "F" ) );
3499 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3502 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3503 p1.getNode( "ab" ) );
3504 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3507 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3508 p1.getNode( "E" ) );
3509 if ( !abcde.getName().equals( "abcde" ) ) {
3512 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3513 p1.getNode( "A" ) );
3514 if ( !abcde2.getName().equals( "abcde" ) ) {
3517 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3518 p1.getNode( "abcdefgh" ) );
3519 if ( !r.getName().equals( "abcdefgh" ) ) {
3522 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3523 p1.getNode( "H" ) );
3524 if ( !r2.getName().equals( "abcdefgh" ) ) {
3527 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3528 p1.getNode( "A" ) );
3529 if ( !r3.getName().equals( "abcdefgh" ) ) {
3532 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3533 p1.getNode( "abcde" ) );
3534 if ( !abcde3.getName().equals( "abcde" ) ) {
3537 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3538 p1.getNode( "E" ) );
3539 if ( !abcde4.getName().equals( "abcde" ) ) {
3542 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3543 p1.getNode( "B" ) );
3544 if ( !ab3.getName().equals( "ab" ) ) {
3547 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3548 p1.getNode( "ab" ) );
3549 if ( !ab4.getName().equals( "ab" ) ) {
3552 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3553 PhylogenyMethods.preOrderReId( p2 );
3554 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3555 p2.getNode( "d" ) );
3556 if ( !cd.getName().equals( "cd" ) ) {
3559 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3560 p2.getNode( "c" ) );
3561 if ( !cd2.getName().equals( "cd" ) ) {
3564 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3565 p2.getNode( "e" ) );
3566 if ( !cde.getName().equals( "cde" ) ) {
3569 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3570 p2.getNode( "c" ) );
3571 if ( !cde2.getName().equals( "cde" ) ) {
3574 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3575 p2.getNode( "f" ) );
3576 if ( !cdef.getName().equals( "cdef" ) ) {
3579 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3580 p2.getNode( "f" ) );
3581 if ( !cdef2.getName().equals( "cdef" ) ) {
3584 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3585 p2.getNode( "d" ) );
3586 if ( !cdef3.getName().equals( "cdef" ) ) {
3589 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3590 p2.getNode( "a" ) );
3591 if ( !rt.getName().equals( "r" ) ) {
3594 final Phylogeny p3 = factory
3595 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3596 new NHXParser() )[ 0 ];
3597 PhylogenyMethods.preOrderReId( p3 );
3598 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3599 p3.getNode( "c" ) );
3600 if ( !bc_3.getName().equals( "bc" ) ) {
3603 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3604 p3.getNode( "c" ) );
3605 if ( !ac_3.getName().equals( "abc" ) ) {
3608 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3609 p3.getNode( "d" ) );
3610 if ( !ad_3.getName().equals( "abcde" ) ) {
3613 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3614 p3.getNode( "f" ) );
3615 if ( !af_3.getName().equals( "abcdef" ) ) {
3618 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3619 p3.getNode( "g" ) );
3620 if ( !ag_3.getName().equals( "" ) ) {
3623 if ( !ag_3.isRoot() ) {
3626 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3627 p3.getNode( "l" ) );
3628 if ( !al_3.getName().equals( "" ) ) {
3631 if ( !al_3.isRoot() ) {
3634 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3635 p3.getNode( "l" ) );
3636 if ( !kl_3.getName().equals( "" ) ) {
3639 if ( !kl_3.isRoot() ) {
3642 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3643 p3.getNode( "l" ) );
3644 if ( !fl_3.getName().equals( "" ) ) {
3647 if ( !fl_3.isRoot() ) {
3650 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3651 p3.getNode( "k" ) );
3652 if ( !gk_3.getName().equals( "ghijk" ) ) {
3655 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3656 PhylogenyMethods.preOrderReId( p4 );
3657 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3658 p4.getNode( "c" ) );
3659 if ( !r_4.getName().equals( "r" ) ) {
3662 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3663 PhylogenyMethods.preOrderReId( p5 );
3664 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3665 p5.getNode( "c" ) );
3666 if ( !r_5.getName().equals( "root" ) ) {
3669 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3670 PhylogenyMethods.preOrderReId( p6 );
3671 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3672 p6.getNode( "a" ) );
3673 if ( !r_6.getName().equals( "rot" ) ) {
3676 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3677 PhylogenyMethods.preOrderReId( p7 );
3678 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3679 p7.getNode( "e" ) );
3680 if ( !r_7.getName().equals( "rott" ) ) {
3683 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3684 p7.getNode( "a" ) );
3685 if ( !r_71.getName().equals( "rott" ) ) {
3688 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3689 p7.getNode( "rott" ) );
3690 if ( !r_72.getName().equals( "rott" ) ) {
3693 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3694 p7.getNode( "a" ) );
3695 if ( !r_73.getName().equals( "rott" ) ) {
3698 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3699 p7.getNode( "rott" ) );
3700 if ( !r_74.getName().equals( "rott" ) ) {
3703 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3704 p7.getNode( "e" ) );
3705 if ( !r_75.getName().equals( "e" ) ) {
3709 catch ( final Exception e ) {
3710 e.printStackTrace( System.out );
3716 private static boolean testHmmscanOutputParser() {
3717 final String test_dir = Test.PATH_TO_TEST_DATA;
3719 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3720 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3722 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3723 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3724 final List<Protein> proteins = parser2.parse();
3725 if ( parser2.getProteinsEncountered() != 4 ) {
3728 if ( proteins.size() != 4 ) {
3731 if ( parser2.getDomainsEncountered() != 69 ) {
3734 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3737 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3740 final Protein p1 = proteins.get( 0 );
3741 if ( p1.getNumberOfProteinDomains() != 15 ) {
3744 if ( p1.getLength() != 850 ) {
3747 final Protein p2 = proteins.get( 1 );
3748 if ( p2.getNumberOfProteinDomains() != 51 ) {
3751 if ( p2.getLength() != 1291 ) {
3754 final Protein p3 = proteins.get( 2 );
3755 if ( p3.getNumberOfProteinDomains() != 2 ) {
3758 final Protein p4 = proteins.get( 3 );
3759 if ( p4.getNumberOfProteinDomains() != 1 ) {
3762 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3765 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3768 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3771 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3774 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3777 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3780 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3783 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3786 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3790 catch ( final Exception e ) {
3791 e.printStackTrace( System.out );
3797 private static boolean testLastExternalNodeMethods() {
3799 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3800 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3801 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3802 final PhylogenyNode n1 = t0.getNode( "A" );
3803 if ( n1.isLastExternalNode() ) {
3806 final PhylogenyNode n2 = t0.getNode( "B" );
3807 if ( n2.isLastExternalNode() ) {
3810 final PhylogenyNode n3 = t0.getNode( "C" );
3811 if ( n3.isLastExternalNode() ) {
3814 final PhylogenyNode n4 = t0.getNode( "D" );
3815 if ( !n4.isLastExternalNode() ) {
3819 catch ( final Exception e ) {
3820 e.printStackTrace( System.out );
3826 private static boolean testLevelOrderIterator() {
3828 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3829 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3830 PhylogenyNodeIterator it0;
3831 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3834 for( it0.reset(); it0.hasNext(); ) {
3837 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3838 if ( !it.next().getName().equals( "r" ) ) {
3841 if ( !it.next().getName().equals( "ab" ) ) {
3844 if ( !it.next().getName().equals( "cd" ) ) {
3847 if ( !it.next().getName().equals( "A" ) ) {
3850 if ( !it.next().getName().equals( "B" ) ) {
3853 if ( !it.next().getName().equals( "C" ) ) {
3856 if ( !it.next().getName().equals( "D" ) ) {
3859 if ( it.hasNext() ) {
3862 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",
3863 new NHXParser() )[ 0 ];
3864 PhylogenyNodeIterator it2;
3865 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3868 for( it2.reset(); it2.hasNext(); ) {
3871 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3872 if ( !it3.next().getName().equals( "r" ) ) {
3875 if ( !it3.next().getName().equals( "abc" ) ) {
3878 if ( !it3.next().getName().equals( "defg" ) ) {
3881 if ( !it3.next().getName().equals( "A" ) ) {
3884 if ( !it3.next().getName().equals( "B" ) ) {
3887 if ( !it3.next().getName().equals( "C" ) ) {
3890 if ( !it3.next().getName().equals( "D" ) ) {
3893 if ( !it3.next().getName().equals( "E" ) ) {
3896 if ( !it3.next().getName().equals( "F" ) ) {
3899 if ( !it3.next().getName().equals( "G" ) ) {
3902 if ( !it3.next().getName().equals( "1" ) ) {
3905 if ( !it3.next().getName().equals( "2" ) ) {
3908 if ( !it3.next().getName().equals( "3" ) ) {
3911 if ( !it3.next().getName().equals( "4" ) ) {
3914 if ( !it3.next().getName().equals( "5" ) ) {
3917 if ( !it3.next().getName().equals( "6" ) ) {
3920 if ( !it3.next().getName().equals( "f1" ) ) {
3923 if ( !it3.next().getName().equals( "f2" ) ) {
3926 if ( !it3.next().getName().equals( "f3" ) ) {
3929 if ( !it3.next().getName().equals( "a" ) ) {
3932 if ( !it3.next().getName().equals( "b" ) ) {
3935 if ( !it3.next().getName().equals( "f21" ) ) {
3938 if ( !it3.next().getName().equals( "X" ) ) {
3941 if ( !it3.next().getName().equals( "Y" ) ) {
3944 if ( !it3.next().getName().equals( "Z" ) ) {
3947 if ( it3.hasNext() ) {
3950 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3951 PhylogenyNodeIterator it4;
3952 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3955 for( it4.reset(); it4.hasNext(); ) {
3958 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3959 if ( !it5.next().getName().equals( "r" ) ) {
3962 if ( !it5.next().getName().equals( "A" ) ) {
3965 if ( !it5.next().getName().equals( "B" ) ) {
3968 if ( !it5.next().getName().equals( "C" ) ) {
3971 if ( !it5.next().getName().equals( "D" ) ) {
3974 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3975 PhylogenyNodeIterator it6;
3976 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3979 for( it6.reset(); it6.hasNext(); ) {
3982 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3983 if ( !it7.next().getName().equals( "A" ) ) {
3986 if ( it.hasNext() ) {
3990 catch ( final Exception e ) {
3991 e.printStackTrace( System.out );
3997 private static boolean testNodeRemoval() {
3999 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4000 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
4001 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
4002 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
4005 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
4006 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
4007 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4010 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4011 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4012 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4016 catch ( final Exception e ) {
4017 e.printStackTrace( System.out );
4023 private static boolean testMidpointrooting() {
4025 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4026 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4027 PhylogenyMethods.midpointRoot( t0 );
4028 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4031 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4034 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4038 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",
4039 new NHXParser() )[ 0 ];
4040 if ( !t1.isRooted() ) {
4043 PhylogenyMethods.midpointRoot( t1 );
4044 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4047 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4050 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4053 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4056 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4059 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4062 t1.reRoot( t1.getNode( "A" ) );
4063 PhylogenyMethods.midpointRoot( t1 );
4064 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4067 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4070 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4073 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4076 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4080 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4084 catch ( final Exception e ) {
4085 e.printStackTrace( System.out );
4091 private static boolean testNexusCharactersParsing() {
4093 final NexusCharactersParser parser = new NexusCharactersParser();
4094 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4096 String[] labels = parser.getCharStateLabels();
4097 if ( labels.length != 7 ) {
4100 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4103 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4106 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4109 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4112 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4115 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4118 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4121 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4123 labels = parser.getCharStateLabels();
4124 if ( labels.length != 7 ) {
4127 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4130 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4133 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4136 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4139 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4142 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4145 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4149 catch ( final Exception e ) {
4150 e.printStackTrace( System.out );
4156 private static boolean testNexusMatrixParsing() {
4158 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4159 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4161 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4162 if ( m.getNumberOfCharacters() != 9 ) {
4165 if ( m.getNumberOfIdentifiers() != 5 ) {
4168 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4171 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4174 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4177 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4180 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4183 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4186 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4189 // if ( labels.length != 7 ) {
4192 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4195 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4198 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4201 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4204 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4207 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4210 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4213 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4215 // labels = parser.getCharStateLabels();
4216 // if ( labels.length != 7 ) {
4219 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4222 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4225 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4228 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4231 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4234 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4237 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4241 catch ( final Exception e ) {
4242 e.printStackTrace( System.out );
4248 private static boolean testNexusTreeParsing() {
4250 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4251 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4252 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4253 if ( phylogenies.length != 1 ) {
4256 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4259 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4263 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4264 if ( phylogenies.length != 1 ) {
4267 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4270 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4274 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4275 if ( phylogenies.length != 1 ) {
4278 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4281 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4284 if ( phylogenies[ 0 ].isRooted() ) {
4288 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4289 if ( phylogenies.length != 18 ) {
4292 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4295 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4298 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4301 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4304 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4307 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4310 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4313 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4316 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4319 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4322 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4325 if ( phylogenies[ 8 ].isRooted() ) {
4328 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4331 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4334 if ( !phylogenies[ 9 ].isRooted() ) {
4337 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4340 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4343 if ( !phylogenies[ 10 ].isRooted() ) {
4346 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4349 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4352 if ( phylogenies[ 11 ].isRooted() ) {
4355 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4358 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4361 if ( !phylogenies[ 12 ].isRooted() ) {
4364 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4367 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4370 if ( !phylogenies[ 13 ].isRooted() ) {
4373 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4376 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4379 if ( !phylogenies[ 14 ].isRooted() ) {
4382 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4385 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4388 if ( phylogenies[ 15 ].isRooted() ) {
4391 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4394 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4397 if ( !phylogenies[ 16 ].isRooted() ) {
4400 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4403 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4406 if ( phylogenies[ 17 ].isRooted() ) {
4409 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4413 catch ( final Exception e ) {
4414 e.printStackTrace( System.out );
4420 private static boolean testNexusTreeParsingIterating() {
4422 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
4423 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
4424 if ( !p.hasNext() ) {
4427 Phylogeny phy = p.next();
4428 if ( phy == null ) {
4431 if ( phy.getNumberOfExternalNodes() != 25 ) {
4434 if ( !phy.getName().equals( "" ) ) {
4437 if ( p.hasNext() ) {
4441 if ( phy != null ) {
4446 if ( !p.hasNext() ) {
4450 if ( phy == null ) {
4453 if ( phy.getNumberOfExternalNodes() != 25 ) {
4456 if ( !phy.getName().equals( "" ) ) {
4459 if ( p.hasNext() ) {
4463 if ( phy != null ) {
4467 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
4468 if ( !p.hasNext() ) {
4472 if ( phy == null ) {
4475 if ( phy.getNumberOfExternalNodes() != 10 ) {
4478 if ( !phy.getName().equals( "name" ) ) {
4481 if ( p.hasNext() ) {
4485 if ( phy != null ) {
4490 if ( !p.hasNext() ) {
4494 if ( phy == null ) {
4497 if ( phy.getNumberOfExternalNodes() != 10 ) {
4500 if ( !phy.getName().equals( "name" ) ) {
4503 if ( p.hasNext() ) {
4507 if ( phy != null ) {
4511 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
4512 if ( !p.hasNext() ) {
4516 if ( phy == null ) {
4519 if ( phy.getNumberOfExternalNodes() != 3 ) {
4522 if ( !phy.getName().equals( "" ) ) {
4525 if ( phy.isRooted() ) {
4528 if ( p.hasNext() ) {
4532 if ( phy != null ) {
4537 if ( !p.hasNext() ) {
4541 if ( phy == null ) {
4544 if ( phy.getNumberOfExternalNodes() != 3 ) {
4547 if ( !phy.getName().equals( "" ) ) {
4550 if ( p.hasNext() ) {
4554 if ( phy != null ) {
4558 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
4559 // if ( phylogenies.length != 18 ) {
4563 if ( !p.hasNext() ) {
4567 if ( phy == null ) {
4570 if ( phy.getNumberOfExternalNodes() != 10 ) {
4573 if ( !phy.getName().equals( "tree 0" ) ) {
4577 if ( !p.hasNext() ) {
4581 if ( phy == null ) {
4584 if ( phy.getNumberOfExternalNodes() != 10 ) {
4587 if ( !phy.getName().equals( "tree 1" ) ) {
4591 if ( !p.hasNext() ) {
4595 if ( phy == null ) {
4598 if ( phy.getNumberOfExternalNodes() != 3 ) {
4601 if ( !phy.getName().equals( "" ) ) {
4604 if ( phy.isRooted() ) {
4608 if ( !p.hasNext() ) {
4612 if ( phy == null ) {
4615 if ( phy.getNumberOfExternalNodes() != 4 ) {
4618 if ( !phy.getName().equals( "" ) ) {
4621 if ( !phy.isRooted() ) {
4625 if ( !p.hasNext() ) {
4629 if ( phy == null ) {
4632 if ( phy.getNumberOfExternalNodes() != 5 ) {
4633 System.out.println( phy.getNumberOfExternalNodes() );
4636 if ( !phy.getName().equals( "" ) ) {
4639 if ( !phy.isRooted() ) {
4643 if ( !p.hasNext() ) {
4647 if ( phy == null ) {
4650 if ( phy.getNumberOfExternalNodes() != 3 ) {
4653 if ( !phy.getName().equals( "" ) ) {
4656 if ( phy.isRooted() ) {
4660 if ( !p.hasNext() ) {
4664 if ( phy == null ) {
4667 if ( phy.getNumberOfExternalNodes() != 2 ) {
4670 if ( !phy.getName().equals( "" ) ) {
4673 if ( !phy.isRooted() ) {
4677 if ( !p.hasNext() ) {
4681 if ( phy.getNumberOfExternalNodes() != 3 ) {
4684 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4687 if ( !phy.isRooted() ) {
4691 if ( !p.hasNext() ) {
4695 if ( phy.getNumberOfExternalNodes() != 3 ) {
4698 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
4701 if ( !phy.getName().equals( "tree 8" ) ) {
4705 if ( !p.hasNext() ) {
4709 if ( phy.getNumberOfExternalNodes() != 3 ) {
4712 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
4715 if ( !phy.getName().equals( "tree 9" ) ) {
4719 if ( !p.hasNext() ) {
4723 if ( phy.getNumberOfExternalNodes() != 3 ) {
4726 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4729 if ( !phy.getName().equals( "tree 10" ) ) {
4732 if ( !phy.isRooted() ) {
4736 if ( !p.hasNext() ) {
4740 if ( phy.getNumberOfExternalNodes() != 3 ) {
4743 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
4746 if ( !phy.getName().equals( "tree 11" ) ) {
4749 if ( phy.isRooted() ) {
4753 if ( !p.hasNext() ) {
4757 if ( phy.getNumberOfExternalNodes() != 3 ) {
4760 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
4763 if ( !phy.getName().equals( "tree 12" ) ) {
4766 if ( !phy.isRooted() ) {
4770 if ( !p.hasNext() ) {
4774 if ( phy.getNumberOfExternalNodes() != 3 ) {
4777 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4780 if ( !phy.getName().equals( "tree 13" ) ) {
4783 if ( !phy.isRooted() ) {
4787 if ( !p.hasNext() ) {
4791 if ( phy.getNumberOfExternalNodes() != 10 ) {
4792 System.out.println( phy.getNumberOfExternalNodes() );
4797 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4798 System.out.println( phy.toNewHampshire() );
4801 if ( !phy.getName().equals( "tree 14" ) ) {
4804 if ( !phy.isRooted() ) {
4808 if ( !p.hasNext() ) {
4812 if ( phy.getNumberOfExternalNodes() != 10 ) {
4813 System.out.println( phy.getNumberOfExternalNodes() );
4818 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4819 System.out.println( phy.toNewHampshire() );
4822 if ( !phy.getName().equals( "tree 15" ) ) {
4825 if ( phy.isRooted() ) {
4829 if ( !p.hasNext() ) {
4833 if ( phy.getNumberOfExternalNodes() != 10 ) {
4834 System.out.println( phy.getNumberOfExternalNodes() );
4839 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4840 System.out.println( phy.toNewHampshire() );
4843 if ( !phy.getName().equals( "tree 16" ) ) {
4846 if ( !phy.isRooted() ) {
4850 if ( !p.hasNext() ) {
4854 if ( phy.getNumberOfExternalNodes() != 10 ) {
4855 System.out.println( phy.getNumberOfExternalNodes() );
4860 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4861 System.out.println( phy.toNewHampshire() );
4864 if ( !phy.getName().equals( "tree 17" ) ) {
4867 if ( phy.isRooted() ) {
4871 if ( p.hasNext() ) {
4875 if ( phy != null ) {
4880 if ( !p.hasNext() ) {
4884 if ( phy == null ) {
4887 if ( phy.getNumberOfExternalNodes() != 10 ) {
4890 if ( !phy.getName().equals( "tree 0" ) ) {
4894 if ( !p.hasNext() ) {
4898 if ( phy == null ) {
4901 if ( phy.getNumberOfExternalNodes() != 10 ) {
4904 if ( !phy.getName().equals( "tree 1" ) ) {
4908 if ( !p.hasNext() ) {
4912 if ( phy == null ) {
4915 if ( phy.getNumberOfExternalNodes() != 3 ) {
4918 if ( !phy.getName().equals( "" ) ) {
4921 if ( phy.isRooted() ) {
4925 if ( !p.hasNext() ) {
4929 if ( phy == null ) {
4932 if ( phy.getNumberOfExternalNodes() != 4 ) {
4935 if ( !phy.getName().equals( "" ) ) {
4938 if ( !phy.isRooted() ) {
4942 if ( !p.hasNext() ) {
4946 if ( phy == null ) {
4949 if ( phy.getNumberOfExternalNodes() != 5 ) {
4950 System.out.println( phy.getNumberOfExternalNodes() );
4953 if ( !phy.getName().equals( "" ) ) {
4956 if ( !phy.isRooted() ) {
4960 if ( !p.hasNext() ) {
4964 if ( phy == null ) {
4967 if ( phy.getNumberOfExternalNodes() != 3 ) {
4970 if ( !phy.getName().equals( "" ) ) {
4973 if ( phy.isRooted() ) {
4977 catch ( final Exception e ) {
4978 e.printStackTrace( System.out );
4984 private static boolean testNexusTreeParsingTranslating() {
4986 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4987 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4988 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4989 if ( phylogenies.length != 1 ) {
4992 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4995 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4998 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5001 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5004 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5005 .equals( "Aranaeus" ) ) {
5009 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
5010 if ( phylogenies.length != 3 ) {
5013 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5016 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5019 if ( phylogenies[ 0 ].isRooted() ) {
5022 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5025 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5028 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5029 .equals( "Aranaeus" ) ) {
5032 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
5035 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
5038 if ( phylogenies[ 1 ].isRooted() ) {
5041 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5044 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5047 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5048 .equals( "Aranaeus" ) ) {
5051 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
5054 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
5057 if ( !phylogenies[ 2 ].isRooted() ) {
5060 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5063 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5066 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5067 .equals( "Aranaeus" ) ) {
5071 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
5072 if ( phylogenies.length != 3 ) {
5075 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5078 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5081 if ( phylogenies[ 0 ].isRooted() ) {
5084 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5087 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5090 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5091 .equals( "Aranaeus" ) ) {
5094 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
5097 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
5100 if ( phylogenies[ 1 ].isRooted() ) {
5103 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5106 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5109 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5110 .equals( "Aranaeus" ) ) {
5113 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
5116 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
5119 if ( !phylogenies[ 2 ].isRooted() ) {
5122 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5125 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5128 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5129 .equals( "Aranaeus" ) ) {
5133 catch ( final Exception e ) {
5134 e.printStackTrace( System.out );
5140 private static boolean testNHParsing() {
5142 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5143 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
5144 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
5147 final NHXParser nhxp = new NHXParser();
5148 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
5149 nhxp.setReplaceUnderscores( true );
5150 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
5151 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
5154 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
5157 final Phylogeny p1b = factory
5158 .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 ",
5159 new NHXParser() )[ 0 ];
5160 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
5163 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
5166 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
5167 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
5168 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
5169 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
5170 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
5171 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
5172 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
5173 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
5174 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
5175 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
5176 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
5177 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
5178 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
5180 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
5183 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
5186 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
5189 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
5192 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
5193 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
5194 final String p16_S = "((A,B),C)";
5195 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
5196 if ( p16.length != 1 ) {
5199 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
5202 final String p17_S = "(C,(A,B))";
5203 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
5204 if ( p17.length != 1 ) {
5207 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
5210 final String p18_S = "((A,B),(C,D))";
5211 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
5212 if ( p18.length != 1 ) {
5215 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
5218 final String p19_S = "(((A,B),C),D)";
5219 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
5220 if ( p19.length != 1 ) {
5223 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
5226 final String p20_S = "(A,(B,(C,D)))";
5227 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
5228 if ( p20.length != 1 ) {
5231 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
5234 final String p21_S = "(A,(B,(C,(D,E))))";
5235 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
5236 if ( p21.length != 1 ) {
5239 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
5242 final String p22_S = "((((A,B),C),D),E)";
5243 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
5244 if ( p22.length != 1 ) {
5247 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
5250 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5251 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
5252 if ( p23.length != 1 ) {
5253 System.out.println( "xl=" + p23.length );
5257 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
5260 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5261 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
5262 if ( p24.length != 1 ) {
5265 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
5268 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5269 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5270 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
5271 if ( p241.length != 2 ) {
5274 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
5277 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
5280 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
5281 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
5282 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
5283 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
5284 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
5285 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
5286 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
5287 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
5288 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
5289 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
5292 final String p26_S = "(A,B)ab";
5293 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
5294 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
5297 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5298 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
5299 if ( p27s.length != 1 ) {
5300 System.out.println( "xxl=" + p27s.length );
5304 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
5305 System.out.println( p27s[ 0 ].toNewHampshireX() );
5309 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
5311 if ( p27.length != 1 ) {
5312 System.out.println( "yl=" + p27.length );
5316 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
5317 System.out.println( p27[ 0 ].toNewHampshireX() );
5321 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5322 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5323 final String p28_S3 = "(A,B)ab";
5324 final String p28_S4 = "((((A,B),C),D),;E;)";
5325 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
5327 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
5330 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
5333 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
5336 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
5339 if ( p28.length != 4 ) {
5342 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";
5343 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
5344 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
5347 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";
5348 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
5349 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
5352 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
5353 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
5354 if ( ( p32.length != 0 ) ) {
5357 final String p33_S = "A";
5358 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
5359 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
5362 final String p34_S = "B;";
5363 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
5364 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
5367 final String p35_S = "B:0.2";
5368 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
5369 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
5372 final String p36_S = "(A)";
5373 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
5374 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
5377 final String p37_S = "((A))";
5378 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
5379 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
5382 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
5383 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
5384 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
5387 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
5388 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
5389 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
5392 final String p40_S = "(A,B,C)";
5393 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
5394 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
5397 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
5398 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
5399 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
5402 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
5403 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
5404 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
5407 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)";
5408 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
5409 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
5412 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)))";
5413 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
5414 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
5417 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
5418 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
5419 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
5422 final String p46_S = "";
5423 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
5424 if ( p46.length != 0 ) {
5427 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
5428 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5431 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5432 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5435 final Phylogeny p49 = factory
5436 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
5437 new NHXParser() )[ 0 ];
5438 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5441 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5442 if ( p50.getNode( "A" ) == null ) {
5445 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
5446 .equals( "((A,B)ab:2.0[88],C);" ) ) {
5449 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
5452 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
5453 .equals( "((A,B)88:2.0,C);" ) ) {
5456 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5457 if ( p51.getNode( "A(A" ) == null ) {
5460 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5461 if ( p52.getNode( "A(A" ) == null ) {
5464 final Phylogeny p53 = factory
5465 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
5466 new NHXParser() )[ 0 ];
5467 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
5471 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
5472 if ( p54.getNode( "A" ) == null ) {
5475 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
5476 .equals( "((A,B)[88],C);" ) ) {
5480 catch ( final Exception e ) {
5481 e.printStackTrace( System.out );
5487 private static boolean testNHParsingIter() {
5489 final String p0_str = "(A,B);";
5490 final NHXParser p = new NHXParser();
5491 p.setSource( p0_str );
5492 if ( !p.hasNext() ) {
5495 final Phylogeny p0 = p.next();
5496 if ( !p0.toNewHampshire().equals( p0_str ) ) {
5497 System.out.println( p0.toNewHampshire() );
5500 if ( p.hasNext() ) {
5503 if ( p.next() != null ) {
5507 final String p00_str = "(A,B)root;";
5508 p.setSource( p00_str );
5509 final Phylogeny p00 = p.next();
5510 if ( !p00.toNewHampshire().equals( p00_str ) ) {
5511 System.out.println( p00.toNewHampshire() );
5515 final String p000_str = "A;";
5516 p.setSource( p000_str );
5517 final Phylogeny p000 = p.next();
5518 if ( !p000.toNewHampshire().equals( p000_str ) ) {
5519 System.out.println( p000.toNewHampshire() );
5523 final String p0000_str = "A";
5524 p.setSource( p0000_str );
5525 final Phylogeny p0000 = p.next();
5526 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
5527 System.out.println( p0000.toNewHampshire() );
5531 p.setSource( "(A)" );
5532 final Phylogeny p00000 = p.next();
5533 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
5534 System.out.println( p00000.toNewHampshire() );
5538 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
5539 p.setSource( p1_str );
5540 if ( !p.hasNext() ) {
5543 final Phylogeny p1_0 = p.next();
5544 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
5545 System.out.println( p1_0.toNewHampshire() );
5548 if ( !p.hasNext() ) {
5551 final Phylogeny p1_1 = p.next();
5552 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
5553 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
5556 if ( !p.hasNext() ) {
5559 final Phylogeny p1_2 = p.next();
5560 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
5561 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
5564 if ( !p.hasNext() ) {
5567 final Phylogeny p1_3 = p.next();
5568 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
5569 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
5572 if ( p.hasNext() ) {
5575 if ( p.next() != null ) {
5579 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
5580 p.setSource( p2_str );
5581 if ( !p.hasNext() ) {
5584 Phylogeny p2_0 = p.next();
5585 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5586 System.out.println( p2_0.toNewHampshire() );
5589 if ( !p.hasNext() ) {
5592 Phylogeny p2_1 = p.next();
5593 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5594 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5597 if ( !p.hasNext() ) {
5600 Phylogeny p2_2 = p.next();
5601 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5602 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5605 if ( !p.hasNext() ) {
5608 Phylogeny p2_3 = p.next();
5609 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5610 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5613 if ( !p.hasNext() ) {
5616 Phylogeny p2_4 = p.next();
5617 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5618 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5621 if ( p.hasNext() ) {
5624 if ( p.next() != null ) {
5629 if ( !p.hasNext() ) {
5633 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5634 System.out.println( p2_0.toNewHampshire() );
5637 if ( !p.hasNext() ) {
5641 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5642 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5645 if ( !p.hasNext() ) {
5649 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5650 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5653 if ( !p.hasNext() ) {
5657 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5658 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5661 if ( !p.hasNext() ) {
5665 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5666 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5669 if ( p.hasNext() ) {
5672 if ( p.next() != null ) {
5676 final String p3_str = "((A,B),C)abc";
5677 p.setSource( p3_str );
5678 if ( !p.hasNext() ) {
5681 final Phylogeny p3_0 = p.next();
5682 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
5685 if ( p.hasNext() ) {
5688 if ( p.next() != null ) {
5692 final String p4_str = "((A,B)ab,C)abc";
5693 p.setSource( p4_str );
5694 if ( !p.hasNext() ) {
5697 final Phylogeny p4_0 = p.next();
5698 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
5701 if ( p.hasNext() ) {
5704 if ( p.next() != null ) {
5708 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
5709 p.setSource( p5_str );
5710 if ( !p.hasNext() ) {
5713 final Phylogeny p5_0 = p.next();
5714 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
5717 if ( p.hasNext() ) {
5720 if ( p.next() != null ) {
5724 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5725 p.setSource( p6_str );
5726 if ( !p.hasNext() ) {
5729 Phylogeny p6_0 = p.next();
5730 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5733 if ( p.hasNext() ) {
5736 if ( p.next() != null ) {
5740 if ( !p.hasNext() ) {
5744 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5747 if ( p.hasNext() ) {
5750 if ( p.next() != null ) {
5754 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5755 p.setSource( p7_str );
5756 if ( !p.hasNext() ) {
5759 Phylogeny p7_0 = p.next();
5760 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5763 if ( p.hasNext() ) {
5766 if ( p.next() != null ) {
5770 if ( !p.hasNext() ) {
5774 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5777 if ( p.hasNext() ) {
5780 if ( p.next() != null ) {
5784 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
5785 p.setSource( p8_str );
5786 if ( !p.hasNext() ) {
5789 Phylogeny p8_0 = p.next();
5790 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5793 if ( !p.hasNext() ) {
5796 if ( !p.hasNext() ) {
5799 Phylogeny p8_1 = p.next();
5800 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5803 if ( p.hasNext() ) {
5806 if ( p.next() != null ) {
5810 if ( !p.hasNext() ) {
5814 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5817 if ( !p.hasNext() ) {
5821 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5824 if ( p.hasNext() ) {
5827 if ( p.next() != null ) {
5833 if ( p.hasNext() ) {
5837 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
5838 if ( !p.hasNext() ) {
5841 Phylogeny p_27 = p.next();
5842 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5843 System.out.println( p_27.toNewHampshireX() );
5847 if ( p.hasNext() ) {
5850 if ( p.next() != null ) {
5854 if ( !p.hasNext() ) {
5858 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5859 System.out.println( p_27.toNewHampshireX() );
5863 if ( p.hasNext() ) {
5866 if ( p.next() != null ) {
5870 catch ( final Exception e ) {
5871 e.printStackTrace( System.out );
5877 private static boolean testNHXconversion() {
5879 final PhylogenyNode n1 = new PhylogenyNode();
5880 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5881 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5882 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5883 final PhylogenyNode n5 = PhylogenyNode
5884 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
5885 final PhylogenyNode n6 = PhylogenyNode
5886 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
5887 if ( !n1.toNewHampshireX().equals( "" ) ) {
5890 if ( !n2.toNewHampshireX().equals( "" ) ) {
5893 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
5896 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
5899 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
5902 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
5906 catch ( final Exception e ) {
5907 e.printStackTrace( System.out );
5913 private static boolean testTaxonomyExtraction() {
5915 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5916 NHXParser.TAXONOMY_EXTRACTION.YES );
5917 if ( n0.getNodeData().isHasTaxonomy() ) {
5920 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
5921 NHXParser.TAXONOMY_EXTRACTION.YES );
5922 if ( n1.getNodeData().isHasTaxonomy() ) {
5923 System.out.println( n1.toString() );
5926 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
5927 NHXParser.TAXONOMY_EXTRACTION.YES );
5928 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5929 System.out.println( n2.toString() );
5932 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
5933 NHXParser.TAXONOMY_EXTRACTION.YES );
5934 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5935 System.out.println( n3.toString() );
5938 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
5939 NHXParser.TAXONOMY_EXTRACTION.YES );
5940 if ( n4.getNodeData().isHasTaxonomy() ) {
5941 System.out.println( n4.toString() );
5944 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
5945 NHXParser.TAXONOMY_EXTRACTION.YES );
5946 if ( n5.getNodeData().isHasTaxonomy() ) {
5947 System.out.println( n5.toString() );
5950 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
5951 NHXParser.TAXONOMY_EXTRACTION.YES );
5952 if ( n6.getNodeData().isHasTaxonomy() ) {
5953 System.out.println( n6.toString() );
5956 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
5957 NHXParser.TAXONOMY_EXTRACTION.YES );
5958 if ( n7.getNodeData().isHasTaxonomy() ) {
5959 System.out.println( n7.toString() );
5962 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
5963 NHXParser.TAXONOMY_EXTRACTION.YES );
5964 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5965 System.out.println( n8.toString() );
5968 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
5969 NHXParser.TAXONOMY_EXTRACTION.YES );
5970 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5971 System.out.println( n9.toString() );
5974 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
5975 NHXParser.TAXONOMY_EXTRACTION.YES );
5976 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
5977 System.out.println( n10.toString() );
5980 final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
5981 NHXParser.TAXONOMY_EXTRACTION.YES );
5982 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
5983 System.out.println( n11.toString() );
5986 final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
5987 NHXParser.TAXONOMY_EXTRACTION.YES );
5988 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
5989 System.out.println( n12.toString() );
5992 final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
5993 NHXParser.TAXONOMY_EXTRACTION.YES );
5994 if ( n13.getNodeData().isHasTaxonomy() ) {
5995 System.out.println( n13.toString() );
5998 final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
5999 NHXParser.TAXONOMY_EXTRACTION.YES );
6000 if ( n14.getNodeData().isHasTaxonomy() ) {
6001 System.out.println( n14.toString() );
6004 final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
6005 NHXParser.TAXONOMY_EXTRACTION.YES );
6006 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
6007 System.out.println( n15.toString() );
6010 final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
6011 NHXParser.TAXONOMY_EXTRACTION.YES );
6012 if ( n16.getNodeData().isHasTaxonomy() ) {
6013 System.out.println( n16.toString() );
6016 final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
6017 NHXParser.TAXONOMY_EXTRACTION.YES );
6018 if ( n17.getNodeData().isHasTaxonomy() ) {
6019 System.out.println( n17.toString() );
6023 catch ( final Exception e ) {
6024 e.printStackTrace( System.out );
6030 private static boolean testNHXNodeParsing() {
6032 final PhylogenyNode n1 = new PhylogenyNode();
6033 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
6034 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
6035 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
6036 final PhylogenyNode n5 = PhylogenyNode
6037 .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]" );
6038 if ( !n3.getName().equals( "n3" ) ) {
6041 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6044 if ( n3.isDuplication() ) {
6047 if ( n3.isHasAssignedEvent() ) {
6050 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
6053 if ( !n4.getName().equals( "n4" ) ) {
6056 if ( n4.getDistanceToParent() != 0.01 ) {
6059 if ( !n5.getName().equals( "n5" ) ) {
6062 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
6065 if ( n5.getDistanceToParent() != 0.1 ) {
6068 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
6071 if ( !n5.isDuplication() ) {
6074 if ( !n5.isHasAssignedEvent() ) {
6077 final PhylogenyNode n8 = PhylogenyNode
6078 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6079 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
6082 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
6085 final PhylogenyNode n9 = PhylogenyNode
6086 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6087 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
6090 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
6093 final PhylogenyNode n10 = PhylogenyNode
6094 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6095 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
6098 final PhylogenyNode n20 = PhylogenyNode
6099 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6100 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
6103 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
6106 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
6107 NHXParser.TAXONOMY_EXTRACTION.YES );
6108 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
6111 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
6114 final PhylogenyNode n20xx = PhylogenyNode
6115 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6116 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
6119 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
6122 final PhylogenyNode n20xxx = PhylogenyNode
6123 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6124 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
6127 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
6130 final PhylogenyNode n20xxxx = PhylogenyNode
6131 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6132 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
6135 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
6138 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
6139 NHXParser.TAXONOMY_EXTRACTION.YES );
6140 if ( !n21.getName().equals( "n21_PIG" ) ) {
6143 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
6146 final PhylogenyNode n21x = PhylogenyNode
6147 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6148 if ( !n21x.getName().equals( "n21_PIG" ) ) {
6151 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
6154 final PhylogenyNode n22 = PhylogenyNode
6155 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6156 if ( !n22.getName().equals( "n22/PIG" ) ) {
6159 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
6162 final PhylogenyNode n23 = PhylogenyNode
6163 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6164 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
6167 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
6170 final PhylogenyNode a = PhylogenyNode
6171 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6172 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
6175 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
6178 final PhylogenyNode b = PhylogenyNode
6179 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6180 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
6183 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
6186 final PhylogenyNode c = PhylogenyNode
6187 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
6188 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6189 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
6192 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
6195 final PhylogenyNode c1 = PhylogenyNode
6196 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
6197 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6198 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
6201 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
6204 final PhylogenyNode c2 = PhylogenyNode
6205 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
6206 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6207 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
6210 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
6213 final PhylogenyNode d = PhylogenyNode
6214 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6215 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
6218 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
6221 final PhylogenyNode e = PhylogenyNode
6222 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6223 if ( !e.getName().equals( "n10_RAT1" ) ) {
6226 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
6229 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
6230 NHXParser.TAXONOMY_EXTRACTION.YES );
6231 if ( !e2.getName().equals( "n10_RAT1" ) ) {
6234 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
6237 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
6238 NHXParser.TAXONOMY_EXTRACTION.YES );
6239 if ( !e3.getName().equals( "n10_RAT~" ) ) {
6242 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
6245 final PhylogenyNode n11 = PhylogenyNode
6246 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
6247 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6248 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
6251 if ( n11.getDistanceToParent() != 0.4 ) {
6254 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
6257 final PhylogenyNode n12 = PhylogenyNode
6258 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
6259 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6260 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
6263 if ( n12.getDistanceToParent() != 0.4 ) {
6266 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
6269 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
6270 NHXParser.TAXONOMY_EXTRACTION.YES );
6271 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
6274 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
6277 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
6278 NHXParser.TAXONOMY_EXTRACTION.YES );
6279 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
6282 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
6285 if ( n1.getName().compareTo( "" ) != 0 ) {
6288 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
6291 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6294 if ( n2.getName().compareTo( "" ) != 0 ) {
6297 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
6300 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6303 final PhylogenyNode n00 = PhylogenyNode
6304 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
6305 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
6308 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
6311 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
6312 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
6315 final PhylogenyNode n13 = PhylogenyNode
6316 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6317 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
6320 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
6323 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
6326 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6329 final PhylogenyNode n14 = PhylogenyNode
6330 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6331 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
6334 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
6337 final PhylogenyNode n15 = PhylogenyNode
6338 .createInstanceFromNhxString( "something_wicked[123]",
6339 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6340 if ( !n15.getName().equals( "something_wicked" ) ) {
6343 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
6346 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
6349 final PhylogenyNode n16 = PhylogenyNode
6350 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6351 if ( !n16.getName().equals( "something_wicked2" ) ) {
6354 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
6357 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
6360 final PhylogenyNode n17 = PhylogenyNode
6361 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6362 if ( !n17.getName().equals( "something_wicked3" ) ) {
6365 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
6368 final PhylogenyNode n18 = PhylogenyNode
6369 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6370 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
6373 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
6376 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
6379 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
6380 NHXParser.TAXONOMY_EXTRACTION.YES );
6381 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
6384 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6387 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
6388 NHXParser.TAXONOMY_EXTRACTION.YES );
6389 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
6392 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6395 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
6396 NHXParser.TAXONOMY_EXTRACTION.YES );
6397 if ( n31.getNodeData().isHasTaxonomy() ) {
6400 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
6401 NHXParser.TAXONOMY_EXTRACTION.YES );
6402 if ( n32.getNodeData().isHasTaxonomy() ) {
6406 catch ( final Exception e ) {
6407 e.printStackTrace( System.out );
6413 private static boolean testNHXParsing() {
6415 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6416 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
6417 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
6420 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]";
6421 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
6422 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6425 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]";
6426 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
6427 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
6430 final Phylogeny[] p3 = factory
6431 .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]",
6433 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6436 final Phylogeny[] p4 = factory
6437 .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(]",
6439 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6442 final Phylogeny[] p5 = factory
6443 .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(((]",
6445 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6448 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)";
6449 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)";
6450 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
6451 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
6454 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)))";
6455 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)))";
6456 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
6457 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
6460 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]) ))[,,, ])))))))";
6461 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
6462 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
6463 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
6466 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
6467 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
6470 final Phylogeny p10 = factory
6471 .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]",
6472 new NHXParser() )[ 0 ];
6473 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
6477 catch ( final Exception e ) {
6478 e.printStackTrace( System.out );
6484 private static boolean testNHXParsingQuotes() {
6486 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6487 final NHXParser p = new NHXParser();
6488 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
6489 if ( phylogenies_0.length != 5 ) {
6492 final Phylogeny phy = phylogenies_0[ 4 ];
6493 if ( phy.getNumberOfExternalNodes() != 7 ) {
6496 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
6499 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
6502 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
6503 .getScientificName().equals( "hsapiens" ) ) {
6506 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
6509 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
6512 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
6515 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
6518 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
6521 final NHXParser p1p = new NHXParser();
6522 p1p.setIgnoreQuotes( true );
6523 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
6524 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
6527 final NHXParser p2p = new NHXParser();
6528 p1p.setIgnoreQuotes( false );
6529 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
6530 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
6533 final NHXParser p3p = new NHXParser();
6534 p3p.setIgnoreQuotes( false );
6535 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
6536 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
6539 final NHXParser p4p = new NHXParser();
6540 p4p.setIgnoreQuotes( false );
6541 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
6542 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
6545 final Phylogeny p10 = factory
6546 .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]",
6547 new NHXParser() )[ 0 ];
6548 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]";
6549 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
6552 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
6553 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
6557 final Phylogeny p12 = factory
6558 .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]",
6559 new NHXParser() )[ 0 ];
6560 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]";
6561 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
6564 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
6565 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
6568 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;";
6569 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
6572 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
6573 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
6577 catch ( final Exception e ) {
6578 e.printStackTrace( System.out );
6584 private static boolean testNHXParsingMB() {
6586 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6587 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
6588 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6589 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6590 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6591 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6592 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6593 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6594 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6595 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
6596 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
6599 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
6602 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
6603 0.1100000000000000e+00 ) ) {
6606 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
6609 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
6612 final Phylogeny p2 = factory
6613 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
6614 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6615 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6616 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6617 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6618 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6619 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6620 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6621 + "7.369400000000000e-02}])",
6622 new NHXParser() )[ 0 ];
6623 if ( p2.getNode( "1" ) == null ) {
6626 if ( p2.getNode( "2" ) == null ) {
6630 catch ( final Exception e ) {
6631 e.printStackTrace( System.out );
6638 private static boolean testPhylogenyBranch() {
6640 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
6641 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
6642 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
6643 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
6644 if ( !a1b1.equals( a1b1 ) ) {
6647 if ( !a1b1.equals( b1a1 ) ) {
6650 if ( !b1a1.equals( a1b1 ) ) {
6653 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
6654 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
6655 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
6656 if ( a1_b1.equals( b1_a1 ) ) {
6659 if ( a1_b1.equals( a1_b1_ ) ) {
6662 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
6663 if ( !a1_b1.equals( b1_a1_ ) ) {
6666 if ( a1_b1_.equals( b1_a1_ ) ) {
6669 if ( !a1_b1_.equals( b1_a1 ) ) {
6673 catch ( final Exception e ) {
6674 e.printStackTrace( System.out );
6680 private static boolean testPhyloXMLparsingOfDistributionElement() {
6682 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6683 PhyloXmlParser xml_parser = null;
6685 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
6687 catch ( final Exception e ) {
6688 // Do nothing -- means were not running from jar.
6690 if ( xml_parser == null ) {
6691 xml_parser = new PhyloXmlParser();
6692 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
6693 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
6696 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
6699 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
6701 if ( xml_parser.getErrorCount() > 0 ) {
6702 System.out.println( xml_parser.getErrorMessages().toString() );
6705 if ( phylogenies_0.length != 1 ) {
6708 final Phylogeny t1 = phylogenies_0[ 0 ];
6709 PhylogenyNode n = null;
6710 Distribution d = null;
6711 n = t1.getNode( "root node" );
6712 if ( !n.getNodeData().isHasDistribution() ) {
6715 if ( n.getNodeData().getDistributions().size() != 1 ) {
6718 d = n.getNodeData().getDistribution();
6719 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6722 if ( d.getPoints().size() != 1 ) {
6725 if ( d.getPolygons() != null ) {
6728 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6731 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6734 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6737 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6740 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6743 n = t1.getNode( "node a" );
6744 if ( !n.getNodeData().isHasDistribution() ) {
6747 if ( n.getNodeData().getDistributions().size() != 2 ) {
6750 d = n.getNodeData().getDistribution( 1 );
6751 if ( !d.getDesc().equals( "San Diego" ) ) {
6754 if ( d.getPoints().size() != 1 ) {
6757 if ( d.getPolygons() != null ) {
6760 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6763 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6766 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6769 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6772 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6775 n = t1.getNode( "node bb" );
6776 if ( !n.getNodeData().isHasDistribution() ) {
6779 if ( n.getNodeData().getDistributions().size() != 1 ) {
6782 d = n.getNodeData().getDistribution( 0 );
6783 if ( d.getPoints().size() != 3 ) {
6786 if ( d.getPolygons().size() != 2 ) {
6789 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6792 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6795 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6798 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6801 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6804 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6807 Polygon p = d.getPolygons().get( 0 );
6808 if ( p.getPoints().size() != 3 ) {
6811 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6814 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6817 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6820 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6823 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6826 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6829 p = d.getPolygons().get( 1 );
6830 if ( p.getPoints().size() != 3 ) {
6833 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6836 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6839 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6843 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
6844 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
6845 if ( rt.length != 1 ) {
6848 final Phylogeny t1_rt = rt[ 0 ];
6849 n = t1_rt.getNode( "root node" );
6850 if ( !n.getNodeData().isHasDistribution() ) {
6853 if ( n.getNodeData().getDistributions().size() != 1 ) {
6856 d = n.getNodeData().getDistribution();
6857 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6860 if ( d.getPoints().size() != 1 ) {
6863 if ( d.getPolygons() != null ) {
6866 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6869 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6872 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6875 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6878 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6881 n = t1_rt.getNode( "node a" );
6882 if ( !n.getNodeData().isHasDistribution() ) {
6885 if ( n.getNodeData().getDistributions().size() != 2 ) {
6888 d = n.getNodeData().getDistribution( 1 );
6889 if ( !d.getDesc().equals( "San Diego" ) ) {
6892 if ( d.getPoints().size() != 1 ) {
6895 if ( d.getPolygons() != null ) {
6898 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6901 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6904 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6907 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6910 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6913 n = t1_rt.getNode( "node bb" );
6914 if ( !n.getNodeData().isHasDistribution() ) {
6917 if ( n.getNodeData().getDistributions().size() != 1 ) {
6920 d = n.getNodeData().getDistribution( 0 );
6921 if ( d.getPoints().size() != 3 ) {
6924 if ( d.getPolygons().size() != 2 ) {
6927 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6930 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6933 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6936 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6939 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6942 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6945 p = d.getPolygons().get( 0 );
6946 if ( p.getPoints().size() != 3 ) {
6949 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6952 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6955 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6958 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6961 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6964 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6967 p = d.getPolygons().get( 1 );
6968 if ( p.getPoints().size() != 3 ) {
6971 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6974 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6977 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6981 catch ( final Exception e ) {
6982 e.printStackTrace( System.out );
6988 private static boolean testPostOrderIterator() {
6990 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6991 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6992 PhylogenyNodeIterator it0;
6993 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
6996 for( it0.reset(); it0.hasNext(); ) {
6999 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
7000 final PhylogenyNodeIterator it = t1.iteratorPostorder();
7001 if ( !it.next().getName().equals( "A" ) ) {
7004 if ( !it.next().getName().equals( "B" ) ) {
7007 if ( !it.next().getName().equals( "ab" ) ) {
7010 if ( !it.next().getName().equals( "C" ) ) {
7013 if ( !it.next().getName().equals( "D" ) ) {
7016 if ( !it.next().getName().equals( "cd" ) ) {
7019 if ( !it.next().getName().equals( "abcd" ) ) {
7022 if ( !it.next().getName().equals( "E" ) ) {
7025 if ( !it.next().getName().equals( "F" ) ) {
7028 if ( !it.next().getName().equals( "ef" ) ) {
7031 if ( !it.next().getName().equals( "G" ) ) {
7034 if ( !it.next().getName().equals( "H" ) ) {
7037 if ( !it.next().getName().equals( "gh" ) ) {
7040 if ( !it.next().getName().equals( "efgh" ) ) {
7043 if ( !it.next().getName().equals( "r" ) ) {
7046 if ( it.hasNext() ) {
7050 catch ( final Exception e ) {
7051 e.printStackTrace( System.out );
7057 private static boolean testPreOrderIterator() {
7059 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7060 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
7061 PhylogenyNodeIterator it0;
7062 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
7065 for( it0.reset(); it0.hasNext(); ) {
7068 PhylogenyNodeIterator it = t0.iteratorPreorder();
7069 if ( !it.next().getName().equals( "r" ) ) {
7072 if ( !it.next().getName().equals( "ab" ) ) {
7075 if ( !it.next().getName().equals( "A" ) ) {
7078 if ( !it.next().getName().equals( "B" ) ) {
7081 if ( !it.next().getName().equals( "cd" ) ) {
7084 if ( !it.next().getName().equals( "C" ) ) {
7087 if ( !it.next().getName().equals( "D" ) ) {
7090 if ( it.hasNext() ) {
7093 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
7094 it = t1.iteratorPreorder();
7095 if ( !it.next().getName().equals( "r" ) ) {
7098 if ( !it.next().getName().equals( "abcd" ) ) {
7101 if ( !it.next().getName().equals( "ab" ) ) {
7104 if ( !it.next().getName().equals( "A" ) ) {
7107 if ( !it.next().getName().equals( "B" ) ) {
7110 if ( !it.next().getName().equals( "cd" ) ) {
7113 if ( !it.next().getName().equals( "C" ) ) {
7116 if ( !it.next().getName().equals( "D" ) ) {
7119 if ( !it.next().getName().equals( "efgh" ) ) {
7122 if ( !it.next().getName().equals( "ef" ) ) {
7125 if ( !it.next().getName().equals( "E" ) ) {
7128 if ( !it.next().getName().equals( "F" ) ) {
7131 if ( !it.next().getName().equals( "gh" ) ) {
7134 if ( !it.next().getName().equals( "G" ) ) {
7137 if ( !it.next().getName().equals( "H" ) ) {
7140 if ( it.hasNext() ) {
7144 catch ( final Exception e ) {
7145 e.printStackTrace( System.out );
7151 private static boolean testPropertiesMap() {
7153 final PropertiesMap pm = new PropertiesMap();
7154 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
7155 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
7156 final Property p2 = new Property( "something:else",
7158 "improbable:research",
7161 pm.addProperty( p0 );
7162 pm.addProperty( p1 );
7163 pm.addProperty( p2 );
7164 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
7167 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
7170 if ( pm.getProperties().size() != 3 ) {
7173 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
7176 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
7179 if ( pm.getProperties().size() != 3 ) {
7182 pm.removeProperty( "dimensions:diameter" );
7183 if ( pm.getProperties().size() != 2 ) {
7186 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
7189 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
7193 catch ( final Exception e ) {
7194 e.printStackTrace( System.out );
7200 private static boolean testReIdMethods() {
7202 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7203 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
7204 final long count = PhylogenyNode.getNodeCount();
7206 if ( p.getNode( "r" ).getId() != count ) {
7209 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
7212 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
7215 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
7218 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
7221 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
7224 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
7227 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
7230 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
7233 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
7236 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
7239 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
7242 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
7245 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
7248 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
7252 catch ( final Exception e ) {
7253 e.printStackTrace( System.out );
7259 private static boolean testRerooting() {
7261 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7262 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",
7263 new NHXParser() )[ 0 ];
7264 if ( !t1.isRooted() ) {
7267 t1.reRoot( t1.getNode( "D" ) );
7268 t1.reRoot( t1.getNode( "CD" ) );
7269 t1.reRoot( t1.getNode( "A" ) );
7270 t1.reRoot( t1.getNode( "B" ) );
7271 t1.reRoot( t1.getNode( "AB" ) );
7272 t1.reRoot( t1.getNode( "D" ) );
7273 t1.reRoot( t1.getNode( "C" ) );
7274 t1.reRoot( t1.getNode( "CD" ) );
7275 t1.reRoot( t1.getNode( "A" ) );
7276 t1.reRoot( t1.getNode( "B" ) );
7277 t1.reRoot( t1.getNode( "AB" ) );
7278 t1.reRoot( t1.getNode( "D" ) );
7279 t1.reRoot( t1.getNode( "D" ) );
7280 t1.reRoot( t1.getNode( "C" ) );
7281 t1.reRoot( t1.getNode( "A" ) );
7282 t1.reRoot( t1.getNode( "B" ) );
7283 t1.reRoot( t1.getNode( "AB" ) );
7284 t1.reRoot( t1.getNode( "C" ) );
7285 t1.reRoot( t1.getNode( "D" ) );
7286 t1.reRoot( t1.getNode( "CD" ) );
7287 t1.reRoot( t1.getNode( "D" ) );
7288 t1.reRoot( t1.getNode( "A" ) );
7289 t1.reRoot( t1.getNode( "B" ) );
7290 t1.reRoot( t1.getNode( "AB" ) );
7291 t1.reRoot( t1.getNode( "C" ) );
7292 t1.reRoot( t1.getNode( "D" ) );
7293 t1.reRoot( t1.getNode( "CD" ) );
7294 t1.reRoot( t1.getNode( "D" ) );
7295 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
7298 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
7301 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
7304 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
7307 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
7310 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
7313 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",
7314 new NHXParser() )[ 0 ];
7315 t2.reRoot( t2.getNode( "A" ) );
7316 t2.reRoot( t2.getNode( "D" ) );
7317 t2.reRoot( t2.getNode( "ABC" ) );
7318 t2.reRoot( t2.getNode( "A" ) );
7319 t2.reRoot( t2.getNode( "B" ) );
7320 t2.reRoot( t2.getNode( "D" ) );
7321 t2.reRoot( t2.getNode( "C" ) );
7322 t2.reRoot( t2.getNode( "ABC" ) );
7323 t2.reRoot( t2.getNode( "A" ) );
7324 t2.reRoot( t2.getNode( "B" ) );
7325 t2.reRoot( t2.getNode( "AB" ) );
7326 t2.reRoot( t2.getNode( "AB" ) );
7327 t2.reRoot( t2.getNode( "D" ) );
7328 t2.reRoot( t2.getNode( "C" ) );
7329 t2.reRoot( t2.getNode( "B" ) );
7330 t2.reRoot( t2.getNode( "AB" ) );
7331 t2.reRoot( t2.getNode( "D" ) );
7332 t2.reRoot( t2.getNode( "D" ) );
7333 t2.reRoot( t2.getNode( "ABC" ) );
7334 t2.reRoot( t2.getNode( "A" ) );
7335 t2.reRoot( t2.getNode( "B" ) );
7336 t2.reRoot( t2.getNode( "AB" ) );
7337 t2.reRoot( t2.getNode( "D" ) );
7338 t2.reRoot( t2.getNode( "C" ) );
7339 t2.reRoot( t2.getNode( "ABC" ) );
7340 t2.reRoot( t2.getNode( "A" ) );
7341 t2.reRoot( t2.getNode( "B" ) );
7342 t2.reRoot( t2.getNode( "AB" ) );
7343 t2.reRoot( t2.getNode( "D" ) );
7344 t2.reRoot( t2.getNode( "D" ) );
7345 t2.reRoot( t2.getNode( "C" ) );
7346 t2.reRoot( t2.getNode( "A" ) );
7347 t2.reRoot( t2.getNode( "B" ) );
7348 t2.reRoot( t2.getNode( "AB" ) );
7349 t2.reRoot( t2.getNode( "C" ) );
7350 t2.reRoot( t2.getNode( "D" ) );
7351 t2.reRoot( t2.getNode( "ABC" ) );
7352 t2.reRoot( t2.getNode( "D" ) );
7353 t2.reRoot( t2.getNode( "A" ) );
7354 t2.reRoot( t2.getNode( "B" ) );
7355 t2.reRoot( t2.getNode( "AB" ) );
7356 t2.reRoot( t2.getNode( "C" ) );
7357 t2.reRoot( t2.getNode( "D" ) );
7358 t2.reRoot( t2.getNode( "ABC" ) );
7359 t2.reRoot( t2.getNode( "D" ) );
7360 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7363 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7366 t2.reRoot( t2.getNode( "ABC" ) );
7367 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7370 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7373 t2.reRoot( t2.getNode( "AB" ) );
7374 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7377 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7380 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7383 t2.reRoot( t2.getNode( "AB" ) );
7384 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7387 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7390 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7393 t2.reRoot( t2.getNode( "D" ) );
7394 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7397 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7400 t2.reRoot( t2.getNode( "ABC" ) );
7401 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7404 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7407 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
7408 new NHXParser() )[ 0 ];
7409 t3.reRoot( t3.getNode( "B" ) );
7410 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7413 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7416 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7419 t3.reRoot( t3.getNode( "B" ) );
7420 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7423 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7426 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7429 t3.reRoot( t3.getRoot() );
7430 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7433 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7436 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7440 catch ( final Exception e ) {
7441 e.printStackTrace( System.out );
7447 private static boolean testSDIse() {
7449 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7450 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
7451 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
7452 gene1.setRooted( true );
7453 species1.setRooted( true );
7454 final SDI sdi = new SDI( gene1, species1 );
7455 if ( !gene1.getRoot().isDuplication() ) {
7458 final Phylogeny species2 = factory
7459 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7460 new NHXParser() )[ 0 ];
7461 final Phylogeny gene2 = factory
7462 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7463 new NHXParser() )[ 0 ];
7464 species2.setRooted( true );
7465 gene2.setRooted( true );
7466 final SDI sdi2 = new SDI( gene2, species2 );
7467 if ( sdi2.getDuplicationsSum() != 0 ) {
7470 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
7473 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
7476 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
7479 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
7482 if ( !gene2.getNode( "r" ).isSpeciation() ) {
7485 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
7488 final Phylogeny species3 = factory
7489 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7490 new NHXParser() )[ 0 ];
7491 final Phylogeny gene3 = factory
7492 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7493 new NHXParser() )[ 0 ];
7494 species3.setRooted( true );
7495 gene3.setRooted( true );
7496 final SDI sdi3 = new SDI( gene3, species3 );
7497 if ( sdi3.getDuplicationsSum() != 1 ) {
7500 if ( !gene3.getNode( "aa" ).isDuplication() ) {
7503 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
7506 final Phylogeny species4 = factory
7507 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7508 new NHXParser() )[ 0 ];
7509 final Phylogeny gene4 = factory
7510 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7511 new NHXParser() )[ 0 ];
7512 species4.setRooted( true );
7513 gene4.setRooted( true );
7514 final SDI sdi4 = new SDI( gene4, species4 );
7515 if ( sdi4.getDuplicationsSum() != 1 ) {
7518 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
7521 if ( !gene4.getNode( "abc" ).isDuplication() ) {
7524 if ( gene4.getNode( "abcd" ).isDuplication() ) {
7527 if ( species4.getNumberOfExternalNodes() != 6 ) {
7530 if ( gene4.getNumberOfExternalNodes() != 6 ) {
7533 final Phylogeny species5 = factory
7534 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7535 new NHXParser() )[ 0 ];
7536 final Phylogeny gene5 = factory
7537 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7538 new NHXParser() )[ 0 ];
7539 species5.setRooted( true );
7540 gene5.setRooted( true );
7541 final SDI sdi5 = new SDI( gene5, species5 );
7542 if ( sdi5.getDuplicationsSum() != 2 ) {
7545 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
7548 if ( !gene5.getNode( "adc" ).isDuplication() ) {
7551 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
7554 if ( species5.getNumberOfExternalNodes() != 6 ) {
7557 if ( gene5.getNumberOfExternalNodes() != 6 ) {
7560 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
7561 // Conjecture for Comparing Molecular Phylogenies"
7562 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
7563 final Phylogeny species6 = factory
7564 .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,"
7565 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7566 new NHXParser() )[ 0 ];
7567 final Phylogeny gene6 = factory
7568 .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,"
7569 + "((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,"
7570 + "(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;",
7571 new NHXParser() )[ 0 ];
7572 species6.setRooted( true );
7573 gene6.setRooted( true );
7574 final SDI sdi6 = new SDI( gene6, species6 );
7575 if ( sdi6.getDuplicationsSum() != 3 ) {
7578 if ( !gene6.getNode( "r" ).isDuplication() ) {
7581 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
7584 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
7587 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
7590 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
7593 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
7596 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
7599 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
7602 sdi6.computeMappingCostL();
7603 if ( sdi6.computeMappingCostL() != 17 ) {
7606 if ( species6.getNumberOfExternalNodes() != 9 ) {
7609 if ( gene6.getNumberOfExternalNodes() != 9 ) {
7612 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
7613 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
7614 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
7615 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
7616 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
7617 species7.setRooted( true );
7618 final Phylogeny gene7_1 = Test
7619 .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])" );
7620 gene7_1.setRooted( true );
7621 final SDI sdi7 = new SDI( gene7_1, species7 );
7622 if ( sdi7.getDuplicationsSum() != 0 ) {
7625 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
7628 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
7631 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
7634 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
7637 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
7640 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
7643 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
7646 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
7649 final Phylogeny gene7_2 = Test
7650 .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])" );
7651 gene7_2.setRooted( true );
7652 final SDI sdi7_2 = new SDI( gene7_2, species7 );
7653 if ( sdi7_2.getDuplicationsSum() != 1 ) {
7656 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
7659 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
7662 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
7665 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
7668 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
7671 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
7674 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
7677 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
7680 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
7684 catch ( final Exception e ) {
7690 private static boolean testSDIunrooted() {
7692 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7693 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
7694 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
7695 final Iterator<PhylogenyBranch> iter = l.iterator();
7696 PhylogenyBranch br = iter.next();
7697 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
7700 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
7704 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7707 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7711 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
7714 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
7718 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7721 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7725 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7728 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7732 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7735 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7739 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7742 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7746 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7749 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7753 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7756 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7760 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7763 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7767 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7770 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7774 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
7777 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
7781 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7784 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7788 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
7791 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
7795 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
7798 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
7801 if ( iter.hasNext() ) {
7804 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
7805 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
7806 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
7808 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7811 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7815 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7818 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7822 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7825 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7828 if ( iter1.hasNext() ) {
7831 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
7832 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
7833 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
7835 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7838 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7842 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7845 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7849 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7852 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7855 if ( iter2.hasNext() ) {
7858 final Phylogeny species0 = factory
7859 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7860 new NHXParser() )[ 0 ];
7861 final Phylogeny gene1 = factory
7862 .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])",
7863 new NHXParser() )[ 0 ];
7864 species0.setRooted( true );
7865 gene1.setRooted( true );
7866 final SDIR sdi_unrooted = new SDIR();
7867 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
7868 if ( sdi_unrooted.getCount() != 1 ) {
7871 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
7874 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
7877 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
7880 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7883 final Phylogeny gene2 = factory
7884 .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])",
7885 new NHXParser() )[ 0 ];
7886 gene2.setRooted( true );
7887 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
7888 if ( sdi_unrooted.getCount() != 1 ) {
7891 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7894 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7897 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7900 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7903 final Phylogeny species6 = factory
7904 .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,"
7905 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7906 new NHXParser() )[ 0 ];
7907 final Phylogeny gene6 = factory
7908 .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],"
7909 + "(((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],"
7910 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7911 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7912 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7913 new NHXParser() )[ 0 ];
7914 species6.setRooted( true );
7915 gene6.setRooted( true );
7916 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7917 if ( sdi_unrooted.getCount() != 1 ) {
7920 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7923 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7926 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7929 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7932 if ( !p6[ 0 ].getRoot().isDuplication() ) {
7935 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7938 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7941 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
7944 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7947 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
7950 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
7953 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7957 final Phylogeny species7 = factory
7958 .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,"
7959 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7960 new NHXParser() )[ 0 ];
7961 final Phylogeny gene7 = factory
7962 .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],"
7963 + "(((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],"
7964 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7965 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7966 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7967 new NHXParser() )[ 0 ];
7968 species7.setRooted( true );
7969 gene7.setRooted( true );
7970 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
7971 if ( sdi_unrooted.getCount() != 1 ) {
7974 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7977 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7980 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7983 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
7986 if ( !p7[ 0 ].getRoot().isDuplication() ) {
7989 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7992 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7995 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
7998 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8001 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
8004 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
8007 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8011 final Phylogeny species8 = factory
8012 .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,"
8013 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
8014 new NHXParser() )[ 0 ];
8015 final Phylogeny gene8 = factory
8016 .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],"
8017 + "(((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],"
8018 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
8019 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
8020 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
8021 new NHXParser() )[ 0 ];
8022 species8.setRooted( true );
8023 gene8.setRooted( true );
8024 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
8025 if ( sdi_unrooted.getCount() != 1 ) {
8028 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
8031 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
8034 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
8037 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
8040 if ( !p8[ 0 ].getRoot().isDuplication() ) {
8043 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
8046 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
8049 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
8052 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8055 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
8058 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
8061 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8066 catch ( final Exception e ) {
8067 e.printStackTrace( System.out );
8073 private static boolean testSplit() {
8075 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8076 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
8077 //Archaeopteryx.createApplication( p0 );
8078 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
8079 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8080 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8081 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8082 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8083 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8084 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8085 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8086 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8087 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8088 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
8089 // System.out.println( s0.toString() );
8091 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
8092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8094 if ( s0.match( query_nodes ) ) {
8097 query_nodes = new HashSet<PhylogenyNode>();
8098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8105 if ( !s0.match( query_nodes ) ) {
8109 query_nodes = new HashSet<PhylogenyNode>();
8110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8113 if ( !s0.match( query_nodes ) ) {
8117 query_nodes = new HashSet<PhylogenyNode>();
8118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8119 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8122 if ( !s0.match( query_nodes ) ) {
8126 query_nodes = new HashSet<PhylogenyNode>();
8127 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8128 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8131 if ( !s0.match( query_nodes ) ) {
8135 query_nodes = new HashSet<PhylogenyNode>();
8136 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8137 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8139 if ( !s0.match( query_nodes ) ) {
8143 query_nodes = new HashSet<PhylogenyNode>();
8144 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8145 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8146 if ( !s0.match( query_nodes ) ) {
8150 query_nodes = new HashSet<PhylogenyNode>();
8151 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8152 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8153 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8156 if ( !s0.match( query_nodes ) ) {
8160 query_nodes = new HashSet<PhylogenyNode>();
8161 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8162 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8163 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8164 if ( !s0.match( query_nodes ) ) {
8168 query_nodes = new HashSet<PhylogenyNode>();
8169 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8170 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8171 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8172 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8173 if ( !s0.match( query_nodes ) ) {
8177 query_nodes = new HashSet<PhylogenyNode>();
8178 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8179 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8180 if ( s0.match( query_nodes ) ) {
8184 query_nodes = new HashSet<PhylogenyNode>();
8185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8188 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8189 if ( s0.match( query_nodes ) ) {
8193 query_nodes = new HashSet<PhylogenyNode>();
8194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8196 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8197 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8199 if ( s0.match( query_nodes ) ) {
8203 query_nodes = new HashSet<PhylogenyNode>();
8204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8205 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8207 if ( s0.match( query_nodes ) ) {
8211 query_nodes = new HashSet<PhylogenyNode>();
8212 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8213 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8214 if ( s0.match( query_nodes ) ) {
8218 query_nodes = new HashSet<PhylogenyNode>();
8219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8221 if ( s0.match( query_nodes ) ) {
8225 query_nodes = new HashSet<PhylogenyNode>();
8226 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8227 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8228 if ( s0.match( query_nodes ) ) {
8232 query_nodes = new HashSet<PhylogenyNode>();
8233 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8234 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8235 if ( s0.match( query_nodes ) ) {
8239 query_nodes = new HashSet<PhylogenyNode>();
8240 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8241 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8242 if ( s0.match( query_nodes ) ) {
8246 query_nodes = new HashSet<PhylogenyNode>();
8247 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8248 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8249 if ( s0.match( query_nodes ) ) {
8253 query_nodes = new HashSet<PhylogenyNode>();
8254 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8255 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8256 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8257 if ( s0.match( query_nodes ) ) {
8261 query_nodes = new HashSet<PhylogenyNode>();
8262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8265 if ( s0.match( query_nodes ) ) {
8269 query_nodes = new HashSet<PhylogenyNode>();
8270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8271 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8273 if ( s0.match( query_nodes ) ) {
8277 query_nodes = new HashSet<PhylogenyNode>();
8278 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8279 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8280 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8281 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8282 if ( s0.match( query_nodes ) ) {
8286 // query_nodes = new HashSet<PhylogenyNode>();
8287 // query_nodes.add( new PhylogenyNode( "X" ) );
8288 // query_nodes.add( new PhylogenyNode( "Y" ) );
8289 // query_nodes.add( new PhylogenyNode( "A" ) );
8290 // query_nodes.add( new PhylogenyNode( "B" ) );
8291 // query_nodes.add( new PhylogenyNode( "C" ) );
8292 // query_nodes.add( new PhylogenyNode( "D" ) );
8293 // query_nodes.add( new PhylogenyNode( "E" ) );
8294 // query_nodes.add( new PhylogenyNode( "F" ) );
8295 // query_nodes.add( new PhylogenyNode( "G" ) );
8296 // if ( !s0.match( query_nodes ) ) {
8299 // query_nodes = new HashSet<PhylogenyNode>();
8300 // query_nodes.add( new PhylogenyNode( "X" ) );
8301 // query_nodes.add( new PhylogenyNode( "Y" ) );
8302 // query_nodes.add( new PhylogenyNode( "A" ) );
8303 // query_nodes.add( new PhylogenyNode( "B" ) );
8304 // query_nodes.add( new PhylogenyNode( "C" ) );
8305 // if ( !s0.match( query_nodes ) ) {
8309 // query_nodes = new HashSet<PhylogenyNode>();
8310 // query_nodes.add( new PhylogenyNode( "X" ) );
8311 // query_nodes.add( new PhylogenyNode( "Y" ) );
8312 // query_nodes.add( new PhylogenyNode( "D" ) );
8313 // query_nodes.add( new PhylogenyNode( "E" ) );
8314 // query_nodes.add( new PhylogenyNode( "F" ) );
8315 // query_nodes.add( new PhylogenyNode( "G" ) );
8316 // if ( !s0.match( query_nodes ) ) {
8320 // query_nodes = new HashSet<PhylogenyNode>();
8321 // query_nodes.add( new PhylogenyNode( "X" ) );
8322 // query_nodes.add( new PhylogenyNode( "Y" ) );
8323 // query_nodes.add( new PhylogenyNode( "A" ) );
8324 // query_nodes.add( new PhylogenyNode( "B" ) );
8325 // query_nodes.add( new PhylogenyNode( "C" ) );
8326 // query_nodes.add( new PhylogenyNode( "D" ) );
8327 // if ( !s0.match( query_nodes ) ) {
8331 // query_nodes = new HashSet<PhylogenyNode>();
8332 // query_nodes.add( new PhylogenyNode( "X" ) );
8333 // query_nodes.add( new PhylogenyNode( "Y" ) );
8334 // query_nodes.add( new PhylogenyNode( "E" ) );
8335 // query_nodes.add( new PhylogenyNode( "F" ) );
8336 // query_nodes.add( new PhylogenyNode( "G" ) );
8337 // if ( !s0.match( query_nodes ) ) {
8341 // query_nodes = new HashSet<PhylogenyNode>();
8342 // query_nodes.add( new PhylogenyNode( "X" ) );
8343 // query_nodes.add( new PhylogenyNode( "Y" ) );
8344 // query_nodes.add( new PhylogenyNode( "F" ) );
8345 // query_nodes.add( new PhylogenyNode( "G" ) );
8346 // if ( !s0.match( query_nodes ) ) {
8350 query_nodes = new HashSet<PhylogenyNode>();
8351 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8352 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8353 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8354 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8355 if ( s0.match( query_nodes ) ) {
8359 query_nodes = new HashSet<PhylogenyNode>();
8360 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8361 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8362 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8363 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8364 if ( s0.match( query_nodes ) ) {
8367 ///////////////////////////
8369 query_nodes = new HashSet<PhylogenyNode>();
8370 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8374 if ( s0.match( query_nodes ) ) {
8378 query_nodes = new HashSet<PhylogenyNode>();
8379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8380 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8383 if ( s0.match( query_nodes ) ) {
8387 query_nodes = new HashSet<PhylogenyNode>();
8388 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8389 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8391 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8392 if ( s0.match( query_nodes ) ) {
8396 query_nodes = new HashSet<PhylogenyNode>();
8397 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8398 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8400 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8401 if ( s0.match( query_nodes ) ) {
8405 query_nodes = new HashSet<PhylogenyNode>();
8406 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8407 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8408 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8409 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8410 if ( s0.match( query_nodes ) ) {
8414 query_nodes = new HashSet<PhylogenyNode>();
8415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8416 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8417 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8418 if ( s0.match( query_nodes ) ) {
8422 query_nodes = new HashSet<PhylogenyNode>();
8423 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8424 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8425 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8426 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8427 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8428 if ( s0.match( query_nodes ) ) {
8432 query_nodes = new HashSet<PhylogenyNode>();
8433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8434 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8435 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8436 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8437 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8438 if ( s0.match( query_nodes ) ) {
8442 query_nodes = new HashSet<PhylogenyNode>();
8443 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8444 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8445 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8446 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8448 if ( s0.match( query_nodes ) ) {
8452 query_nodes = new HashSet<PhylogenyNode>();
8453 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8454 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8455 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8456 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8457 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8458 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8459 if ( s0.match( query_nodes ) ) {
8463 catch ( final Exception e ) {
8464 e.printStackTrace();
8470 private static boolean testSplitStrict() {
8472 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8473 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
8474 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
8475 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8476 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8477 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8478 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8479 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8480 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8481 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8482 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
8483 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
8484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8485 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8486 if ( s0.match( query_nodes ) ) {
8489 query_nodes = new HashSet<PhylogenyNode>();
8490 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8491 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8494 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8495 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8496 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8497 if ( !s0.match( query_nodes ) ) {
8501 query_nodes = new HashSet<PhylogenyNode>();
8502 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8503 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8504 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8505 if ( !s0.match( query_nodes ) ) {
8509 query_nodes = new HashSet<PhylogenyNode>();
8510 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8511 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8512 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8513 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8514 if ( !s0.match( query_nodes ) ) {
8518 query_nodes = new HashSet<PhylogenyNode>();
8519 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8520 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8523 if ( !s0.match( query_nodes ) ) {
8527 query_nodes = new HashSet<PhylogenyNode>();
8528 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8529 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8531 if ( !s0.match( query_nodes ) ) {
8535 query_nodes = new HashSet<PhylogenyNode>();
8536 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8537 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8538 if ( !s0.match( query_nodes ) ) {
8542 query_nodes = new HashSet<PhylogenyNode>();
8543 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8544 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8545 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8548 if ( !s0.match( query_nodes ) ) {
8552 query_nodes = new HashSet<PhylogenyNode>();
8553 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8554 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8556 if ( !s0.match( query_nodes ) ) {
8560 query_nodes = new HashSet<PhylogenyNode>();
8561 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8562 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8563 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8564 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8565 if ( !s0.match( query_nodes ) ) {
8569 query_nodes = new HashSet<PhylogenyNode>();
8570 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8571 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8572 if ( s0.match( query_nodes ) ) {
8576 query_nodes = new HashSet<PhylogenyNode>();
8577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8581 if ( s0.match( query_nodes ) ) {
8585 query_nodes = new HashSet<PhylogenyNode>();
8586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8591 if ( s0.match( query_nodes ) ) {
8595 query_nodes = new HashSet<PhylogenyNode>();
8596 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8599 if ( s0.match( query_nodes ) ) {
8603 query_nodes = new HashSet<PhylogenyNode>();
8604 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8606 if ( s0.match( query_nodes ) ) {
8610 query_nodes = new HashSet<PhylogenyNode>();
8611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8612 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8613 if ( s0.match( query_nodes ) ) {
8617 query_nodes = new HashSet<PhylogenyNode>();
8618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8620 if ( s0.match( query_nodes ) ) {
8624 query_nodes = new HashSet<PhylogenyNode>();
8625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8627 if ( s0.match( query_nodes ) ) {
8631 query_nodes = new HashSet<PhylogenyNode>();
8632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8634 if ( s0.match( query_nodes ) ) {
8638 query_nodes = new HashSet<PhylogenyNode>();
8639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8641 if ( s0.match( query_nodes ) ) {
8645 query_nodes = new HashSet<PhylogenyNode>();
8646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8649 if ( s0.match( query_nodes ) ) {
8653 query_nodes = new HashSet<PhylogenyNode>();
8654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8657 if ( s0.match( query_nodes ) ) {
8661 query_nodes = new HashSet<PhylogenyNode>();
8662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8665 if ( s0.match( query_nodes ) ) {
8669 query_nodes = new HashSet<PhylogenyNode>();
8670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8674 if ( s0.match( query_nodes ) ) {
8678 catch ( final Exception e ) {
8679 e.printStackTrace();
8685 private static boolean testSubtreeDeletion() {
8687 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8688 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8689 t1.deleteSubtree( t1.getNode( "A" ), false );
8690 if ( t1.getNumberOfExternalNodes() != 5 ) {
8693 t1.toNewHampshireX();
8694 t1.deleteSubtree( t1.getNode( "E" ), false );
8695 if ( t1.getNumberOfExternalNodes() != 4 ) {
8698 t1.toNewHampshireX();
8699 t1.deleteSubtree( t1.getNode( "F" ), false );
8700 if ( t1.getNumberOfExternalNodes() != 3 ) {
8703 t1.toNewHampshireX();
8704 t1.deleteSubtree( t1.getNode( "D" ), false );
8705 t1.toNewHampshireX();
8706 if ( t1.getNumberOfExternalNodes() != 3 ) {
8709 t1.deleteSubtree( t1.getNode( "def" ), false );
8710 t1.toNewHampshireX();
8711 if ( t1.getNumberOfExternalNodes() != 2 ) {
8714 t1.deleteSubtree( t1.getNode( "B" ), false );
8715 t1.toNewHampshireX();
8716 if ( t1.getNumberOfExternalNodes() != 1 ) {
8719 t1.deleteSubtree( t1.getNode( "C" ), false );
8720 t1.toNewHampshireX();
8721 if ( t1.getNumberOfExternalNodes() != 1 ) {
8724 t1.deleteSubtree( t1.getNode( "abc" ), false );
8725 t1.toNewHampshireX();
8726 if ( t1.getNumberOfExternalNodes() != 1 ) {
8729 t1.deleteSubtree( t1.getNode( "r" ), false );
8730 if ( t1.getNumberOfExternalNodes() != 0 ) {
8733 if ( !t1.isEmpty() ) {
8736 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8737 t2.deleteSubtree( t2.getNode( "A" ), false );
8738 t2.toNewHampshireX();
8739 if ( t2.getNumberOfExternalNodes() != 5 ) {
8742 t2.deleteSubtree( t2.getNode( "abc" ), false );
8743 t2.toNewHampshireX();
8744 if ( t2.getNumberOfExternalNodes() != 3 ) {
8747 t2.deleteSubtree( t2.getNode( "def" ), false );
8748 t2.toNewHampshireX();
8749 if ( t2.getNumberOfExternalNodes() != 1 ) {
8753 catch ( final Exception e ) {
8754 e.printStackTrace( System.out );
8760 private static boolean testSupportCount() {
8762 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8763 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
8764 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
8765 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
8766 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
8767 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
8768 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
8770 SupportCount.count( t0_1, phylogenies_1, true, false );
8771 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
8772 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
8773 + "(((((A,B),C),D),E),((F,G),X))"
8774 + "(((((A,Y),B),C),D),((F,G),E))"
8775 + "(((((A,B),C),D),E),(F,G))"
8776 + "(((((A,B),C),D),E),(F,G))"
8777 + "(((((A,B),C),D),E),(F,G))"
8778 + "(((((A,B),C),D),E),(F,G),Z)"
8779 + "(((((A,B),C),D),E),(F,G))"
8780 + "((((((A,B),C),D),E),F),G)"
8781 + "(((((X,Y),F,G),E),((A,B),C)),D)",
8783 SupportCount.count( t0_2, phylogenies_2, true, false );
8784 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
8785 while ( it.hasNext() ) {
8786 final PhylogenyNode n = it.next();
8787 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
8791 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
8792 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
8793 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
8794 SupportCount.count( t0_3, phylogenies_3, true, false );
8795 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
8796 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
8799 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
8802 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
8805 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
8808 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
8811 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
8814 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
8817 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
8820 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
8823 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
8826 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8827 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
8828 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
8829 SupportCount.count( t0_4, phylogenies_4, true, false );
8830 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
8831 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
8834 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
8837 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
8840 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
8843 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
8846 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
8849 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
8852 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
8855 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
8858 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
8861 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8862 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8863 double d = SupportCount.compare( b1, a, true, true, true );
8864 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
8867 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8868 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8869 d = SupportCount.compare( b2, a, true, true, true );
8870 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
8873 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8874 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
8875 d = SupportCount.compare( b3, a, true, true, true );
8876 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
8879 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
8880 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
8881 d = SupportCount.compare( b4, a, true, true, false );
8882 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
8886 catch ( final Exception e ) {
8887 e.printStackTrace( System.out );
8893 private static boolean testSupportTransfer() {
8895 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8896 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)",
8897 new NHXParser() )[ 0 ];
8898 final Phylogeny p2 = factory
8899 .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 ];
8900 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8903 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8906 support_transfer.moveBranchLengthsToBootstrap( p1 );
8907 support_transfer.transferSupportValues( p1, p2 );
8908 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8911 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8914 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8917 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8920 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
8923 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
8926 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
8929 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
8933 catch ( final Exception e ) {
8934 e.printStackTrace( System.out );
8940 private static boolean testUniprotTaxonomySearch() {
8942 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
8944 if ( results.size() != 1 ) {
8947 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8950 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8953 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8956 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8959 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8963 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
8964 if ( results.size() != 1 ) {
8967 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8970 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8973 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8976 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8979 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8983 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
8984 if ( results.size() != 1 ) {
8987 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8990 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8993 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8996 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8999 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9003 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
9004 if ( results.size() != 1 ) {
9007 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
9010 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
9013 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
9016 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9019 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9022 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
9025 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
9028 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
9029 .equals( "Nematostella vectensis" ) ) {
9030 System.out.println( results.get( 0 ).getLineage() );
9034 catch ( final IOException e ) {
9035 System.out.println();
9036 System.out.println( "the following might be due to absence internet connection:" );
9037 e.printStackTrace( System.out );
9040 catch ( final Exception e ) {
9046 private static boolean testEmblEntryRetrieval() {
9047 //The format for GenBank Accession numbers are:
9048 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
9049 //Protein: 3 letters + 5 numerals
9050 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
9051 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
9054 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
9057 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
9060 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
9063 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
9066 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
9069 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
9072 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
9075 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
9078 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
9081 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
9084 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
9087 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
9093 private static boolean testUniprotEntryRetrieval() {
9094 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
9097 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
9100 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
9103 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
9106 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
9109 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
9112 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
9115 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
9118 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
9121 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
9124 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
9127 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
9130 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
9134 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
9135 if ( !entry.getAccession().equals( "P12345" ) ) {
9138 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
9141 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
9144 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
9147 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
9151 catch ( final IOException e ) {
9152 System.out.println();
9153 System.out.println( "the following might be due to absence internet connection:" );
9154 e.printStackTrace( System.out );
9157 catch ( final Exception e ) {
9163 private static boolean testWabiTxSearch() {
9166 result = TxSearch.searchSimple( "nematostella" );
9167 result = TxSearch.getTxId( "nematostella" );
9168 if ( !result.equals( "45350" ) ) {
9171 result = TxSearch.getTxName( "45350" );
9172 if ( !result.equals( "Nematostella" ) ) {
9175 result = TxSearch.getTxId( "nematostella vectensis" );
9176 if ( !result.equals( "45351" ) ) {
9179 result = TxSearch.getTxName( "45351" );
9180 if ( !result.equals( "Nematostella vectensis" ) ) {
9183 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
9184 if ( !result.equals( "536089" ) ) {
9187 result = TxSearch.getTxName( "536089" );
9188 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
9191 final List<String> queries = new ArrayList<String>();
9192 queries.add( "Campylobacter coli" );
9193 queries.add( "Escherichia coli" );
9194 queries.add( "Arabidopsis" );
9195 queries.add( "Trichoplax" );
9196 queries.add( "Samanea saman" );
9197 queries.add( "Kluyveromyces marxianus" );
9198 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
9199 queries.add( "Bornavirus parrot/PDD/2008" );
9200 final List<RANKS> ranks = new ArrayList<RANKS>();
9201 ranks.add( RANKS.SUPERKINGDOM );
9202 ranks.add( RANKS.KINGDOM );
9203 ranks.add( RANKS.FAMILY );
9204 ranks.add( RANKS.GENUS );
9205 ranks.add( RANKS.TRIBE );
9206 result = TxSearch.searchLineage( queries, ranks );
9207 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
9208 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
9210 catch ( final Exception e ) {
9211 System.out.println();
9212 System.out.println( "the following might be due to absence internet connection:" );
9213 e.printStackTrace( System.out );
9219 private static boolean testAminoAcidSequence() {
9221 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
9222 if ( aa1.getLength() != 13 ) {
9225 if ( aa1.getResidueAt( 0 ) != 'A' ) {
9228 if ( aa1.getResidueAt( 2 ) != 'K' ) {
9231 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
9234 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
9235 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
9238 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
9239 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
9242 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
9243 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
9247 catch ( final Exception e ) {
9248 e.printStackTrace();
9254 private static boolean testCreateBalancedPhylogeny() {
9256 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
9257 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
9260 if ( p0.getNumberOfExternalNodes() != 15625 ) {
9263 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
9264 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
9267 if ( p1.getNumberOfExternalNodes() != 100 ) {
9271 catch ( final Exception e ) {
9272 e.printStackTrace();
9278 private static boolean testFastaParser() {
9280 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
9283 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
9286 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
9287 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
9290 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
9293 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
9296 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
9299 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
9302 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
9306 catch ( final Exception e ) {
9307 e.printStackTrace();
9313 private static boolean testGeneralMsaParser() {
9315 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
9316 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
9317 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
9318 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
9319 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
9320 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
9321 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
9322 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
9323 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9326 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9329 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9332 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9335 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9338 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9341 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9344 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9347 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9350 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9353 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9356 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9359 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
9360 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
9363 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
9366 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
9369 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
9370 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
9373 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
9376 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
9379 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
9380 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
9383 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
9386 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
9390 catch ( final Exception e ) {
9391 e.printStackTrace();
9397 private static boolean testMafft( final String path ) {
9399 final List<String> opts = new ArrayList<String>();
9400 opts.add( "--maxiterate" );
9402 opts.add( "--localpair" );
9403 opts.add( "--quiet" );
9405 final MsaInferrer mafft = Mafft.createInstance( path );
9406 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
9407 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
9410 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
9414 catch ( final Exception e ) {
9415 e.printStackTrace( System.out );
9421 private static boolean testNextNodeWithCollapsing() {
9423 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9425 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
9426 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9427 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
9428 t0.getNode( "cd" ).setCollapse( true );
9429 t0.getNode( "cde" ).setCollapse( true );
9430 n = t0.getFirstExternalNode();
9431 while ( n != null ) {
9433 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9435 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9438 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9441 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
9444 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
9447 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
9450 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
9454 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9455 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
9456 t1.getNode( "ab" ).setCollapse( true );
9457 t1.getNode( "cd" ).setCollapse( true );
9458 t1.getNode( "cde" ).setCollapse( true );
9459 n = t1.getNode( "ab" );
9460 ext = new ArrayList<PhylogenyNode>();
9461 while ( n != null ) {
9463 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9465 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9468 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9471 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
9474 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
9477 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
9483 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9484 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
9485 t2.getNode( "ab" ).setCollapse( true );
9486 t2.getNode( "cd" ).setCollapse( true );
9487 t2.getNode( "cde" ).setCollapse( true );
9488 t2.getNode( "c" ).setCollapse( true );
9489 t2.getNode( "d" ).setCollapse( true );
9490 t2.getNode( "e" ).setCollapse( true );
9491 t2.getNode( "gh" ).setCollapse( true );
9492 n = t2.getNode( "ab" );
9493 ext = new ArrayList<PhylogenyNode>();
9494 while ( n != null ) {
9496 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9498 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9501 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9504 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
9507 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
9513 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9514 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
9515 t3.getNode( "ab" ).setCollapse( true );
9516 t3.getNode( "cd" ).setCollapse( true );
9517 t3.getNode( "cde" ).setCollapse( true );
9518 t3.getNode( "c" ).setCollapse( true );
9519 t3.getNode( "d" ).setCollapse( true );
9520 t3.getNode( "e" ).setCollapse( true );
9521 t3.getNode( "gh" ).setCollapse( true );
9522 t3.getNode( "fgh" ).setCollapse( true );
9523 n = t3.getNode( "ab" );
9524 ext = new ArrayList<PhylogenyNode>();
9525 while ( n != null ) {
9527 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9529 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9532 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9535 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
9541 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9542 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
9543 t4.getNode( "ab" ).setCollapse( true );
9544 t4.getNode( "cd" ).setCollapse( true );
9545 t4.getNode( "cde" ).setCollapse( true );
9546 t4.getNode( "c" ).setCollapse( true );
9547 t4.getNode( "d" ).setCollapse( true );
9548 t4.getNode( "e" ).setCollapse( true );
9549 t4.getNode( "gh" ).setCollapse( true );
9550 t4.getNode( "fgh" ).setCollapse( true );
9551 t4.getNode( "abcdefgh" ).setCollapse( true );
9552 n = t4.getNode( "abcdefgh" );
9553 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
9558 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9559 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
9561 n = t5.getFirstExternalNode();
9562 while ( n != null ) {
9564 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9566 if ( ext.size() != 8 ) {
9569 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9572 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9575 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9578 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9581 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9584 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9587 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
9590 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
9595 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9596 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
9598 t6.getNode( "ab" ).setCollapse( true );
9599 n = t6.getNode( "ab" );
9600 while ( n != null ) {
9602 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9604 if ( ext.size() != 7 ) {
9607 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9610 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9613 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9616 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9619 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9622 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9625 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9630 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9631 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
9633 t7.getNode( "cd" ).setCollapse( true );
9634 n = t7.getNode( "a" );
9635 while ( n != null ) {
9637 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9639 if ( ext.size() != 7 ) {
9642 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9645 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9648 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9651 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9654 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9657 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9660 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9665 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9666 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
9668 t8.getNode( "cd" ).setCollapse( true );
9669 t8.getNode( "c" ).setCollapse( true );
9670 t8.getNode( "d" ).setCollapse( true );
9671 n = t8.getNode( "a" );
9672 while ( n != null ) {
9674 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9676 if ( ext.size() != 7 ) {
9679 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9682 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9685 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9686 System.out.println( "2 fail" );
9689 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9692 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9695 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9698 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9703 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9704 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
9706 t9.getNode( "gh" ).setCollapse( true );
9707 n = t9.getNode( "a" );
9708 while ( n != null ) {
9710 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9712 if ( ext.size() != 7 ) {
9715 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9718 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9721 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9724 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9727 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9730 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9733 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9738 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9739 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
9741 t10.getNode( "gh" ).setCollapse( true );
9742 t10.getNode( "g" ).setCollapse( true );
9743 t10.getNode( "h" ).setCollapse( true );
9744 n = t10.getNode( "a" );
9745 while ( n != null ) {
9747 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9749 if ( ext.size() != 7 ) {
9752 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9755 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9758 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9761 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9764 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9767 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9770 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9775 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9776 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
9778 t11.getNode( "gh" ).setCollapse( true );
9779 t11.getNode( "fgh" ).setCollapse( true );
9780 n = t11.getNode( "a" );
9781 while ( n != null ) {
9783 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9785 if ( ext.size() != 6 ) {
9788 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9791 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9794 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9797 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9800 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9803 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9808 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9809 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
9811 t12.getNode( "gh" ).setCollapse( true );
9812 t12.getNode( "fgh" ).setCollapse( true );
9813 t12.getNode( "g" ).setCollapse( true );
9814 t12.getNode( "h" ).setCollapse( true );
9815 t12.getNode( "f" ).setCollapse( true );
9816 n = t12.getNode( "a" );
9817 while ( n != null ) {
9819 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9821 if ( ext.size() != 6 ) {
9824 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9827 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9830 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9833 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9836 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9839 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9844 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9845 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
9847 t13.getNode( "ab" ).setCollapse( true );
9848 t13.getNode( "b" ).setCollapse( true );
9849 t13.getNode( "fgh" ).setCollapse( true );
9850 t13.getNode( "gh" ).setCollapse( true );
9851 n = t13.getNode( "ab" );
9852 while ( n != null ) {
9854 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9856 if ( ext.size() != 5 ) {
9859 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9862 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9865 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9868 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9871 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9876 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
9877 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
9879 t14.getNode( "ab" ).setCollapse( true );
9880 t14.getNode( "a" ).setCollapse( true );
9881 t14.getNode( "fgh" ).setCollapse( true );
9882 t14.getNode( "gh" ).setCollapse( true );
9883 n = t14.getNode( "ab" );
9884 while ( n != null ) {
9886 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9888 if ( ext.size() != 5 ) {
9891 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9894 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9897 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9900 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9903 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9908 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" );
9909 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9911 t15.getNode( "ab" ).setCollapse( true );
9912 t15.getNode( "a" ).setCollapse( true );
9913 t15.getNode( "fgh" ).setCollapse( true );
9914 t15.getNode( "gh" ).setCollapse( true );
9915 n = t15.getNode( "ab" );
9916 while ( n != null ) {
9918 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9920 if ( ext.size() != 6 ) {
9923 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9926 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9929 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9932 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9935 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
9938 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9943 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" );
9944 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
9946 t16.getNode( "ab" ).setCollapse( true );
9947 t16.getNode( "a" ).setCollapse( true );
9948 t16.getNode( "fgh" ).setCollapse( true );
9949 t16.getNode( "gh" ).setCollapse( true );
9950 t16.getNode( "cd" ).setCollapse( true );
9951 t16.getNode( "cde" ).setCollapse( true );
9952 t16.getNode( "d" ).setCollapse( true );
9953 t16.getNode( "x" ).setCollapse( true );
9954 n = t16.getNode( "ab" );
9955 while ( n != null ) {
9957 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9959 if ( ext.size() != 4 ) {
9962 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9965 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9968 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
9971 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
9975 catch ( final Exception e ) {
9976 e.printStackTrace( System.out );
9982 private static boolean testMsaQualityMethod() {
9984 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
9985 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
9986 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
9987 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
9988 final List<Sequence> l = new ArrayList<Sequence>();
9993 final Msa msa = BasicMsa.createInstance( l );
9994 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
9997 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
10000 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
10003 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
10007 catch ( final Exception e ) {
10008 e.printStackTrace( System.out );
10014 private static boolean testSequenceIdParsing() {
10016 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
10017 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10018 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10019 if ( id != null ) {
10020 System.out.println( "value =" + id.getValue() );
10021 System.out.println( "provider=" + id.getProvider() );
10026 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
10027 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10028 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10029 if ( id != null ) {
10030 System.out.println( "value =" + id.getValue() );
10031 System.out.println( "provider=" + id.getProvider() );
10036 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
10037 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10038 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10039 if ( id != null ) {
10040 System.out.println( "value =" + id.getValue() );
10041 System.out.println( "provider=" + id.getProvider() );
10046 id = SequenceIdParser.parse( "gb_AAA96518_1" );
10047 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10048 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
10049 if ( id != null ) {
10050 System.out.println( "value =" + id.getValue() );
10051 System.out.println( "provider=" + id.getProvider() );
10056 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
10057 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10058 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
10059 if ( id != null ) {
10060 System.out.println( "value =" + id.getValue() );
10061 System.out.println( "provider=" + id.getProvider() );
10066 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
10067 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10068 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
10069 if ( id != null ) {
10070 System.out.println( "value =" + id.getValue() );
10071 System.out.println( "provider=" + id.getProvider() );
10076 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
10077 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10078 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
10079 if ( id != null ) {
10080 System.out.println( "value =" + id.getValue() );
10081 System.out.println( "provider=" + id.getProvider() );
10086 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
10087 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10088 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
10089 if ( id != null ) {
10090 System.out.println( "value =" + id.getValue() );
10091 System.out.println( "provider=" + id.getProvider() );
10096 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
10097 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10098 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
10099 if ( id != null ) {
10100 System.out.println( "value =" + id.getValue() );
10101 System.out.println( "provider=" + id.getProvider() );
10106 id = SequenceIdParser.parse( "P4A123" );
10107 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10108 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
10109 if ( id != null ) {
10110 System.out.println( "value =" + id.getValue() );
10111 System.out.println( "provider=" + id.getProvider() );
10116 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
10117 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10118 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
10119 if ( id != null ) {
10120 System.out.println( "value =" + id.getValue() );
10121 System.out.println( "provider=" + id.getProvider() );
10126 id = SequenceIdParser.parse( "XP_12345" );
10127 if ( id != null ) {
10128 System.out.println( "value =" + id.getValue() );
10129 System.out.println( "provider=" + id.getProvider() );
10132 // lcl_91970_unknown_
10134 catch ( final Exception e ) {
10135 e.printStackTrace( System.out );