2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.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( "NH parsing: " );
229 if ( Test.testNHParsing() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "Conversion to NHX (node level): " );
238 if ( Test.testNHXconversion() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "NHX parsing: " );
247 if ( Test.testNHXParsing() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "NHX parsing with quotes: " );
256 if ( Test.testNHXParsingQuotes() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "NHX parsing (MrBayes): " );
265 if ( Test.testNHXParsingMB() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "Nexus characters parsing: " );
274 if ( Test.testNexusCharactersParsing() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Nexus tree parsing: " );
283 if ( Test.testNexusTreeParsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Nexus tree parsing (translating): " );
292 if ( Test.testNexusTreeParsingTranslating() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Nexus matrix parsing: " );
301 if ( Test.testNexusMatrixParsing() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "Basic phyloXML parsing: " );
310 if ( Test.testBasicPhyloXMLparsing() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "Basic phyloXML parsing (validating against schema): " );
319 if ( testBasicPhyloXMLparsingValidating() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
328 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "phyloXML Distribution Element: " );
337 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "Tol XML parsing: " );
346 if ( Test.testBasicTolXMLparsing() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "Copying of node data: " );
355 if ( Test.testCopyOfNodeData() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Basic tree methods: " );
364 if ( Test.testBasicTreeMethods() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Postorder Iterator: " );
373 if ( Test.testPostOrderIterator() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Preorder Iterator: " );
382 if ( Test.testPreOrderIterator() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Levelorder Iterator: " );
391 if ( Test.testLevelOrderIterator() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Re-id methods: " );
400 if ( Test.testReIdMethods() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Methods on last external nodes: " );
409 if ( Test.testLastExternalNodeMethods() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Methods on external nodes: " );
418 if ( Test.testExternalNodeRelatedMethods() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Deletion of external nodes: " );
427 if ( Test.testDeletionOfExternalNodes() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Subtree deletion: " );
436 if ( Test.testSubtreeDeletion() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Phylogeny branch: " );
445 if ( Test.testPhylogenyBranch() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Rerooting: " );
454 if ( Test.testRerooting() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Mipoint rooting: " );
463 if ( Test.testMidpointrooting() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Node removal: " );
472 if ( Test.testNodeRemoval() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "Support count: " );
481 if ( Test.testSupportCount() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "Support transfer: " );
490 if ( Test.testSupportTransfer() ) {
491 System.out.println( "OK." );
495 System.out.println( "failed." );
498 System.out.print( "Finding of LCA: " );
499 if ( Test.testGetLCA() ) {
500 System.out.println( "OK." );
504 System.out.println( "failed." );
507 System.out.print( "Finding of LCA 2: " );
508 if ( Test.testGetLCA2() ) {
509 System.out.println( "OK." );
513 System.out.println( "failed." );
516 System.out.print( "Calculation of distance between nodes: " );
517 if ( Test.testGetDistance() ) {
518 System.out.println( "OK." );
522 System.out.println( "failed." );
525 System.out.print( "Descriptive statistics: " );
526 if ( Test.testDescriptiveStatistics() ) {
527 System.out.println( "OK." );
531 System.out.println( "failed." );
534 System.out.print( "Data objects and methods: " );
535 if ( Test.testDataObjects() ) {
536 System.out.println( "OK." );
540 System.out.println( "failed." );
543 System.out.print( "Properties map: " );
544 if ( Test.testPropertiesMap() ) {
545 System.out.println( "OK." );
549 System.out.println( "failed." );
552 System.out.print( "SDIse: " );
553 if ( Test.testSDIse() ) {
554 System.out.println( "OK." );
558 System.out.println( "failed." );
561 System.out.print( "SDIunrooted: " );
562 if ( Test.testSDIunrooted() ) {
563 System.out.println( "OK." );
567 System.out.println( "failed." );
570 System.out.print( "GSDI: " );
571 if ( TestGSDI.test() ) {
572 System.out.println( "OK." );
576 System.out.println( "failed." );
579 System.out.print( "RIO: " );
580 if ( TestRIO.test() ) {
581 System.out.println( "OK." );
585 System.out.println( "failed." );
588 System.out.print( "Phylogeny reconstruction:" );
589 System.out.println();
590 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Analysis of domain architectures: " );
599 System.out.println();
600 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
601 System.out.println( "OK." );
605 System.out.println( "failed." );
608 System.out.print( "GO: " );
609 System.out.println();
610 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
611 System.out.println( "OK." );
615 System.out.println( "failed." );
618 System.out.print( "Modeling tools: " );
619 if ( TestPccx.test() ) {
620 System.out.println( "OK." );
624 System.out.println( "failed." );
627 System.out.print( "Split Matrix strict: " );
628 if ( Test.testSplitStrict() ) {
629 System.out.println( "OK." );
633 System.out.println( "failed." );
636 System.out.print( "Split Matrix: " );
637 if ( Test.testSplit() ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "Confidence Assessor: " );
646 if ( Test.testConfidenceAssessor() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "Basic table: " );
655 if ( Test.testBasicTable() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "General table: " );
664 if ( Test.testGeneralTable() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "Amino acid sequence: " );
673 if ( Test.testAminoAcidSequence() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "General MSA parser: " );
682 if ( Test.testGeneralMsaParser() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
690 System.out.print( "Fasta parser for msa: " );
691 if ( Test.testFastaParser() ) {
692 System.out.println( "OK." );
696 System.out.println( "failed." );
699 System.out.print( "Creation of balanced phylogeny: " );
700 if ( Test.testCreateBalancedPhylogeny() ) {
701 System.out.println( "OK." );
705 System.out.println( "failed." );
708 System.out.print( "EMBL Entry Retrieval: " );
709 if ( Test.testEmblEntryRetrieval() ) {
710 System.out.println( "OK." );
714 System.out.println( "failed." );
717 System.out.print( "Uniprot Entry Retrieval: " );
718 if ( Test.testUniprotEntryRetrieval() ) {
719 System.out.println( "OK." );
723 System.out.println( "failed." );
726 System.out.print( "Uniprot Taxonomy Search: " );
727 if ( Test.testUniprotTaxonomySearch() ) {
728 System.out.println( "OK." );
732 System.out.println( "failed." );
737 final String os = ForesterUtil.OS_NAME.toLowerCase();
738 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
739 path = "/usr/local/bin/mafft";
741 else if ( os.indexOf( "win" ) >= 0 ) {
742 path = "C:\\Program Files\\mafft-win\\mafft.bat";
745 path = "/home/czmasek/bin/mafft";
747 if ( !MsaInferrer.isInstalled( path ) ) {
750 if ( !MsaInferrer.isInstalled( path ) ) {
751 path = "/usr/local/bin/mafft";
753 if ( MsaInferrer.isInstalled( path ) ) {
754 System.out.print( "MAFFT (external program): " );
755 if ( Test.testMafft( path ) ) {
756 System.out.println( "OK." );
760 System.out.println( "failed [will not count towards failed tests]" );
764 System.out.print( "Next nodes with collapsed: " );
765 if ( Test.testNextNodeWithCollapsing() ) {
766 System.out.println( "OK." );
770 System.out.println( "failed." );
773 System.out.print( "Simple MSA quality: " );
774 if ( Test.testMsaQualityMethod() ) {
775 System.out.println( "OK." );
779 System.out.println( "failed." );
782 System.out.println();
783 final Runtime rt = java.lang.Runtime.getRuntime();
784 final long free_memory = rt.freeMemory() / 1000000;
785 final long total_memory = rt.totalMemory() / 1000000;
786 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
787 + free_memory + "MB, total memory: " + total_memory + "MB)" );
788 System.out.println();
789 System.out.println( "Successful tests: " + succeeded );
790 System.out.println( "Failed tests: " + failed );
791 System.out.println();
793 System.out.println( "OK." );
796 System.out.println( "Not OK." );
800 private static boolean testExtractTaxonomyCodeFromNodeName() {
802 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
805 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
808 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
811 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
812 .equals( "MOUSE" ) ) {
815 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
816 .equals( "MOUSE" ) ) {
819 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
820 .equals( "MOUSE" ) ) {
823 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
826 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
829 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
833 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
837 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
841 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
844 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
847 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
850 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
854 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
855 .equals( "MOUSE" ) ) {
858 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
859 .equals( "MOUSE" ) ) {
863 catch ( final Exception e ) {
864 e.printStackTrace( System.out );
870 private static boolean testBasicNodeMethods() {
872 if ( PhylogenyNode.getNodeCount() != 0 ) {
875 final PhylogenyNode n1 = new PhylogenyNode();
876 final PhylogenyNode n2 = PhylogenyNode
877 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
878 final PhylogenyNode n3 = PhylogenyNode
879 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
880 final PhylogenyNode n4 = PhylogenyNode
881 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
882 if ( n1.isHasAssignedEvent() ) {
885 if ( PhylogenyNode.getNodeCount() != 4 ) {
888 if ( n3.getIndicator() != 0 ) {
891 if ( n3.getNumberOfExternalNodes() != 1 ) {
894 if ( !n3.isExternal() ) {
897 if ( !n3.isRoot() ) {
900 if ( !n4.getName().equals( "n4" ) ) {
904 catch ( final Exception e ) {
905 e.printStackTrace( System.out );
911 private static boolean testBasicPhyloXMLparsing() {
913 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
914 final PhyloXmlParser xml_parser = new PhyloXmlParser();
915 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
917 if ( xml_parser.getErrorCount() > 0 ) {
918 System.out.println( xml_parser.getErrorMessages().toString() );
921 if ( phylogenies_0.length != 4 ) {
924 final Phylogeny t1 = phylogenies_0[ 0 ];
925 final Phylogeny t2 = phylogenies_0[ 1 ];
926 final Phylogeny t3 = phylogenies_0[ 2 ];
927 final Phylogeny t4 = phylogenies_0[ 3 ];
928 if ( t1.getNumberOfExternalNodes() != 1 ) {
931 if ( !t1.isRooted() ) {
934 if ( t1.isRerootable() ) {
937 if ( !t1.getType().equals( "gene_tree" ) ) {
940 if ( t2.getNumberOfExternalNodes() != 2 ) {
943 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
946 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
949 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
952 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
955 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
958 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
961 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
962 .startsWith( "actgtgggggt" ) ) {
965 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
966 .startsWith( "ctgtgatgcat" ) ) {
969 if ( t3.getNumberOfExternalNodes() != 4 ) {
972 if ( !t1.getName().equals( "t1" ) ) {
975 if ( !t2.getName().equals( "t2" ) ) {
978 if ( !t3.getName().equals( "t3" ) ) {
981 if ( !t4.getName().equals( "t4" ) ) {
984 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
987 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
990 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
993 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
994 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
997 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1000 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1003 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1006 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1007 .equals( "apoptosis" ) ) {
1010 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1011 .equals( "GO:0006915" ) ) {
1014 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1015 .equals( "UniProtKB" ) ) {
1018 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1019 .equals( "experimental" ) ) {
1022 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1023 .equals( "function" ) ) {
1026 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1027 .getValue() != 1 ) {
1030 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1031 .getType().equals( "ml" ) ) {
1034 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1035 .equals( "apoptosis" ) ) {
1038 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1039 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1042 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1043 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1046 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1047 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1050 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1051 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1054 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1055 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1058 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1059 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1062 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1063 .equals( "GO:0005829" ) ) {
1066 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1067 .equals( "intracellular organelle" ) ) {
1070 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1073 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1074 .equals( "UniProt link" ) ) ) {
1077 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1081 catch ( final Exception e ) {
1082 e.printStackTrace( System.out );
1088 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1090 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1091 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1092 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1093 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1096 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1098 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1100 if ( xml_parser.getErrorCount() > 0 ) {
1101 System.out.println( xml_parser.getErrorMessages().toString() );
1104 if ( phylogenies_0.length != 4 ) {
1107 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1108 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1109 if ( phylogenies_t1.length != 1 ) {
1112 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1113 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1116 if ( !t1_rt.isRooted() ) {
1119 if ( t1_rt.isRerootable() ) {
1122 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1125 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1126 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1127 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1128 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1131 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1134 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1137 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1140 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1141 .startsWith( "actgtgggggt" ) ) {
1144 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1145 .startsWith( "ctgtgatgcat" ) ) {
1148 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1149 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1150 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1151 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1152 if ( phylogenies_1.length != 1 ) {
1155 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1156 if ( !t3_rt.getName().equals( "t3" ) ) {
1159 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1162 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1165 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1168 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1171 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1172 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1175 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1178 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1181 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1182 .equals( "UniProtKB" ) ) {
1185 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1186 .equals( "apoptosis" ) ) {
1189 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1190 .equals( "GO:0006915" ) ) {
1193 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1194 .equals( "UniProtKB" ) ) {
1197 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1198 .equals( "experimental" ) ) {
1201 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1202 .equals( "function" ) ) {
1205 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1206 .getValue() != 1 ) {
1209 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1210 .getType().equals( "ml" ) ) {
1213 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1214 .equals( "apoptosis" ) ) {
1217 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1218 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1221 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1222 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1225 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1226 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1229 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1230 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1233 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1234 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1237 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1238 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1241 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1242 .equals( "GO:0005829" ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1246 .equals( "intracellular organelle" ) ) {
1249 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1253 .equals( "UniProt link" ) ) ) {
1256 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1262 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1263 .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." ) ) ) {
1266 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1269 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1272 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1275 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1278 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1279 .equals( "ncbi" ) ) {
1282 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1285 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1286 .getName().equals( "B" ) ) {
1289 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1290 .getFrom() != 21 ) {
1293 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1296 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1297 .getLength() != 24 ) {
1300 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1301 .getConfidence() != 2144 ) {
1304 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1305 .equals( "pfam" ) ) {
1308 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1311 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1314 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1317 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1320 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1321 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1324 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1327 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1330 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1333 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1336 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1339 if ( taxbb.getSynonyms().size() != 2 ) {
1342 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1345 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1348 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1351 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1354 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1357 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1358 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1362 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1365 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1368 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1371 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1374 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1377 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1380 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1384 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1387 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1388 .equalsIgnoreCase( "435" ) ) {
1391 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1394 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1395 .equalsIgnoreCase( "443.7" ) ) {
1398 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1401 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1404 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1405 .equalsIgnoreCase( "433" ) ) {
1409 catch ( final Exception e ) {
1410 e.printStackTrace( System.out );
1416 private static boolean testBasicPhyloXMLparsingValidating() {
1418 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1419 PhyloXmlParser xml_parser = null;
1421 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1423 catch ( final Exception e ) {
1424 // Do nothing -- means were not running from jar.
1426 if ( xml_parser == null ) {
1427 xml_parser = new PhyloXmlParser();
1428 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1429 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1432 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1435 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1437 if ( xml_parser.getErrorCount() > 0 ) {
1438 System.out.println( xml_parser.getErrorMessages().toString() );
1441 if ( phylogenies_0.length != 4 ) {
1444 final Phylogeny t1 = phylogenies_0[ 0 ];
1445 final Phylogeny t2 = phylogenies_0[ 1 ];
1446 final Phylogeny t3 = phylogenies_0[ 2 ];
1447 final Phylogeny t4 = phylogenies_0[ 3 ];
1448 if ( !t1.getName().equals( "t1" ) ) {
1451 if ( !t2.getName().equals( "t2" ) ) {
1454 if ( !t3.getName().equals( "t3" ) ) {
1457 if ( !t4.getName().equals( "t4" ) ) {
1460 if ( t1.getNumberOfExternalNodes() != 1 ) {
1463 if ( t2.getNumberOfExternalNodes() != 2 ) {
1466 if ( t3.getNumberOfExternalNodes() != 4 ) {
1469 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1470 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1471 if ( xml_parser.getErrorCount() > 0 ) {
1472 System.out.println( "errors:" );
1473 System.out.println( xml_parser.getErrorMessages().toString() );
1476 if ( phylogenies_1.length != 4 ) {
1479 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1481 if ( xml_parser.getErrorCount() > 0 ) {
1482 System.out.println( "errors:" );
1483 System.out.println( xml_parser.getErrorMessages().toString() );
1486 if ( phylogenies_2.length != 1 ) {
1489 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1492 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1494 if ( xml_parser.getErrorCount() > 0 ) {
1495 System.out.println( xml_parser.getErrorMessages().toString() );
1498 if ( phylogenies_3.length != 2 ) {
1501 final Phylogeny a = phylogenies_3[ 0 ];
1502 if ( !a.getName().equals( "tree 4" ) ) {
1505 if ( a.getNumberOfExternalNodes() != 3 ) {
1508 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1511 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1514 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1516 if ( xml_parser.getErrorCount() > 0 ) {
1517 System.out.println( xml_parser.getErrorMessages().toString() );
1520 if ( phylogenies_4.length != 1 ) {
1523 final Phylogeny s = phylogenies_4[ 0 ];
1524 if ( s.getNumberOfExternalNodes() != 6 ) {
1527 s.getNode( "first" );
1529 s.getNode( "\"<a'b&c'd\">\"" );
1530 s.getNode( "'''\"" );
1531 s.getNode( "\"\"\"" );
1532 s.getNode( "dick & doof" );
1534 catch ( final Exception e ) {
1535 e.printStackTrace( System.out );
1541 private static boolean testBasicTable() {
1543 final BasicTable<String> t0 = new BasicTable<String>();
1544 if ( t0.getNumberOfColumns() != 0 ) {
1547 if ( t0.getNumberOfRows() != 0 ) {
1550 t0.setValue( 3, 2, "23" );
1551 t0.setValue( 10, 1, "error" );
1552 t0.setValue( 10, 1, "110" );
1553 t0.setValue( 9, 1, "19" );
1554 t0.setValue( 1, 10, "101" );
1555 t0.setValue( 10, 10, "1010" );
1556 t0.setValue( 100, 10, "10100" );
1557 t0.setValue( 0, 0, "00" );
1558 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1561 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1564 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1567 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1570 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1573 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1576 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1579 if ( t0.getNumberOfColumns() != 101 ) {
1582 if ( t0.getNumberOfRows() != 11 ) {
1585 if ( t0.getValueAsString( 49, 4 ) != null ) {
1588 final String l = ForesterUtil.getLineSeparator();
1589 final StringBuffer source = new StringBuffer();
1590 source.append( "" + l );
1591 source.append( "# 1 1 1 1 1 1 1 1" + l );
1592 source.append( " 00 01 02 03" + l );
1593 source.append( " 10 11 12 13 " + l );
1594 source.append( "20 21 22 23 " + l );
1595 source.append( " 30 31 32 33" + l );
1596 source.append( "40 41 42 43" + l );
1597 source.append( " # 1 1 1 1 1 " + l );
1598 source.append( "50 51 52 53 54" + l );
1599 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1600 if ( t1.getNumberOfColumns() != 5 ) {
1603 if ( t1.getNumberOfRows() != 6 ) {
1606 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1609 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1612 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1615 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1618 final StringBuffer source1 = new StringBuffer();
1619 source1.append( "" + l );
1620 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1621 source1.append( " 00; 01 ;02;03" + l );
1622 source1.append( " 10; 11; 12; 13 " + l );
1623 source1.append( "20; 21; 22; 23 " + l );
1624 source1.append( " 30; 31; 32; 33" + l );
1625 source1.append( "40;41;42;43" + l );
1626 source1.append( " # 1 1 1 1 1 " + l );
1627 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1628 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1629 if ( t2.getNumberOfColumns() != 5 ) {
1632 if ( t2.getNumberOfRows() != 6 ) {
1635 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1638 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1641 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1644 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1647 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1650 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1653 final StringBuffer source2 = new StringBuffer();
1654 source2.append( "" + l );
1655 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1656 source2.append( " 00; 01 ;02;03" + l );
1657 source2.append( " 10; 11; 12; 13 " + l );
1658 source2.append( "20; 21; 22; 23 " + l );
1659 source2.append( " " + l );
1660 source2.append( " 30; 31; 32; 33" + l );
1661 source2.append( "40;41;42;43" + l );
1662 source2.append( " comment: 1 1 1 1 1 " + l );
1663 source2.append( ";;;50 ; 52; 53;;54 " + l );
1664 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1670 if ( tl.size() != 2 ) {
1673 final BasicTable<String> t3 = tl.get( 0 );
1674 final BasicTable<String> t4 = tl.get( 1 );
1675 if ( t3.getNumberOfColumns() != 4 ) {
1678 if ( t3.getNumberOfRows() != 3 ) {
1681 if ( t4.getNumberOfColumns() != 4 ) {
1684 if ( t4.getNumberOfRows() != 3 ) {
1687 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1690 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1694 catch ( final Exception e ) {
1695 e.printStackTrace( System.out );
1701 private static boolean testBasicTolXMLparsing() {
1703 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1704 final TolParser parser = new TolParser();
1705 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1706 if ( parser.getErrorCount() > 0 ) {
1707 System.out.println( parser.getErrorMessages().toString() );
1710 if ( phylogenies_0.length != 1 ) {
1713 final Phylogeny t1 = phylogenies_0[ 0 ];
1714 if ( t1.getNumberOfExternalNodes() != 5 ) {
1717 if ( !t1.isRooted() ) {
1720 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1723 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1726 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1729 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1732 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1733 if ( parser.getErrorCount() > 0 ) {
1734 System.out.println( parser.getErrorMessages().toString() );
1737 if ( phylogenies_1.length != 1 ) {
1740 final Phylogeny t2 = phylogenies_1[ 0 ];
1741 if ( t2.getNumberOfExternalNodes() != 664 ) {
1744 if ( !t2.isRooted() ) {
1747 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1750 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1753 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1756 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1759 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1762 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1763 .equals( "Aquifex" ) ) {
1766 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1767 if ( parser.getErrorCount() > 0 ) {
1768 System.out.println( parser.getErrorMessages().toString() );
1771 if ( phylogenies_2.length != 1 ) {
1774 final Phylogeny t3 = phylogenies_2[ 0 ];
1775 if ( t3.getNumberOfExternalNodes() != 184 ) {
1778 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1781 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1784 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1787 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1788 if ( parser.getErrorCount() > 0 ) {
1789 System.out.println( parser.getErrorMessages().toString() );
1792 if ( phylogenies_3.length != 1 ) {
1795 final Phylogeny t4 = phylogenies_3[ 0 ];
1796 if ( t4.getNumberOfExternalNodes() != 1 ) {
1799 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1802 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1805 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1808 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1809 if ( parser.getErrorCount() > 0 ) {
1810 System.out.println( parser.getErrorMessages().toString() );
1813 if ( phylogenies_4.length != 1 ) {
1816 final Phylogeny t5 = phylogenies_4[ 0 ];
1817 if ( t5.getNumberOfExternalNodes() != 13 ) {
1820 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1823 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1826 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1830 catch ( final Exception e ) {
1831 e.printStackTrace( System.out );
1837 private static boolean testBasicTreeMethods() {
1839 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1840 final Phylogeny t1 = factory.create();
1841 if ( !t1.isEmpty() ) {
1844 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1845 if ( t2.getNumberOfExternalNodes() != 4 ) {
1848 if ( t2.getHeight() != 8.5 ) {
1851 if ( !t2.isCompletelyBinary() ) {
1854 if ( t2.isEmpty() ) {
1857 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1858 if ( t3.getNumberOfExternalNodes() != 5 ) {
1861 if ( t3.getHeight() != 11 ) {
1864 if ( t3.isCompletelyBinary() ) {
1867 final PhylogenyNode n = t3.getNode( "ABC" );
1868 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 ];
1869 if ( t4.getNumberOfExternalNodes() != 9 ) {
1872 if ( t4.getHeight() != 11 ) {
1875 if ( t4.isCompletelyBinary() ) {
1878 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)" );
1879 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1880 if ( t5.getNumberOfExternalNodes() != 8 ) {
1883 if ( t5.getHeight() != 15 ) {
1886 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)" );
1887 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1888 if ( t6.getHeight() != 15 ) {
1891 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)" );
1892 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1893 if ( t7.getHeight() != 15 ) {
1896 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)" );
1897 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1898 if ( t8.getNumberOfExternalNodes() != 10 ) {
1901 if ( t8.getHeight() != 15 ) {
1904 final char[] a9 = new char[] {};
1905 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1906 if ( t9.getHeight() != 0 ) {
1909 final char[] a10 = new char[] { 'a', ':', '6' };
1910 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1911 if ( t10.getHeight() != 6 ) {
1915 catch ( final Exception e ) {
1916 e.printStackTrace( System.out );
1922 private static boolean testConfidenceAssessor() {
1924 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1925 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1926 final Phylogeny[] ev0 = factory
1927 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1929 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1930 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1933 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1936 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1937 final Phylogeny[] ev1 = factory
1938 .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)));",
1940 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1941 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1944 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1947 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1948 final Phylogeny[] ev_b = factory
1949 .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",
1951 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1952 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1955 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1959 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1960 final Phylogeny[] ev1x = factory
1961 .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)));",
1963 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1964 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1967 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1970 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1971 final Phylogeny[] ev_bx = factory
1972 .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",
1974 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1975 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1978 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1982 final Phylogeny[] t2 = factory
1983 .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);",
1985 final Phylogeny[] ev2 = factory
1986 .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);",
1988 for( final Phylogeny target : t2 ) {
1989 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
1992 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
1993 new NHXParser() )[ 0 ];
1994 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
1995 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
1996 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1999 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2002 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2006 catch ( final Exception e ) {
2007 e.printStackTrace();
2013 private static boolean testCopyOfNodeData() {
2015 final PhylogenyNode n1 = PhylogenyNode
2016 .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]" );
2017 final PhylogenyNode n2 = n1.copyNodeData();
2018 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2022 catch ( final Exception e ) {
2023 e.printStackTrace();
2029 private static boolean testDataObjects() {
2031 final Confidence s0 = new Confidence();
2032 final Confidence s1 = new Confidence();
2033 if ( !s0.isEqual( s1 ) ) {
2036 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2037 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2038 if ( s2.isEqual( s1 ) ) {
2041 if ( !s2.isEqual( s3 ) ) {
2044 final Confidence s4 = ( Confidence ) s3.copy();
2045 if ( !s4.isEqual( s3 ) ) {
2052 final Taxonomy t1 = new Taxonomy();
2053 final Taxonomy t2 = new Taxonomy();
2054 final Taxonomy t3 = new Taxonomy();
2055 final Taxonomy t4 = new Taxonomy();
2056 final Taxonomy t5 = new Taxonomy();
2057 t1.setIdentifier( new Identifier( "ecoli" ) );
2058 t1.setTaxonomyCode( "ECOLI" );
2059 t1.setScientificName( "E. coli" );
2060 t1.setCommonName( "coli" );
2061 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2062 if ( !t1.isEqual( t0 ) ) {
2065 t2.setIdentifier( new Identifier( "ecoli" ) );
2066 t2.setTaxonomyCode( "OTHER" );
2067 t2.setScientificName( "what" );
2068 t2.setCommonName( "something" );
2069 if ( !t1.isEqual( t2 ) ) {
2072 t2.setIdentifier( new Identifier( "nemve" ) );
2073 if ( t1.isEqual( t2 ) ) {
2076 t1.setIdentifier( null );
2077 t3.setTaxonomyCode( "ECOLI" );
2078 t3.setScientificName( "what" );
2079 t3.setCommonName( "something" );
2080 if ( !t1.isEqual( t3 ) ) {
2083 t1.setIdentifier( null );
2084 t1.setTaxonomyCode( "" );
2085 t4.setScientificName( "E. ColI" );
2086 t4.setCommonName( "something" );
2087 if ( !t1.isEqual( t4 ) ) {
2090 t4.setScientificName( "B. subtilis" );
2091 t4.setCommonName( "something" );
2092 if ( t1.isEqual( t4 ) ) {
2095 t1.setIdentifier( null );
2096 t1.setTaxonomyCode( "" );
2097 t1.setScientificName( "" );
2098 t5.setCommonName( "COLI" );
2099 if ( !t1.isEqual( t5 ) ) {
2102 t5.setCommonName( "vibrio" );
2103 if ( t1.isEqual( t5 ) ) {
2108 final Identifier id0 = new Identifier( "123", "pfam" );
2109 final Identifier id1 = ( Identifier ) id0.copy();
2110 if ( !id1.isEqual( id1 ) ) {
2113 if ( !id1.isEqual( id0 ) ) {
2116 if ( !id0.isEqual( id1 ) ) {
2123 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2124 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2125 if ( !pd1.isEqual( pd1 ) ) {
2128 if ( !pd1.isEqual( pd0 ) ) {
2133 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2134 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2135 if ( !pd3.isEqual( pd3 ) ) {
2138 if ( !pd2.isEqual( pd3 ) ) {
2141 if ( !pd0.isEqual( pd3 ) ) {
2146 // DomainArchitecture
2147 // ------------------
2148 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2149 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2150 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2151 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2152 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2153 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2158 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2159 if ( ds0.getNumberOfDomains() != 4 ) {
2162 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2163 if ( !ds0.isEqual( ds0 ) ) {
2166 if ( !ds0.isEqual( ds1 ) ) {
2169 if ( ds1.getNumberOfDomains() != 4 ) {
2172 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2177 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2178 if ( ds0.isEqual( ds2 ) ) {
2184 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2185 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2186 System.out.println( ds3.toNHX() );
2189 if ( ds3.getNumberOfDomains() != 3 ) {
2194 final Event e1 = new Event( Event.EventType.fusion );
2195 if ( e1.isDuplication() ) {
2198 if ( !e1.isFusion() ) {
2201 if ( !e1.asText().toString().equals( "fusion" ) ) {
2204 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2207 final Event e11 = new Event( Event.EventType.fusion );
2208 if ( !e11.isEqual( e1 ) ) {
2211 if ( !e11.toNHX().toString().equals( "" ) ) {
2214 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2215 if ( e2.isDuplication() ) {
2218 if ( !e2.isSpeciationOrDuplication() ) {
2221 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2224 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2227 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2230 if ( e11.isEqual( e2 ) ) {
2233 final Event e2c = ( Event ) e2.copy();
2234 if ( !e2c.isEqual( e2 ) ) {
2237 Event e3 = new Event( 1, 2, 3 );
2238 if ( e3.isDuplication() ) {
2241 if ( e3.isSpeciation() ) {
2244 if ( e3.isGeneLoss() ) {
2247 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2250 final Event e3c = ( Event ) e3.copy();
2251 final Event e3cc = ( Event ) e3c.copy();
2252 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2256 if ( !e3c.isEqual( e3cc ) ) {
2259 Event e4 = new Event( 1, 2, 3 );
2260 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2263 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2266 final Event e4c = ( Event ) e4.copy();
2268 final Event e4cc = ( Event ) e4c.copy();
2269 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2272 if ( !e4c.isEqual( e4cc ) ) {
2275 final Event e5 = new Event();
2276 if ( !e5.isUnassigned() ) {
2279 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2282 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2285 final Event e6 = new Event( 1, 0, 0 );
2286 if ( !e6.asText().toString().equals( "duplication" ) ) {
2289 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2292 final Event e7 = new Event( 0, 1, 0 );
2293 if ( !e7.asText().toString().equals( "speciation" ) ) {
2296 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2299 final Event e8 = new Event( 0, 0, 1 );
2300 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2303 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2307 catch ( final Exception e ) {
2308 e.printStackTrace( System.out );
2314 private static boolean testDeletionOfExternalNodes() {
2316 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2317 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2318 final PhylogenyWriter w = new PhylogenyWriter();
2319 if ( t0.isEmpty() ) {
2322 if ( t0.getNumberOfExternalNodes() != 1 ) {
2325 t0.deleteSubtree( t0.getNode( "A" ), false );
2326 if ( t0.getNumberOfExternalNodes() != 0 ) {
2329 if ( !t0.isEmpty() ) {
2332 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2333 if ( t1.getNumberOfExternalNodes() != 2 ) {
2336 t1.deleteSubtree( t1.getNode( "A" ), false );
2337 if ( t1.getNumberOfExternalNodes() != 1 ) {
2340 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2343 t1.deleteSubtree( t1.getNode( "B" ), false );
2344 if ( t1.getNumberOfExternalNodes() != 1 ) {
2347 t1.deleteSubtree( t1.getNode( "r" ), false );
2348 if ( !t1.isEmpty() ) {
2351 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2352 if ( t2.getNumberOfExternalNodes() != 3 ) {
2355 t2.deleteSubtree( t2.getNode( "B" ), false );
2356 if ( t2.getNumberOfExternalNodes() != 2 ) {
2359 t2.toNewHampshireX();
2360 PhylogenyNode n = t2.getNode( "A" );
2361 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2364 t2.deleteSubtree( t2.getNode( "A" ), false );
2365 if ( t2.getNumberOfExternalNodes() != 2 ) {
2368 t2.deleteSubtree( t2.getNode( "C" ), true );
2369 if ( t2.getNumberOfExternalNodes() != 1 ) {
2372 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2373 if ( t3.getNumberOfExternalNodes() != 4 ) {
2376 t3.deleteSubtree( t3.getNode( "B" ), true );
2377 if ( t3.getNumberOfExternalNodes() != 3 ) {
2380 n = t3.getNode( "A" );
2381 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2384 n = n.getNextExternalNode();
2385 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2388 t3.deleteSubtree( t3.getNode( "A" ), true );
2389 if ( t3.getNumberOfExternalNodes() != 2 ) {
2392 n = t3.getNode( "C" );
2393 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2396 t3.deleteSubtree( t3.getNode( "C" ), true );
2397 if ( t3.getNumberOfExternalNodes() != 1 ) {
2400 t3.deleteSubtree( t3.getNode( "D" ), true );
2401 if ( t3.getNumberOfExternalNodes() != 0 ) {
2404 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2405 if ( t4.getNumberOfExternalNodes() != 6 ) {
2408 t4.deleteSubtree( t4.getNode( "B2" ), true );
2409 if ( t4.getNumberOfExternalNodes() != 5 ) {
2412 String s = w.toNewHampshire( t4, false, true ).toString();
2413 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2416 t4.deleteSubtree( t4.getNode( "B11" ), true );
2417 if ( t4.getNumberOfExternalNodes() != 4 ) {
2420 t4.deleteSubtree( t4.getNode( "C" ), true );
2421 if ( t4.getNumberOfExternalNodes() != 3 ) {
2424 n = t4.getNode( "A" );
2425 n = n.getNextExternalNode();
2426 if ( !n.getName().equals( "B12" ) ) {
2429 n = n.getNextExternalNode();
2430 if ( !n.getName().equals( "D" ) ) {
2433 s = w.toNewHampshire( t4, false, true ).toString();
2434 if ( !s.equals( "((A,B12),D);" ) ) {
2437 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2438 t5.deleteSubtree( t5.getNode( "A" ), true );
2439 if ( t5.getNumberOfExternalNodes() != 5 ) {
2442 s = w.toNewHampshire( t5, false, true ).toString();
2443 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2446 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2447 t6.deleteSubtree( t6.getNode( "B11" ), true );
2448 if ( t6.getNumberOfExternalNodes() != 5 ) {
2451 s = w.toNewHampshire( t6, false, false ).toString();
2452 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2455 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2456 t7.deleteSubtree( t7.getNode( "B12" ), true );
2457 if ( t7.getNumberOfExternalNodes() != 5 ) {
2460 s = w.toNewHampshire( t7, false, true ).toString();
2461 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2464 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2465 t8.deleteSubtree( t8.getNode( "B2" ), true );
2466 if ( t8.getNumberOfExternalNodes() != 5 ) {
2469 s = w.toNewHampshire( t8, false, false ).toString();
2470 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2473 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2474 t9.deleteSubtree( t9.getNode( "C" ), true );
2475 if ( t9.getNumberOfExternalNodes() != 5 ) {
2478 s = w.toNewHampshire( t9, false, true ).toString();
2479 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2482 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2483 t10.deleteSubtree( t10.getNode( "D" ), true );
2484 if ( t10.getNumberOfExternalNodes() != 5 ) {
2487 s = w.toNewHampshire( t10, false, true ).toString();
2488 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2491 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2492 t11.deleteSubtree( t11.getNode( "A" ), true );
2493 if ( t11.getNumberOfExternalNodes() != 2 ) {
2496 s = w.toNewHampshire( t11, false, true ).toString();
2497 if ( !s.equals( "(B,C);" ) ) {
2500 t11.deleteSubtree( t11.getNode( "C" ), true );
2501 if ( t11.getNumberOfExternalNodes() != 1 ) {
2504 s = w.toNewHampshire( t11, false, false ).toString();
2505 if ( !s.equals( "B;" ) ) {
2508 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2509 t12.deleteSubtree( t12.getNode( "B2" ), true );
2510 if ( t12.getNumberOfExternalNodes() != 8 ) {
2513 s = w.toNewHampshire( t12, false, true ).toString();
2514 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2517 t12.deleteSubtree( t12.getNode( "B3" ), true );
2518 if ( t12.getNumberOfExternalNodes() != 7 ) {
2521 s = w.toNewHampshire( t12, false, true ).toString();
2522 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2525 t12.deleteSubtree( t12.getNode( "C3" ), true );
2526 if ( t12.getNumberOfExternalNodes() != 6 ) {
2529 s = w.toNewHampshire( t12, false, true ).toString();
2530 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2533 t12.deleteSubtree( t12.getNode( "A1" ), true );
2534 if ( t12.getNumberOfExternalNodes() != 5 ) {
2537 s = w.toNewHampshire( t12, false, true ).toString();
2538 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2541 t12.deleteSubtree( t12.getNode( "B1" ), true );
2542 if ( t12.getNumberOfExternalNodes() != 4 ) {
2545 s = w.toNewHampshire( t12, false, true ).toString();
2546 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2549 t12.deleteSubtree( t12.getNode( "A3" ), true );
2550 if ( t12.getNumberOfExternalNodes() != 3 ) {
2553 s = w.toNewHampshire( t12, false, true ).toString();
2554 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2557 t12.deleteSubtree( t12.getNode( "A2" ), true );
2558 if ( t12.getNumberOfExternalNodes() != 2 ) {
2561 s = w.toNewHampshire( t12, false, true ).toString();
2562 if ( !s.equals( "(C1,C2);" ) ) {
2565 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2566 t13.deleteSubtree( t13.getNode( "D" ), true );
2567 if ( t13.getNumberOfExternalNodes() != 4 ) {
2570 s = w.toNewHampshire( t13, false, true ).toString();
2571 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2574 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2575 t14.deleteSubtree( t14.getNode( "E" ), true );
2576 if ( t14.getNumberOfExternalNodes() != 5 ) {
2579 s = w.toNewHampshire( t14, false, true ).toString();
2580 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2583 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2584 t15.deleteSubtree( t15.getNode( "B2" ), true );
2585 if ( t15.getNumberOfExternalNodes() != 11 ) {
2588 t15.deleteSubtree( t15.getNode( "B1" ), true );
2589 if ( t15.getNumberOfExternalNodes() != 10 ) {
2592 t15.deleteSubtree( t15.getNode( "B3" ), true );
2593 if ( t15.getNumberOfExternalNodes() != 9 ) {
2596 t15.deleteSubtree( t15.getNode( "B4" ), true );
2597 if ( t15.getNumberOfExternalNodes() != 8 ) {
2600 t15.deleteSubtree( t15.getNode( "A1" ), true );
2601 if ( t15.getNumberOfExternalNodes() != 7 ) {
2604 t15.deleteSubtree( t15.getNode( "C4" ), true );
2605 if ( t15.getNumberOfExternalNodes() != 6 ) {
2609 catch ( final Exception e ) {
2610 e.printStackTrace( System.out );
2616 private static boolean testDescriptiveStatistics() {
2618 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2619 dss1.addValue( 82 );
2620 dss1.addValue( 78 );
2621 dss1.addValue( 70 );
2622 dss1.addValue( 58 );
2623 dss1.addValue( 42 );
2624 if ( dss1.getN() != 5 ) {
2627 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2630 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2633 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2636 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2639 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2642 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2645 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2648 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2651 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2654 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2657 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2660 dss1.addValue( 123 );
2661 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2664 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2667 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2670 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2671 dss2.addValue( -1.85 );
2672 dss2.addValue( 57.5 );
2673 dss2.addValue( 92.78 );
2674 dss2.addValue( 57.78 );
2675 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2678 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2681 final double[] a = dss2.getDataAsDoubleArray();
2682 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2685 dss2.addValue( -100 );
2686 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2689 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2692 final double[] ds = new double[ 14 ];
2707 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2708 if ( bins.length != 4 ) {
2711 if ( bins[ 0 ] != 2 ) {
2714 if ( bins[ 1 ] != 3 ) {
2717 if ( bins[ 2 ] != 4 ) {
2720 if ( bins[ 3 ] != 5 ) {
2723 final double[] ds1 = new double[ 9 ];
2733 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2734 if ( bins1.length != 4 ) {
2737 if ( bins1[ 0 ] != 2 ) {
2740 if ( bins1[ 1 ] != 3 ) {
2743 if ( bins1[ 2 ] != 0 ) {
2746 if ( bins1[ 3 ] != 4 ) {
2749 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2750 if ( bins1_1.length != 3 ) {
2753 if ( bins1_1[ 0 ] != 3 ) {
2756 if ( bins1_1[ 1 ] != 2 ) {
2759 if ( bins1_1[ 2 ] != 4 ) {
2762 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2763 if ( bins1_2.length != 3 ) {
2766 if ( bins1_2[ 0 ] != 2 ) {
2769 if ( bins1_2[ 1 ] != 2 ) {
2772 if ( bins1_2[ 2 ] != 2 ) {
2775 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2789 dss3.addValue( 10 );
2790 dss3.addValue( 10 );
2791 dss3.addValue( 10 );
2792 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2793 histo.toStringBuffer( 10, '=', 40, 5 );
2794 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2796 catch ( final Exception e ) {
2797 e.printStackTrace( System.out );
2803 private static boolean testDir( final String file ) {
2805 final File f = new File( file );
2806 if ( !f.exists() ) {
2809 if ( !f.isDirectory() ) {
2812 if ( !f.canRead() ) {
2816 catch ( final Exception e ) {
2822 private static boolean testExternalNodeRelatedMethods() {
2824 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2825 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2826 PhylogenyNode n = t1.getNode( "A" );
2827 n = n.getNextExternalNode();
2828 if ( !n.getName().equals( "B" ) ) {
2831 n = n.getNextExternalNode();
2832 if ( !n.getName().equals( "C" ) ) {
2835 n = n.getNextExternalNode();
2836 if ( !n.getName().equals( "D" ) ) {
2839 n = t1.getNode( "B" );
2840 while ( !n.isLastExternalNode() ) {
2841 n = n.getNextExternalNode();
2843 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2844 n = t2.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 = t2.getNode( "B" );
2858 while ( !n.isLastExternalNode() ) {
2859 n = n.getNextExternalNode();
2861 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2862 n = t3.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 = n.getNextExternalNode();
2876 if ( !n.getName().equals( "E" ) ) {
2879 n = n.getNextExternalNode();
2880 if ( !n.getName().equals( "F" ) ) {
2883 n = n.getNextExternalNode();
2884 if ( !n.getName().equals( "G" ) ) {
2887 n = n.getNextExternalNode();
2888 if ( !n.getName().equals( "H" ) ) {
2891 n = t3.getNode( "B" );
2892 while ( !n.isLastExternalNode() ) {
2893 n = n.getNextExternalNode();
2895 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2896 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2897 final PhylogenyNode node = iter.next();
2899 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2900 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2901 final PhylogenyNode node = iter.next();
2903 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2904 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2905 if ( !iter.next().getName().equals( "A" ) ) {
2908 if ( !iter.next().getName().equals( "B" ) ) {
2911 if ( !iter.next().getName().equals( "C" ) ) {
2914 if ( !iter.next().getName().equals( "D" ) ) {
2917 if ( !iter.next().getName().equals( "E" ) ) {
2920 if ( !iter.next().getName().equals( "F" ) ) {
2923 if ( iter.hasNext() ) {
2927 catch ( final Exception e ) {
2928 e.printStackTrace( System.out );
2934 private static boolean testGeneralTable() {
2936 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2937 t0.setValue( 3, 2, "23" );
2938 t0.setValue( 10, 1, "error" );
2939 t0.setValue( 10, 1, "110" );
2940 t0.setValue( 9, 1, "19" );
2941 t0.setValue( 1, 10, "101" );
2942 t0.setValue( 10, 10, "1010" );
2943 t0.setValue( 100, 10, "10100" );
2944 t0.setValue( 0, 0, "00" );
2945 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2948 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2951 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2954 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2957 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2960 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2963 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2966 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2969 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2972 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2973 t1.setValue( "3", "2", "23" );
2974 t1.setValue( "10", "1", "error" );
2975 t1.setValue( "10", "1", "110" );
2976 t1.setValue( "9", "1", "19" );
2977 t1.setValue( "1", "10", "101" );
2978 t1.setValue( "10", "10", "1010" );
2979 t1.setValue( "100", "10", "10100" );
2980 t1.setValue( "0", "0", "00" );
2981 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2982 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2985 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2988 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2991 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2994 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2997 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3000 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3003 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3006 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3009 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3013 catch ( final Exception e ) {
3014 e.printStackTrace( System.out );
3020 private static boolean testGetDistance() {
3022 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3023 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",
3024 new NHXParser() )[ 0 ];
3025 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3028 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3031 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3034 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3037 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3040 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3043 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3046 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3049 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3052 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3055 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3058 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3061 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3064 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3067 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3070 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3073 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3076 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3079 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3082 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3085 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3088 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3091 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3094 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3097 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3100 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3103 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3106 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3109 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3112 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3115 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3118 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",
3119 new NHXParser() )[ 0 ];
3120 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3123 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3126 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3129 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3132 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3135 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3138 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3141 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3144 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3147 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3150 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3154 catch ( final Exception e ) {
3155 e.printStackTrace( System.out );
3161 private static boolean testGetLCA() {
3163 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3164 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3165 new NHXParser() )[ 0 ];
3166 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3167 if ( !A.getName().equals( "A" ) ) {
3170 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3171 if ( !gh.getName().equals( "gh" ) ) {
3174 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3175 if ( !ab.getName().equals( "ab" ) ) {
3178 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3179 if ( !ab2.getName().equals( "ab" ) ) {
3182 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3183 if ( !gh2.getName().equals( "gh" ) ) {
3186 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3187 if ( !gh3.getName().equals( "gh" ) ) {
3190 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3191 if ( !abc.getName().equals( "abc" ) ) {
3194 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3195 if ( !abc2.getName().equals( "abc" ) ) {
3198 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3199 if ( !abcd.getName().equals( "abcd" ) ) {
3202 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3203 if ( !abcd2.getName().equals( "abcd" ) ) {
3206 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3207 if ( !abcdef.getName().equals( "abcdef" ) ) {
3210 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3211 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3214 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3215 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3218 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3219 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3222 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3223 if ( !abcde.getName().equals( "abcde" ) ) {
3226 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3227 if ( !abcde2.getName().equals( "abcde" ) ) {
3230 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3231 if ( !r.getName().equals( "abcdefgh" ) ) {
3234 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3235 if ( !r2.getName().equals( "abcdefgh" ) ) {
3238 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3239 if ( !r3.getName().equals( "abcdefgh" ) ) {
3242 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3243 if ( !abcde3.getName().equals( "abcde" ) ) {
3246 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3247 if ( !abcde4.getName().equals( "abcde" ) ) {
3250 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3251 if ( !ab3.getName().equals( "ab" ) ) {
3254 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3255 if ( !ab4.getName().equals( "ab" ) ) {
3258 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3259 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3260 if ( !cd.getName().equals( "cd" ) ) {
3263 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3264 if ( !cd2.getName().equals( "cd" ) ) {
3267 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3268 if ( !cde.getName().equals( "cde" ) ) {
3271 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3272 if ( !cde2.getName().equals( "cde" ) ) {
3275 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3276 if ( !cdef.getName().equals( "cdef" ) ) {
3279 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3280 if ( !cdef2.getName().equals( "cdef" ) ) {
3283 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3284 if ( !cdef3.getName().equals( "cdef" ) ) {
3287 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3288 if ( !rt.getName().equals( "r" ) ) {
3291 final Phylogeny p3 = factory
3292 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3293 new NHXParser() )[ 0 ];
3294 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3295 if ( !bc_3.getName().equals( "bc" ) ) {
3298 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3299 if ( !ac_3.getName().equals( "abc" ) ) {
3302 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3303 if ( !ad_3.getName().equals( "abcde" ) ) {
3306 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3307 if ( !af_3.getName().equals( "abcdef" ) ) {
3310 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3311 if ( !ag_3.getName().equals( "" ) ) {
3314 if ( !ag_3.isRoot() ) {
3317 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3318 if ( !al_3.getName().equals( "" ) ) {
3321 if ( !al_3.isRoot() ) {
3324 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3325 if ( !kl_3.getName().equals( "" ) ) {
3328 if ( !kl_3.isRoot() ) {
3331 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3332 if ( !fl_3.getName().equals( "" ) ) {
3335 if ( !fl_3.isRoot() ) {
3338 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3339 if ( !gk_3.getName().equals( "ghijk" ) ) {
3342 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3343 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3344 if ( !r_4.getName().equals( "r" ) ) {
3347 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3348 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3349 if ( !r_5.getName().equals( "root" ) ) {
3352 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3353 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3354 if ( !r_6.getName().equals( "rot" ) ) {
3357 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3358 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3359 if ( !r_7.getName().equals( "rott" ) ) {
3363 catch ( final Exception e ) {
3364 e.printStackTrace( System.out );
3370 private static boolean testGetLCA2() {
3372 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3373 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3374 PhylogenyMethods.preOrderReId( p_a );
3375 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3376 p_a.getNode( "a" ) );
3377 if ( !p_a_1.getName().equals( "a" ) ) {
3380 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3381 PhylogenyMethods.preOrderReId( p_b );
3382 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3383 p_b.getNode( "a" ) );
3384 if ( !p_b_1.getName().equals( "b" ) ) {
3387 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3388 p_b.getNode( "b" ) );
3389 if ( !p_b_2.getName().equals( "b" ) ) {
3392 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3393 PhylogenyMethods.preOrderReId( p_c );
3394 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3395 p_c.getNode( "a" ) );
3396 if ( !p_c_1.getName().equals( "b" ) ) {
3399 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3400 p_c.getNode( "c" ) );
3401 if ( !p_c_2.getName().equals( "c" ) ) {
3402 System.out.println( p_c_2.getName() );
3406 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3407 p_c.getNode( "b" ) );
3408 if ( !p_c_3.getName().equals( "b" ) ) {
3411 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3412 p_c.getNode( "a" ) );
3413 if ( !p_c_4.getName().equals( "c" ) ) {
3416 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3417 new NHXParser() )[ 0 ];
3418 PhylogenyMethods.preOrderReId( p1 );
3419 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3420 p1.getNode( "A" ) );
3421 if ( !A.getName().equals( "A" ) ) {
3424 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3425 p1.getNode( "gh" ) );
3426 if ( !gh.getName().equals( "gh" ) ) {
3429 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3430 p1.getNode( "B" ) );
3431 if ( !ab.getName().equals( "ab" ) ) {
3434 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3435 p1.getNode( "A" ) );
3436 if ( !ab2.getName().equals( "ab" ) ) {
3439 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3440 p1.getNode( "G" ) );
3441 if ( !gh2.getName().equals( "gh" ) ) {
3444 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3445 p1.getNode( "H" ) );
3446 if ( !gh3.getName().equals( "gh" ) ) {
3449 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3450 p1.getNode( "A" ) );
3451 if ( !abc.getName().equals( "abc" ) ) {
3454 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3455 p1.getNode( "C" ) );
3456 if ( !abc2.getName().equals( "abc" ) ) {
3459 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3460 p1.getNode( "D" ) );
3461 if ( !abcd.getName().equals( "abcd" ) ) {
3464 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3465 p1.getNode( "A" ) );
3466 if ( !abcd2.getName().equals( "abcd" ) ) {
3469 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3470 p1.getNode( "F" ) );
3471 if ( !abcdef.getName().equals( "abcdef" ) ) {
3474 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3475 p1.getNode( "A" ) );
3476 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3479 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3480 p1.getNode( "F" ) );
3481 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3484 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3485 p1.getNode( "ab" ) );
3486 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3489 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3490 p1.getNode( "E" ) );
3491 if ( !abcde.getName().equals( "abcde" ) ) {
3494 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3495 p1.getNode( "A" ) );
3496 if ( !abcde2.getName().equals( "abcde" ) ) {
3499 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3500 p1.getNode( "abcdefgh" ) );
3501 if ( !r.getName().equals( "abcdefgh" ) ) {
3504 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3505 p1.getNode( "H" ) );
3506 if ( !r2.getName().equals( "abcdefgh" ) ) {
3509 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3510 p1.getNode( "A" ) );
3511 if ( !r3.getName().equals( "abcdefgh" ) ) {
3514 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3515 p1.getNode( "abcde" ) );
3516 if ( !abcde3.getName().equals( "abcde" ) ) {
3519 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3520 p1.getNode( "E" ) );
3521 if ( !abcde4.getName().equals( "abcde" ) ) {
3524 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3525 p1.getNode( "B" ) );
3526 if ( !ab3.getName().equals( "ab" ) ) {
3529 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3530 p1.getNode( "ab" ) );
3531 if ( !ab4.getName().equals( "ab" ) ) {
3534 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3535 PhylogenyMethods.preOrderReId( p2 );
3536 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3537 p2.getNode( "d" ) );
3538 if ( !cd.getName().equals( "cd" ) ) {
3541 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3542 p2.getNode( "c" ) );
3543 if ( !cd2.getName().equals( "cd" ) ) {
3546 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3547 p2.getNode( "e" ) );
3548 if ( !cde.getName().equals( "cde" ) ) {
3551 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3552 p2.getNode( "c" ) );
3553 if ( !cde2.getName().equals( "cde" ) ) {
3556 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3557 p2.getNode( "f" ) );
3558 if ( !cdef.getName().equals( "cdef" ) ) {
3561 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3562 p2.getNode( "f" ) );
3563 if ( !cdef2.getName().equals( "cdef" ) ) {
3566 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3567 p2.getNode( "d" ) );
3568 if ( !cdef3.getName().equals( "cdef" ) ) {
3571 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3572 p2.getNode( "a" ) );
3573 if ( !rt.getName().equals( "r" ) ) {
3576 final Phylogeny p3 = factory
3577 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3578 new NHXParser() )[ 0 ];
3579 PhylogenyMethods.preOrderReId( p3 );
3580 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3581 p3.getNode( "c" ) );
3582 if ( !bc_3.getName().equals( "bc" ) ) {
3585 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3586 p3.getNode( "c" ) );
3587 if ( !ac_3.getName().equals( "abc" ) ) {
3590 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3591 p3.getNode( "d" ) );
3592 if ( !ad_3.getName().equals( "abcde" ) ) {
3595 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3596 p3.getNode( "f" ) );
3597 if ( !af_3.getName().equals( "abcdef" ) ) {
3600 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3601 p3.getNode( "g" ) );
3602 if ( !ag_3.getName().equals( "" ) ) {
3605 if ( !ag_3.isRoot() ) {
3608 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3609 p3.getNode( "l" ) );
3610 if ( !al_3.getName().equals( "" ) ) {
3613 if ( !al_3.isRoot() ) {
3616 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3617 p3.getNode( "l" ) );
3618 if ( !kl_3.getName().equals( "" ) ) {
3621 if ( !kl_3.isRoot() ) {
3624 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3625 p3.getNode( "l" ) );
3626 if ( !fl_3.getName().equals( "" ) ) {
3629 if ( !fl_3.isRoot() ) {
3632 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3633 p3.getNode( "k" ) );
3634 if ( !gk_3.getName().equals( "ghijk" ) ) {
3637 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3638 PhylogenyMethods.preOrderReId( p4 );
3639 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3640 p4.getNode( "c" ) );
3641 if ( !r_4.getName().equals( "r" ) ) {
3644 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3645 PhylogenyMethods.preOrderReId( p5 );
3646 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3647 p5.getNode( "c" ) );
3648 if ( !r_5.getName().equals( "root" ) ) {
3651 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3652 PhylogenyMethods.preOrderReId( p6 );
3653 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3654 p6.getNode( "a" ) );
3655 if ( !r_6.getName().equals( "rot" ) ) {
3658 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3659 PhylogenyMethods.preOrderReId( p7 );
3660 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3661 p7.getNode( "e" ) );
3662 if ( !r_7.getName().equals( "rott" ) ) {
3665 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3666 p7.getNode( "a" ) );
3667 if ( !r_71.getName().equals( "rott" ) ) {
3670 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3671 p7.getNode( "rott" ) );
3672 if ( !r_72.getName().equals( "rott" ) ) {
3675 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3676 p7.getNode( "a" ) );
3677 if ( !r_73.getName().equals( "rott" ) ) {
3680 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3681 p7.getNode( "rott" ) );
3682 if ( !r_74.getName().equals( "rott" ) ) {
3685 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3686 p7.getNode( "e" ) );
3687 if ( !r_75.getName().equals( "e" ) ) {
3691 catch ( final Exception e ) {
3692 e.printStackTrace( System.out );
3698 private static boolean testHmmscanOutputParser() {
3699 final String test_dir = Test.PATH_TO_TEST_DATA;
3701 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3702 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3704 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3705 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3706 final List<Protein> proteins = parser2.parse();
3707 if ( parser2.getProteinsEncountered() != 4 ) {
3710 if ( proteins.size() != 4 ) {
3713 if ( parser2.getDomainsEncountered() != 69 ) {
3716 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3719 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3722 final Protein p1 = proteins.get( 0 );
3723 if ( p1.getNumberOfProteinDomains() != 15 ) {
3726 if ( p1.getLength() != 850 ) {
3729 final Protein p2 = proteins.get( 1 );
3730 if ( p2.getNumberOfProteinDomains() != 51 ) {
3733 if ( p2.getLength() != 1291 ) {
3736 final Protein p3 = proteins.get( 2 );
3737 if ( p3.getNumberOfProteinDomains() != 2 ) {
3740 final Protein p4 = proteins.get( 3 );
3741 if ( p4.getNumberOfProteinDomains() != 1 ) {
3744 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3747 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3750 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3753 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3756 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3759 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3762 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3765 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3768 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3772 catch ( final Exception e ) {
3773 e.printStackTrace( System.out );
3779 private static boolean testLastExternalNodeMethods() {
3781 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3782 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3783 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3784 final PhylogenyNode n1 = t0.getNode( "A" );
3785 if ( n1.isLastExternalNode() ) {
3788 final PhylogenyNode n2 = t0.getNode( "B" );
3789 if ( n2.isLastExternalNode() ) {
3792 final PhylogenyNode n3 = t0.getNode( "C" );
3793 if ( n3.isLastExternalNode() ) {
3796 final PhylogenyNode n4 = t0.getNode( "D" );
3797 if ( !n4.isLastExternalNode() ) {
3801 catch ( final Exception e ) {
3802 e.printStackTrace( System.out );
3808 private static boolean testLevelOrderIterator() {
3810 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3811 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3812 PhylogenyNodeIterator it0;
3813 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3816 for( it0.reset(); it0.hasNext(); ) {
3819 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3820 if ( !it.next().getName().equals( "r" ) ) {
3823 if ( !it.next().getName().equals( "ab" ) ) {
3826 if ( !it.next().getName().equals( "cd" ) ) {
3829 if ( !it.next().getName().equals( "A" ) ) {
3832 if ( !it.next().getName().equals( "B" ) ) {
3835 if ( !it.next().getName().equals( "C" ) ) {
3838 if ( !it.next().getName().equals( "D" ) ) {
3841 if ( it.hasNext() ) {
3844 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",
3845 new NHXParser() )[ 0 ];
3846 PhylogenyNodeIterator it2;
3847 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3850 for( it2.reset(); it2.hasNext(); ) {
3853 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3854 if ( !it3.next().getName().equals( "r" ) ) {
3857 if ( !it3.next().getName().equals( "abc" ) ) {
3860 if ( !it3.next().getName().equals( "defg" ) ) {
3863 if ( !it3.next().getName().equals( "A" ) ) {
3866 if ( !it3.next().getName().equals( "B" ) ) {
3869 if ( !it3.next().getName().equals( "C" ) ) {
3872 if ( !it3.next().getName().equals( "D" ) ) {
3875 if ( !it3.next().getName().equals( "E" ) ) {
3878 if ( !it3.next().getName().equals( "F" ) ) {
3881 if ( !it3.next().getName().equals( "G" ) ) {
3884 if ( !it3.next().getName().equals( "1" ) ) {
3887 if ( !it3.next().getName().equals( "2" ) ) {
3890 if ( !it3.next().getName().equals( "3" ) ) {
3893 if ( !it3.next().getName().equals( "4" ) ) {
3896 if ( !it3.next().getName().equals( "5" ) ) {
3899 if ( !it3.next().getName().equals( "6" ) ) {
3902 if ( !it3.next().getName().equals( "f1" ) ) {
3905 if ( !it3.next().getName().equals( "f2" ) ) {
3908 if ( !it3.next().getName().equals( "f3" ) ) {
3911 if ( !it3.next().getName().equals( "a" ) ) {
3914 if ( !it3.next().getName().equals( "b" ) ) {
3917 if ( !it3.next().getName().equals( "f21" ) ) {
3920 if ( !it3.next().getName().equals( "X" ) ) {
3923 if ( !it3.next().getName().equals( "Y" ) ) {
3926 if ( !it3.next().getName().equals( "Z" ) ) {
3929 if ( it3.hasNext() ) {
3932 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3933 PhylogenyNodeIterator it4;
3934 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3937 for( it4.reset(); it4.hasNext(); ) {
3940 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3941 if ( !it5.next().getName().equals( "r" ) ) {
3944 if ( !it5.next().getName().equals( "A" ) ) {
3947 if ( !it5.next().getName().equals( "B" ) ) {
3950 if ( !it5.next().getName().equals( "C" ) ) {
3953 if ( !it5.next().getName().equals( "D" ) ) {
3956 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3957 PhylogenyNodeIterator it6;
3958 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3961 for( it6.reset(); it6.hasNext(); ) {
3964 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3965 if ( !it7.next().getName().equals( "A" ) ) {
3968 if ( it.hasNext() ) {
3972 catch ( final Exception e ) {
3973 e.printStackTrace( System.out );
3979 private static boolean testNodeRemoval() {
3981 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3982 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3983 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
3984 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
3987 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
3988 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
3989 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
3992 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
3993 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
3994 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
3998 catch ( final Exception e ) {
3999 e.printStackTrace( System.out );
4005 private static boolean testMidpointrooting() {
4007 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4008 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4009 PhylogenyMethods.midpointRoot( t0 );
4010 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4013 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4016 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4020 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",
4021 new NHXParser() )[ 0 ];
4022 if ( !t1.isRooted() ) {
4025 PhylogenyMethods.midpointRoot( t1 );
4026 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4029 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4032 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4035 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4038 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4041 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4044 t1.reRoot( t1.getNode( "A" ) );
4045 PhylogenyMethods.midpointRoot( t1 );
4046 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4049 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4052 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4055 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4058 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4062 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4066 catch ( final Exception e ) {
4067 e.printStackTrace( System.out );
4073 private static boolean testNexusCharactersParsing() {
4075 final NexusCharactersParser parser = new NexusCharactersParser();
4076 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4078 String[] labels = parser.getCharStateLabels();
4079 if ( labels.length != 7 ) {
4082 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4085 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4088 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4091 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4094 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4097 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4100 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4103 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4105 labels = parser.getCharStateLabels();
4106 if ( labels.length != 7 ) {
4109 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4112 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4115 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4118 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4121 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4124 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4127 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4131 catch ( final Exception e ) {
4132 e.printStackTrace( System.out );
4138 private static boolean testNexusMatrixParsing() {
4140 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4141 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4143 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4144 if ( m.getNumberOfCharacters() != 9 ) {
4147 if ( m.getNumberOfIdentifiers() != 5 ) {
4150 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4153 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4156 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4159 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4162 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4165 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4168 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4171 // if ( labels.length != 7 ) {
4174 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4177 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4180 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4183 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4186 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4189 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4192 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4195 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4197 // labels = parser.getCharStateLabels();
4198 // if ( labels.length != 7 ) {
4201 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4204 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4207 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4210 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4213 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4216 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4219 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4223 catch ( final Exception e ) {
4224 e.printStackTrace( System.out );
4230 private static boolean testNexusTreeParsing() {
4232 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4233 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4234 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4235 if ( phylogenies.length != 1 ) {
4238 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4241 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4245 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4246 if ( phylogenies.length != 1 ) {
4249 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4252 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4256 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4257 if ( phylogenies.length != 1 ) {
4260 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4263 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4266 if ( phylogenies[ 0 ].isRooted() ) {
4270 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4271 if ( phylogenies.length != 18 ) {
4274 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4277 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4280 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4283 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4286 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4289 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4292 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4295 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4298 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4301 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4304 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4307 if ( phylogenies[ 8 ].isRooted() ) {
4310 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4313 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4316 if ( !phylogenies[ 9 ].isRooted() ) {
4319 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4322 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4325 if ( !phylogenies[ 10 ].isRooted() ) {
4328 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4331 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4334 if ( phylogenies[ 11 ].isRooted() ) {
4337 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4340 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4343 if ( !phylogenies[ 12 ].isRooted() ) {
4346 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4349 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4352 if ( !phylogenies[ 13 ].isRooted() ) {
4355 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4358 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4361 if ( !phylogenies[ 14 ].isRooted() ) {
4364 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4367 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4370 if ( phylogenies[ 15 ].isRooted() ) {
4373 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4376 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4379 if ( !phylogenies[ 16 ].isRooted() ) {
4382 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4385 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4388 if ( phylogenies[ 17 ].isRooted() ) {
4391 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4395 catch ( final Exception e ) {
4396 e.printStackTrace( System.out );
4402 private static boolean testNexusTreeParsingTranslating() {
4404 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4405 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4406 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4407 if ( phylogenies.length != 1 ) {
4410 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4413 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4416 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4419 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4422 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4423 .equals( "Aranaeus" ) ) {
4427 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4428 if ( phylogenies.length != 3 ) {
4431 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4434 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4437 if ( phylogenies[ 0 ].isRooted() ) {
4440 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4443 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4446 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4447 .equals( "Aranaeus" ) ) {
4450 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4453 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4456 if ( phylogenies[ 1 ].isRooted() ) {
4459 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4462 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4465 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4466 .equals( "Aranaeus" ) ) {
4469 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4472 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4475 if ( !phylogenies[ 2 ].isRooted() ) {
4478 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4481 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4484 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4485 .equals( "Aranaeus" ) ) {
4489 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4490 if ( phylogenies.length != 3 ) {
4493 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4496 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4499 if ( phylogenies[ 0 ].isRooted() ) {
4502 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4505 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4508 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4509 .equals( "Aranaeus" ) ) {
4512 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4515 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4518 if ( phylogenies[ 1 ].isRooted() ) {
4521 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4524 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4527 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4528 .equals( "Aranaeus" ) ) {
4531 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4534 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4537 if ( !phylogenies[ 2 ].isRooted() ) {
4540 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4543 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4546 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4547 .equals( "Aranaeus" ) ) {
4551 catch ( final Exception e ) {
4552 e.printStackTrace( System.out );
4558 private static boolean testNHParsing() {
4560 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4561 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4562 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4565 final NHXParser nhxp = new NHXParser();
4566 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4567 nhxp.setReplaceUnderscores( true );
4568 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4569 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4572 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4575 final Phylogeny p1b = factory
4576 .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 ",
4577 new NHXParser() )[ 0 ];
4578 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4581 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4584 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4585 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4586 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4587 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4588 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4589 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4590 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4591 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4592 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4593 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4594 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4595 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4596 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4598 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4601 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4604 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4607 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4610 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4611 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4612 final String p16_S = "((A,B),C)";
4613 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4614 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4617 final String p17_S = "(C,(A,B))";
4618 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4619 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4622 final String p18_S = "((A,B),(C,D))";
4623 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4624 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4627 final String p19_S = "(((A,B),C),D)";
4628 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4629 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4632 final String p20_S = "(A,(B,(C,D)))";
4633 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4634 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4637 final String p21_S = "(A,(B,(C,(D,E))))";
4638 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4639 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4642 final String p22_S = "((((A,B),C),D),E)";
4643 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4644 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4647 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4648 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4649 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4652 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4653 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4654 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4657 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4658 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4659 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4660 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4663 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4666 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4667 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4668 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4669 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4670 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4671 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4672 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4673 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4674 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4675 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4678 final String p26_S = "(A,B)ab";
4679 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4680 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4683 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4684 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4686 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4689 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4690 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4691 final String p28_S3 = "(A,B)ab";
4692 final String p28_S4 = "((((A,B),C),D),;E;)";
4693 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4695 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4698 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4701 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4704 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4707 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";
4708 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4709 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4712 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";
4713 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4714 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4717 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4718 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4719 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4722 final String p33_S = "A";
4723 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4724 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4727 final String p34_S = "B;";
4728 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4729 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4732 final String p35_S = "B:0.2";
4733 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4734 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4737 final String p36_S = "(A)";
4738 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4739 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4742 final String p37_S = "((A))";
4743 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4744 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4747 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4748 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4749 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4752 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4753 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4754 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4757 final String p40_S = "(A,B,C)";
4758 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4759 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4762 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4763 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4764 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4767 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4768 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4769 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4772 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)";
4773 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4774 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4777 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)))";
4778 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4779 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4782 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4783 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4784 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4787 final String p46_S = "";
4788 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4789 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4792 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4793 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4796 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4797 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4800 final Phylogeny p49 = factory
4801 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4802 new NHXParser() )[ 0 ];
4803 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4806 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4807 if ( p50.getNode( "A" ) == null ) {
4810 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4811 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4814 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4817 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4818 .equals( "((A,B)88:2.0,C);" ) ) {
4821 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4822 if ( p51.getNode( "A(A" ) == null ) {
4825 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4826 if ( p52.getNode( "A(A" ) == null ) {
4829 final Phylogeny p53 = factory
4830 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4831 new NHXParser() )[ 0 ];
4832 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4836 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4837 if ( p54.getNode( "A" ) == null ) {
4840 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4841 .equals( "((A,B)[88],C);" ) ) {
4845 catch ( final Exception e ) {
4846 e.printStackTrace( System.out );
4852 private static boolean testNHXconversion() {
4854 final PhylogenyNode n1 = new PhylogenyNode();
4855 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4856 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4857 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4858 final PhylogenyNode n5 = PhylogenyNode
4859 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4860 final PhylogenyNode n6 = PhylogenyNode
4861 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4862 if ( !n1.toNewHampshireX().equals( "" ) ) {
4865 if ( !n2.toNewHampshireX().equals( "" ) ) {
4868 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4871 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4874 if ( !n5.toNewHampshireX()
4875 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
4878 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
4882 catch ( final Exception e ) {
4883 e.printStackTrace( System.out );
4889 private static boolean testTaxonomyExtraction() {
4891 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
4892 NHXParser.TAXONOMY_EXTRACTION.YES );
4893 if ( n0.getNodeData().isHasTaxonomy() ) {
4896 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
4897 NHXParser.TAXONOMY_EXTRACTION.YES );
4898 if ( n1.getNodeData().isHasTaxonomy() ) {
4899 System.out.println( n1.toString() );
4902 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
4903 NHXParser.TAXONOMY_EXTRACTION.YES );
4904 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4905 System.out.println( n2.toString() );
4908 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
4909 NHXParser.TAXONOMY_EXTRACTION.YES );
4910 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4911 System.out.println( n3.toString() );
4914 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
4915 NHXParser.TAXONOMY_EXTRACTION.YES );
4916 if ( n4.getNodeData().isHasTaxonomy() ) {
4917 System.out.println( n4.toString() );
4920 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
4921 NHXParser.TAXONOMY_EXTRACTION.YES );
4922 if ( n5.getNodeData().isHasTaxonomy() ) {
4923 System.out.println( n5.toString() );
4926 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
4927 NHXParser.TAXONOMY_EXTRACTION.YES );
4928 if ( n6.getNodeData().isHasTaxonomy() ) {
4929 System.out.println( n6.toString() );
4932 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
4933 NHXParser.TAXONOMY_EXTRACTION.YES );
4934 if ( n7.getNodeData().isHasTaxonomy() ) {
4935 System.out.println( n7.toString() );
4938 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
4939 NHXParser.TAXONOMY_EXTRACTION.YES );
4940 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4941 System.out.println( n8.toString() );
4944 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
4945 NHXParser.TAXONOMY_EXTRACTION.YES );
4946 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
4947 System.out.println( n9.toString() );
4950 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
4951 NHXParser.TAXONOMY_EXTRACTION.YES );
4952 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
4953 System.out.println( n10.toString() );
4957 catch ( final Exception e ) {
4958 e.printStackTrace( System.out );
4964 private static boolean testNHXNodeParsing() {
4966 final PhylogenyNode n1 = new PhylogenyNode();
4967 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4968 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4969 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4970 final PhylogenyNode n5 = PhylogenyNode
4971 .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]" );
4972 if ( !n3.getName().equals( "n3" ) ) {
4975 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4978 if ( n3.isDuplication() ) {
4981 if ( n3.isHasAssignedEvent() ) {
4984 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4987 if ( !n4.getName().equals( "n4" ) ) {
4990 if ( n4.getDistanceToParent() != 0.01 ) {
4993 if ( !n5.getName().equals( "n5" ) ) {
4996 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4999 if ( n5.getDistanceToParent() != 0.1 ) {
5002 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
5005 if ( !n5.isDuplication() ) {
5008 if ( !n5.isHasAssignedEvent() ) {
5011 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
5014 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
5017 final PhylogenyNode n8 = PhylogenyNode
5018 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5019 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
5022 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
5025 final PhylogenyNode n9 = PhylogenyNode
5026 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5027 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
5030 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
5033 final PhylogenyNode n10 = PhylogenyNode
5034 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5035 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
5038 final PhylogenyNode n20 = PhylogenyNode
5039 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5040 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
5043 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
5046 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
5047 NHXParser.TAXONOMY_EXTRACTION.YES );
5048 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
5051 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
5054 final PhylogenyNode n20xx = PhylogenyNode
5055 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5056 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
5059 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
5062 final PhylogenyNode n20xxx = PhylogenyNode
5063 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5064 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
5067 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
5070 final PhylogenyNode n20xxxx = PhylogenyNode
5071 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5072 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
5075 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
5078 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
5079 NHXParser.TAXONOMY_EXTRACTION.YES );
5080 if ( !n21.getName().equals( "n21_PIG" ) ) {
5083 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
5086 final PhylogenyNode n21x = PhylogenyNode
5087 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5088 if ( !n21x.getName().equals( "n21_PIG" ) ) {
5091 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
5094 final PhylogenyNode n22 = PhylogenyNode
5095 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5096 if ( !n22.getName().equals( "n22/PIG" ) ) {
5099 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
5102 final PhylogenyNode n23 = PhylogenyNode
5103 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5104 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
5107 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
5110 final PhylogenyNode a = PhylogenyNode
5111 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5112 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
5115 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
5118 final PhylogenyNode b = PhylogenyNode
5119 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5120 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
5123 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
5126 final PhylogenyNode c = PhylogenyNode
5127 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
5128 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5129 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
5132 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
5135 final PhylogenyNode c1 = PhylogenyNode
5136 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
5137 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5138 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
5141 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
5144 final PhylogenyNode c2 = PhylogenyNode
5145 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
5146 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5147 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5150 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5153 final PhylogenyNode d = PhylogenyNode
5154 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5155 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5158 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5161 final PhylogenyNode e = PhylogenyNode
5162 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5163 if ( !e.getName().equals( "n10_RAT1" ) ) {
5166 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5169 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5170 NHXParser.TAXONOMY_EXTRACTION.YES );
5171 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5174 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5177 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5178 NHXParser.TAXONOMY_EXTRACTION.YES );
5179 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5182 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5185 final PhylogenyNode n11 = PhylogenyNode
5186 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5187 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5188 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5191 if ( n11.getDistanceToParent() != 0.4 ) {
5194 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5197 final PhylogenyNode n12 = PhylogenyNode
5198 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5199 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5200 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5203 if ( n12.getDistanceToParent() != 0.4 ) {
5206 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5209 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5210 NHXParser.TAXONOMY_EXTRACTION.YES );
5211 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5214 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5217 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5218 NHXParser.TAXONOMY_EXTRACTION.YES );
5219 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5222 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5225 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
5226 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
5227 if ( !tvu1.getRef().equals( "tag1" ) ) {
5230 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
5233 if ( !tvu1.getUnit().equals( "unit1" ) ) {
5236 if ( !tvu1.getValue().equals( "value1" ) ) {
5239 if ( !tvu3.getRef().equals( "tag3" ) ) {
5242 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
5245 if ( !tvu3.getUnit().equals( "unit3" ) ) {
5248 if ( !tvu3.getValue().equals( "value3" ) ) {
5251 if ( n1.getName().compareTo( "" ) != 0 ) {
5254 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5257 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5260 if ( n2.getName().compareTo( "" ) != 0 ) {
5263 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5266 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5269 final PhylogenyNode n00 = PhylogenyNode
5270 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
5271 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
5274 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5277 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5280 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
5283 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
5286 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
5289 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
5292 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
5295 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5296 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5299 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
5300 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
5303 final PhylogenyNode n13 = PhylogenyNode
5304 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5305 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5308 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5311 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5314 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5317 final PhylogenyNode n14 = PhylogenyNode
5318 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5319 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5322 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5325 final PhylogenyNode n15 = PhylogenyNode
5326 .createInstanceFromNhxString( "something_wicked[123]",
5327 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5328 if ( !n15.getName().equals( "something_wicked" ) ) {
5331 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5334 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5337 final PhylogenyNode n16 = PhylogenyNode
5338 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5339 if ( !n16.getName().equals( "something_wicked2" ) ) {
5342 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5345 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5348 final PhylogenyNode n17 = PhylogenyNode
5349 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5350 if ( !n17.getName().equals( "something_wicked3" ) ) {
5353 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5356 final PhylogenyNode n18 = PhylogenyNode
5357 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5358 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5361 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5364 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5367 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
5368 NHXParser.TAXONOMY_EXTRACTION.YES );
5369 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
5372 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5375 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
5376 NHXParser.TAXONOMY_EXTRACTION.YES );
5377 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
5380 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5383 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
5384 NHXParser.TAXONOMY_EXTRACTION.YES );
5385 if ( n31.getNodeData().isHasTaxonomy() ) {
5388 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5389 NHXParser.TAXONOMY_EXTRACTION.YES );
5390 if ( n32.getNodeData().isHasTaxonomy() ) {
5394 catch ( final Exception e ) {
5395 e.printStackTrace( System.out );
5401 private static boolean testNHXParsing() {
5403 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5404 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5405 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5408 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]";
5409 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5410 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5413 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]";
5414 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5415 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5418 final Phylogeny[] p3 = factory
5419 .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]",
5421 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5424 final Phylogeny[] p4 = factory
5425 .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(]",
5427 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5430 final Phylogeny[] p5 = factory
5431 .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(((]",
5433 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5436 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)";
5437 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)";
5438 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5439 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5442 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)))";
5443 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)))";
5444 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5445 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5448 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]) ))[,,, ])))))))";
5449 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5450 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5451 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5454 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5455 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5458 final Phylogeny p10 = factory
5459 .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]",
5460 new NHXParser() )[ 0 ];
5461 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5465 catch ( final Exception e ) {
5466 e.printStackTrace( System.out );
5472 private static boolean testNHXParsingQuotes() {
5474 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5475 final NHXParser p = new NHXParser();
5476 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5477 if ( phylogenies_0.length != 5 ) {
5480 final Phylogeny phy = phylogenies_0[ 4 ];
5481 if ( phy.getNumberOfExternalNodes() != 7 ) {
5484 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5487 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5490 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5491 .getScientificName().equals( "hsapiens" ) ) {
5494 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5497 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5500 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5503 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5506 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5509 final NHXParser p1p = new NHXParser();
5510 p1p.setIgnoreQuotes( true );
5511 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5512 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5515 final NHXParser p2p = new NHXParser();
5516 p1p.setIgnoreQuotes( false );
5517 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5518 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5521 final NHXParser p3p = new NHXParser();
5522 p3p.setIgnoreQuotes( false );
5523 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5524 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5527 final NHXParser p4p = new NHXParser();
5528 p4p.setIgnoreQuotes( false );
5529 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5530 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5533 final Phylogeny p10 = factory
5534 .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]",
5535 new NHXParser() )[ 0 ];
5536 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]";
5537 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5540 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5541 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5545 final Phylogeny p12 = factory
5546 .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]",
5547 new NHXParser() )[ 0 ];
5548 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]";
5549 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5552 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5553 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5556 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;";
5557 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5560 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5561 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5565 catch ( final Exception e ) {
5566 e.printStackTrace( System.out );
5572 private static boolean testNHXParsingMB() {
5574 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5575 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5576 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5577 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5578 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5579 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5580 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5581 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5582 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5583 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5584 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5587 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5590 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5591 0.1100000000000000e+00 ) ) {
5594 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5597 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5600 final Phylogeny p2 = factory
5601 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5602 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5603 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5604 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5605 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5606 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5607 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5608 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5609 + "7.369400000000000e-02}])",
5610 new NHXParser() )[ 0 ];
5611 if ( p2.getNode( "1" ) == null ) {
5614 if ( p2.getNode( "2" ) == null ) {
5618 catch ( final Exception e ) {
5619 e.printStackTrace( System.out );
5626 private static boolean testPhylogenyBranch() {
5628 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5629 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5630 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5631 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5632 if ( !a1b1.equals( a1b1 ) ) {
5635 if ( !a1b1.equals( b1a1 ) ) {
5638 if ( !b1a1.equals( a1b1 ) ) {
5641 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5642 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5643 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5644 if ( a1_b1.equals( b1_a1 ) ) {
5647 if ( a1_b1.equals( a1_b1_ ) ) {
5650 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5651 if ( !a1_b1.equals( b1_a1_ ) ) {
5654 if ( a1_b1_.equals( b1_a1_ ) ) {
5657 if ( !a1_b1_.equals( b1_a1 ) ) {
5661 catch ( final Exception e ) {
5662 e.printStackTrace( System.out );
5668 private static boolean testPhyloXMLparsingOfDistributionElement() {
5670 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5671 PhyloXmlParser xml_parser = null;
5673 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5675 catch ( final Exception e ) {
5676 // Do nothing -- means were not running from jar.
5678 if ( xml_parser == null ) {
5679 xml_parser = new PhyloXmlParser();
5680 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5681 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5684 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5687 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5689 if ( xml_parser.getErrorCount() > 0 ) {
5690 System.out.println( xml_parser.getErrorMessages().toString() );
5693 if ( phylogenies_0.length != 1 ) {
5696 final Phylogeny t1 = phylogenies_0[ 0 ];
5697 PhylogenyNode n = null;
5698 Distribution d = null;
5699 n = t1.getNode( "root node" );
5700 if ( !n.getNodeData().isHasDistribution() ) {
5703 if ( n.getNodeData().getDistributions().size() != 1 ) {
5706 d = n.getNodeData().getDistribution();
5707 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5710 if ( d.getPoints().size() != 1 ) {
5713 if ( d.getPolygons() != null ) {
5716 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5719 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5722 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5725 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5728 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5731 n = t1.getNode( "node a" );
5732 if ( !n.getNodeData().isHasDistribution() ) {
5735 if ( n.getNodeData().getDistributions().size() != 2 ) {
5738 d = n.getNodeData().getDistribution( 1 );
5739 if ( !d.getDesc().equals( "San Diego" ) ) {
5742 if ( d.getPoints().size() != 1 ) {
5745 if ( d.getPolygons() != null ) {
5748 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5751 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5754 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5757 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5760 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5763 n = t1.getNode( "node bb" );
5764 if ( !n.getNodeData().isHasDistribution() ) {
5767 if ( n.getNodeData().getDistributions().size() != 1 ) {
5770 d = n.getNodeData().getDistribution( 0 );
5771 if ( d.getPoints().size() != 3 ) {
5774 if ( d.getPolygons().size() != 2 ) {
5777 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5780 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5783 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5786 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5789 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5792 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5795 Polygon p = d.getPolygons().get( 0 );
5796 if ( p.getPoints().size() != 3 ) {
5799 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5802 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5805 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5808 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5811 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5814 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5817 p = d.getPolygons().get( 1 );
5818 if ( p.getPoints().size() != 3 ) {
5821 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5824 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5827 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5831 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5832 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5833 if ( rt.length != 1 ) {
5836 final Phylogeny t1_rt = rt[ 0 ];
5837 n = t1_rt.getNode( "root node" );
5838 if ( !n.getNodeData().isHasDistribution() ) {
5841 if ( n.getNodeData().getDistributions().size() != 1 ) {
5844 d = n.getNodeData().getDistribution();
5845 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5848 if ( d.getPoints().size() != 1 ) {
5851 if ( d.getPolygons() != null ) {
5854 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5857 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5860 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5863 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5866 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5869 n = t1_rt.getNode( "node a" );
5870 if ( !n.getNodeData().isHasDistribution() ) {
5873 if ( n.getNodeData().getDistributions().size() != 2 ) {
5876 d = n.getNodeData().getDistribution( 1 );
5877 if ( !d.getDesc().equals( "San Diego" ) ) {
5880 if ( d.getPoints().size() != 1 ) {
5883 if ( d.getPolygons() != null ) {
5886 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5889 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5892 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5895 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5898 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5901 n = t1_rt.getNode( "node bb" );
5902 if ( !n.getNodeData().isHasDistribution() ) {
5905 if ( n.getNodeData().getDistributions().size() != 1 ) {
5908 d = n.getNodeData().getDistribution( 0 );
5909 if ( d.getPoints().size() != 3 ) {
5912 if ( d.getPolygons().size() != 2 ) {
5915 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5918 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5921 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5924 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5927 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5930 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5933 p = d.getPolygons().get( 0 );
5934 if ( p.getPoints().size() != 3 ) {
5937 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5940 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5943 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5946 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5949 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5952 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5955 p = d.getPolygons().get( 1 );
5956 if ( p.getPoints().size() != 3 ) {
5959 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5962 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5965 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5969 catch ( final Exception e ) {
5970 e.printStackTrace( System.out );
5976 private static boolean testPostOrderIterator() {
5978 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5979 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5980 PhylogenyNodeIterator it0;
5981 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5984 for( it0.reset(); it0.hasNext(); ) {
5987 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5988 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5989 if ( !it.next().getName().equals( "A" ) ) {
5992 if ( !it.next().getName().equals( "B" ) ) {
5995 if ( !it.next().getName().equals( "ab" ) ) {
5998 if ( !it.next().getName().equals( "C" ) ) {
6001 if ( !it.next().getName().equals( "D" ) ) {
6004 if ( !it.next().getName().equals( "cd" ) ) {
6007 if ( !it.next().getName().equals( "abcd" ) ) {
6010 if ( !it.next().getName().equals( "E" ) ) {
6013 if ( !it.next().getName().equals( "F" ) ) {
6016 if ( !it.next().getName().equals( "ef" ) ) {
6019 if ( !it.next().getName().equals( "G" ) ) {
6022 if ( !it.next().getName().equals( "H" ) ) {
6025 if ( !it.next().getName().equals( "gh" ) ) {
6028 if ( !it.next().getName().equals( "efgh" ) ) {
6031 if ( !it.next().getName().equals( "r" ) ) {
6034 if ( it.hasNext() ) {
6038 catch ( final Exception e ) {
6039 e.printStackTrace( System.out );
6045 private static boolean testPreOrderIterator() {
6047 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6048 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6049 PhylogenyNodeIterator it0;
6050 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
6053 for( it0.reset(); it0.hasNext(); ) {
6056 PhylogenyNodeIterator it = t0.iteratorPreorder();
6057 if ( !it.next().getName().equals( "r" ) ) {
6060 if ( !it.next().getName().equals( "ab" ) ) {
6063 if ( !it.next().getName().equals( "A" ) ) {
6066 if ( !it.next().getName().equals( "B" ) ) {
6069 if ( !it.next().getName().equals( "cd" ) ) {
6072 if ( !it.next().getName().equals( "C" ) ) {
6075 if ( !it.next().getName().equals( "D" ) ) {
6078 if ( it.hasNext() ) {
6081 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6082 it = t1.iteratorPreorder();
6083 if ( !it.next().getName().equals( "r" ) ) {
6086 if ( !it.next().getName().equals( "abcd" ) ) {
6089 if ( !it.next().getName().equals( "ab" ) ) {
6092 if ( !it.next().getName().equals( "A" ) ) {
6095 if ( !it.next().getName().equals( "B" ) ) {
6098 if ( !it.next().getName().equals( "cd" ) ) {
6101 if ( !it.next().getName().equals( "C" ) ) {
6104 if ( !it.next().getName().equals( "D" ) ) {
6107 if ( !it.next().getName().equals( "efgh" ) ) {
6110 if ( !it.next().getName().equals( "ef" ) ) {
6113 if ( !it.next().getName().equals( "E" ) ) {
6116 if ( !it.next().getName().equals( "F" ) ) {
6119 if ( !it.next().getName().equals( "gh" ) ) {
6122 if ( !it.next().getName().equals( "G" ) ) {
6125 if ( !it.next().getName().equals( "H" ) ) {
6128 if ( it.hasNext() ) {
6132 catch ( final Exception e ) {
6133 e.printStackTrace( System.out );
6139 private static boolean testPropertiesMap() {
6141 final PropertiesMap pm = new PropertiesMap();
6142 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6143 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6144 final Property p2 = new Property( "something:else",
6146 "improbable:research",
6149 pm.addProperty( p0 );
6150 pm.addProperty( p1 );
6151 pm.addProperty( p2 );
6152 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
6155 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
6158 if ( pm.getProperties().size() != 3 ) {
6161 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
6164 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6167 if ( pm.getProperties().size() != 3 ) {
6170 pm.removeProperty( "dimensions:diameter" );
6171 if ( pm.getProperties().size() != 2 ) {
6174 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
6177 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6181 catch ( final Exception e ) {
6182 e.printStackTrace( System.out );
6188 private static boolean testReIdMethods() {
6190 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6191 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6192 final int count = PhylogenyNode.getNodeCount();
6194 if ( p.getNode( "r" ).getId() != count ) {
6197 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6200 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6203 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6206 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6209 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6212 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6215 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6218 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6221 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6224 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6227 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6230 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6233 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6236 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6240 catch ( final Exception e ) {
6241 e.printStackTrace( System.out );
6247 private static boolean testRerooting() {
6249 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6250 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",
6251 new NHXParser() )[ 0 ];
6252 if ( !t1.isRooted() ) {
6255 t1.reRoot( t1.getNode( "D" ) );
6256 t1.reRoot( t1.getNode( "CD" ) );
6257 t1.reRoot( t1.getNode( "A" ) );
6258 t1.reRoot( t1.getNode( "B" ) );
6259 t1.reRoot( t1.getNode( "AB" ) );
6260 t1.reRoot( t1.getNode( "D" ) );
6261 t1.reRoot( t1.getNode( "C" ) );
6262 t1.reRoot( t1.getNode( "CD" ) );
6263 t1.reRoot( t1.getNode( "A" ) );
6264 t1.reRoot( t1.getNode( "B" ) );
6265 t1.reRoot( t1.getNode( "AB" ) );
6266 t1.reRoot( t1.getNode( "D" ) );
6267 t1.reRoot( t1.getNode( "D" ) );
6268 t1.reRoot( t1.getNode( "C" ) );
6269 t1.reRoot( t1.getNode( "A" ) );
6270 t1.reRoot( t1.getNode( "B" ) );
6271 t1.reRoot( t1.getNode( "AB" ) );
6272 t1.reRoot( t1.getNode( "C" ) );
6273 t1.reRoot( t1.getNode( "D" ) );
6274 t1.reRoot( t1.getNode( "CD" ) );
6275 t1.reRoot( t1.getNode( "D" ) );
6276 t1.reRoot( t1.getNode( "A" ) );
6277 t1.reRoot( t1.getNode( "B" ) );
6278 t1.reRoot( t1.getNode( "AB" ) );
6279 t1.reRoot( t1.getNode( "C" ) );
6280 t1.reRoot( t1.getNode( "D" ) );
6281 t1.reRoot( t1.getNode( "CD" ) );
6282 t1.reRoot( t1.getNode( "D" ) );
6283 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6286 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6289 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6292 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6295 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6298 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6301 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",
6302 new NHXParser() )[ 0 ];
6303 t2.reRoot( t2.getNode( "A" ) );
6304 t2.reRoot( t2.getNode( "D" ) );
6305 t2.reRoot( t2.getNode( "ABC" ) );
6306 t2.reRoot( t2.getNode( "A" ) );
6307 t2.reRoot( t2.getNode( "B" ) );
6308 t2.reRoot( t2.getNode( "D" ) );
6309 t2.reRoot( t2.getNode( "C" ) );
6310 t2.reRoot( t2.getNode( "ABC" ) );
6311 t2.reRoot( t2.getNode( "A" ) );
6312 t2.reRoot( t2.getNode( "B" ) );
6313 t2.reRoot( t2.getNode( "AB" ) );
6314 t2.reRoot( t2.getNode( "AB" ) );
6315 t2.reRoot( t2.getNode( "D" ) );
6316 t2.reRoot( t2.getNode( "C" ) );
6317 t2.reRoot( t2.getNode( "B" ) );
6318 t2.reRoot( t2.getNode( "AB" ) );
6319 t2.reRoot( t2.getNode( "D" ) );
6320 t2.reRoot( t2.getNode( "D" ) );
6321 t2.reRoot( t2.getNode( "ABC" ) );
6322 t2.reRoot( t2.getNode( "A" ) );
6323 t2.reRoot( t2.getNode( "B" ) );
6324 t2.reRoot( t2.getNode( "AB" ) );
6325 t2.reRoot( t2.getNode( "D" ) );
6326 t2.reRoot( t2.getNode( "C" ) );
6327 t2.reRoot( t2.getNode( "ABC" ) );
6328 t2.reRoot( t2.getNode( "A" ) );
6329 t2.reRoot( t2.getNode( "B" ) );
6330 t2.reRoot( t2.getNode( "AB" ) );
6331 t2.reRoot( t2.getNode( "D" ) );
6332 t2.reRoot( t2.getNode( "D" ) );
6333 t2.reRoot( t2.getNode( "C" ) );
6334 t2.reRoot( t2.getNode( "A" ) );
6335 t2.reRoot( t2.getNode( "B" ) );
6336 t2.reRoot( t2.getNode( "AB" ) );
6337 t2.reRoot( t2.getNode( "C" ) );
6338 t2.reRoot( t2.getNode( "D" ) );
6339 t2.reRoot( t2.getNode( "ABC" ) );
6340 t2.reRoot( t2.getNode( "D" ) );
6341 t2.reRoot( t2.getNode( "A" ) );
6342 t2.reRoot( t2.getNode( "B" ) );
6343 t2.reRoot( t2.getNode( "AB" ) );
6344 t2.reRoot( t2.getNode( "C" ) );
6345 t2.reRoot( t2.getNode( "D" ) );
6346 t2.reRoot( t2.getNode( "ABC" ) );
6347 t2.reRoot( t2.getNode( "D" ) );
6348 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6351 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6354 t2.reRoot( t2.getNode( "ABC" ) );
6355 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6358 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6361 t2.reRoot( t2.getNode( "AB" ) );
6362 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6365 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6368 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6371 t2.reRoot( t2.getNode( "AB" ) );
6372 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6375 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6378 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6381 t2.reRoot( t2.getNode( "D" ) );
6382 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6385 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6388 t2.reRoot( t2.getNode( "ABC" ) );
6389 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6392 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6395 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6396 new NHXParser() )[ 0 ];
6397 t3.reRoot( t3.getNode( "B" ) );
6398 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6401 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6404 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6407 t3.reRoot( t3.getNode( "B" ) );
6408 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6411 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6414 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6417 t3.reRoot( t3.getRoot() );
6418 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6421 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6424 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6428 catch ( final Exception e ) {
6429 e.printStackTrace( System.out );
6435 private static boolean testSDIse() {
6437 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6438 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6439 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6440 gene1.setRooted( true );
6441 species1.setRooted( true );
6442 final SDI sdi = new SDI( gene1, species1 );
6443 if ( !gene1.getRoot().isDuplication() ) {
6446 final Phylogeny species2 = factory
6447 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6448 new NHXParser() )[ 0 ];
6449 final Phylogeny gene2 = factory
6450 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6451 new NHXParser() )[ 0 ];
6452 species2.setRooted( true );
6453 gene2.setRooted( true );
6454 final SDI sdi2 = new SDI( gene2, species2 );
6455 if ( sdi2.getDuplicationsSum() != 0 ) {
6458 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6461 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6464 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6467 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6470 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6473 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6476 final Phylogeny species3 = factory
6477 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6478 new NHXParser() )[ 0 ];
6479 final Phylogeny gene3 = factory
6480 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6481 new NHXParser() )[ 0 ];
6482 species3.setRooted( true );
6483 gene3.setRooted( true );
6484 final SDI sdi3 = new SDI( gene3, species3 );
6485 if ( sdi3.getDuplicationsSum() != 1 ) {
6488 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6491 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6494 final Phylogeny species4 = factory
6495 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6496 new NHXParser() )[ 0 ];
6497 final Phylogeny gene4 = factory
6498 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6499 new NHXParser() )[ 0 ];
6500 species4.setRooted( true );
6501 gene4.setRooted( true );
6502 final SDI sdi4 = new SDI( gene4, species4 );
6503 if ( sdi4.getDuplicationsSum() != 1 ) {
6506 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6509 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6512 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6515 if ( species4.getNumberOfExternalNodes() != 6 ) {
6518 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6521 final Phylogeny species5 = factory
6522 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6523 new NHXParser() )[ 0 ];
6524 final Phylogeny gene5 = factory
6525 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6526 new NHXParser() )[ 0 ];
6527 species5.setRooted( true );
6528 gene5.setRooted( true );
6529 final SDI sdi5 = new SDI( gene5, species5 );
6530 if ( sdi5.getDuplicationsSum() != 2 ) {
6533 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6536 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6539 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6542 if ( species5.getNumberOfExternalNodes() != 6 ) {
6545 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6548 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6549 // Conjecture for Comparing Molecular Phylogenies"
6550 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6551 final Phylogeny species6 = factory
6552 .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,"
6553 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6554 new NHXParser() )[ 0 ];
6555 final Phylogeny gene6 = factory
6556 .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,"
6557 + "((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,"
6558 + "(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;",
6559 new NHXParser() )[ 0 ];
6560 species6.setRooted( true );
6561 gene6.setRooted( true );
6562 final SDI sdi6 = new SDI( gene6, species6 );
6563 if ( sdi6.getDuplicationsSum() != 3 ) {
6566 if ( !gene6.getNode( "r" ).isDuplication() ) {
6569 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6572 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6575 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6578 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6581 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6584 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6587 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6590 sdi6.computeMappingCostL();
6591 if ( sdi6.computeMappingCostL() != 17 ) {
6594 if ( species6.getNumberOfExternalNodes() != 9 ) {
6597 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6600 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6601 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6602 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6603 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6604 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6605 species7.setRooted( true );
6606 final Phylogeny gene7_1 = Test
6607 .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])" );
6608 gene7_1.setRooted( true );
6609 final SDI sdi7 = new SDI( gene7_1, species7 );
6610 if ( sdi7.getDuplicationsSum() != 0 ) {
6613 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6616 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6619 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6622 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6625 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6628 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6631 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6634 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6637 final Phylogeny gene7_2 = Test
6638 .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])" );
6639 gene7_2.setRooted( true );
6640 final SDI sdi7_2 = new SDI( gene7_2, species7 );
6641 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6644 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6647 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6650 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6653 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6656 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6659 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6662 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6665 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6668 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6672 catch ( final Exception e ) {
6678 private static boolean testSDIunrooted() {
6680 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6681 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6682 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6683 final Iterator<PhylogenyBranch> iter = l.iterator();
6684 PhylogenyBranch br = iter.next();
6685 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6688 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6692 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6695 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6699 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6702 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6706 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6709 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6713 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6716 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6720 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6723 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6727 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6730 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6734 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6737 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6741 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6744 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6748 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6751 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6755 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6758 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6762 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6765 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6769 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6772 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6776 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6779 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6783 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6786 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6789 if ( iter.hasNext() ) {
6792 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6793 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6794 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6796 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6799 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6803 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6806 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6810 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6813 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6816 if ( iter1.hasNext() ) {
6819 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6820 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6821 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6823 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6826 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6830 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6833 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6837 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6840 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6843 if ( iter2.hasNext() ) {
6846 final Phylogeny species0 = factory
6847 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6848 new NHXParser() )[ 0 ];
6849 final Phylogeny gene1 = factory
6850 .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])",
6851 new NHXParser() )[ 0 ];
6852 species0.setRooted( true );
6853 gene1.setRooted( true );
6854 final SDIR sdi_unrooted = new SDIR();
6855 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6856 if ( sdi_unrooted.getCount() != 1 ) {
6859 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6862 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6865 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6868 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6871 final Phylogeny gene2 = factory
6872 .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])",
6873 new NHXParser() )[ 0 ];
6874 gene2.setRooted( true );
6875 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6876 if ( sdi_unrooted.getCount() != 1 ) {
6879 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6882 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6885 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6888 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6891 final Phylogeny species6 = factory
6892 .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,"
6893 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6894 new NHXParser() )[ 0 ];
6895 final Phylogeny gene6 = factory
6896 .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],"
6897 + "(((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],"
6898 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6899 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6900 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6901 new NHXParser() )[ 0 ];
6902 species6.setRooted( true );
6903 gene6.setRooted( true );
6904 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6905 if ( sdi_unrooted.getCount() != 1 ) {
6908 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6911 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6914 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6917 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6920 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6923 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6926 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6929 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6932 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6935 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6938 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6941 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6945 final Phylogeny species7 = factory
6946 .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,"
6947 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6948 new NHXParser() )[ 0 ];
6949 final Phylogeny gene7 = factory
6950 .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],"
6951 + "(((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],"
6952 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6953 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6954 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6955 new NHXParser() )[ 0 ];
6956 species7.setRooted( true );
6957 gene7.setRooted( true );
6958 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6959 if ( sdi_unrooted.getCount() != 1 ) {
6962 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6965 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6968 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6971 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6974 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6977 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6980 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6983 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6986 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6989 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6992 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6995 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6999 final Phylogeny species8 = factory
7000 .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,"
7001 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7002 new NHXParser() )[ 0 ];
7003 final Phylogeny gene8 = factory
7004 .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],"
7005 + "(((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],"
7006 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7007 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7008 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7009 new NHXParser() )[ 0 ];
7010 species8.setRooted( true );
7011 gene8.setRooted( true );
7012 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
7013 if ( sdi_unrooted.getCount() != 1 ) {
7016 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7019 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7022 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7025 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7028 if ( !p8[ 0 ].getRoot().isDuplication() ) {
7031 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7034 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7037 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
7040 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7043 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
7046 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
7049 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7054 catch ( final Exception e ) {
7055 e.printStackTrace( System.out );
7061 private static boolean testSplit() {
7063 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7064 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7065 //Archaeopteryx.createApplication( p0 );
7066 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7067 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7068 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7069 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7070 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7071 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7072 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7073 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7074 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7075 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7076 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
7077 // System.out.println( s0.toString() );
7079 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7081 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7082 if ( s0.match( query_nodes ) ) {
7085 query_nodes = new HashSet<PhylogenyNode>();
7086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7090 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7093 if ( !s0.match( query_nodes ) ) {
7097 query_nodes = new HashSet<PhylogenyNode>();
7098 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7101 if ( !s0.match( query_nodes ) ) {
7105 query_nodes = new HashSet<PhylogenyNode>();
7106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7107 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7108 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7109 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7110 if ( !s0.match( query_nodes ) ) {
7114 query_nodes = new HashSet<PhylogenyNode>();
7115 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7116 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7119 if ( !s0.match( query_nodes ) ) {
7123 query_nodes = new HashSet<PhylogenyNode>();
7124 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7125 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7126 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7127 if ( !s0.match( query_nodes ) ) {
7131 query_nodes = new HashSet<PhylogenyNode>();
7132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7133 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7134 if ( !s0.match( query_nodes ) ) {
7138 query_nodes = new HashSet<PhylogenyNode>();
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7141 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7142 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7143 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7144 if ( !s0.match( query_nodes ) ) {
7148 query_nodes = new HashSet<PhylogenyNode>();
7149 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7150 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7151 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7152 if ( !s0.match( query_nodes ) ) {
7156 query_nodes = new HashSet<PhylogenyNode>();
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7159 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7160 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7161 if ( !s0.match( query_nodes ) ) {
7165 query_nodes = new HashSet<PhylogenyNode>();
7166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7168 if ( s0.match( query_nodes ) ) {
7172 query_nodes = new HashSet<PhylogenyNode>();
7173 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7177 if ( s0.match( query_nodes ) ) {
7181 query_nodes = new HashSet<PhylogenyNode>();
7182 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7184 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7187 if ( s0.match( query_nodes ) ) {
7191 query_nodes = new HashSet<PhylogenyNode>();
7192 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7195 if ( s0.match( query_nodes ) ) {
7199 query_nodes = new HashSet<PhylogenyNode>();
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7202 if ( s0.match( query_nodes ) ) {
7206 query_nodes = new HashSet<PhylogenyNode>();
7207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7209 if ( s0.match( query_nodes ) ) {
7213 query_nodes = new HashSet<PhylogenyNode>();
7214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7216 if ( s0.match( query_nodes ) ) {
7220 query_nodes = new HashSet<PhylogenyNode>();
7221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7223 if ( s0.match( query_nodes ) ) {
7227 query_nodes = new HashSet<PhylogenyNode>();
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7230 if ( s0.match( query_nodes ) ) {
7234 query_nodes = new HashSet<PhylogenyNode>();
7235 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7236 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7237 if ( s0.match( query_nodes ) ) {
7241 query_nodes = new HashSet<PhylogenyNode>();
7242 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7244 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7245 if ( s0.match( query_nodes ) ) {
7249 query_nodes = new HashSet<PhylogenyNode>();
7250 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7253 if ( s0.match( query_nodes ) ) {
7257 query_nodes = new HashSet<PhylogenyNode>();
7258 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7259 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7260 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7261 if ( s0.match( query_nodes ) ) {
7265 query_nodes = new HashSet<PhylogenyNode>();
7266 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7267 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7268 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7269 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7270 if ( s0.match( query_nodes ) ) {
7274 // query_nodes = new HashSet<PhylogenyNode>();
7275 // query_nodes.add( new PhylogenyNode( "X" ) );
7276 // query_nodes.add( new PhylogenyNode( "Y" ) );
7277 // query_nodes.add( new PhylogenyNode( "A" ) );
7278 // query_nodes.add( new PhylogenyNode( "B" ) );
7279 // query_nodes.add( new PhylogenyNode( "C" ) );
7280 // query_nodes.add( new PhylogenyNode( "D" ) );
7281 // query_nodes.add( new PhylogenyNode( "E" ) );
7282 // query_nodes.add( new PhylogenyNode( "F" ) );
7283 // query_nodes.add( new PhylogenyNode( "G" ) );
7284 // if ( !s0.match( query_nodes ) ) {
7287 // query_nodes = new HashSet<PhylogenyNode>();
7288 // query_nodes.add( new PhylogenyNode( "X" ) );
7289 // query_nodes.add( new PhylogenyNode( "Y" ) );
7290 // query_nodes.add( new PhylogenyNode( "A" ) );
7291 // query_nodes.add( new PhylogenyNode( "B" ) );
7292 // query_nodes.add( new PhylogenyNode( "C" ) );
7293 // if ( !s0.match( query_nodes ) ) {
7297 // query_nodes = new HashSet<PhylogenyNode>();
7298 // query_nodes.add( new PhylogenyNode( "X" ) );
7299 // query_nodes.add( new PhylogenyNode( "Y" ) );
7300 // query_nodes.add( new PhylogenyNode( "D" ) );
7301 // query_nodes.add( new PhylogenyNode( "E" ) );
7302 // query_nodes.add( new PhylogenyNode( "F" ) );
7303 // query_nodes.add( new PhylogenyNode( "G" ) );
7304 // if ( !s0.match( query_nodes ) ) {
7308 // query_nodes = new HashSet<PhylogenyNode>();
7309 // query_nodes.add( new PhylogenyNode( "X" ) );
7310 // query_nodes.add( new PhylogenyNode( "Y" ) );
7311 // query_nodes.add( new PhylogenyNode( "A" ) );
7312 // query_nodes.add( new PhylogenyNode( "B" ) );
7313 // query_nodes.add( new PhylogenyNode( "C" ) );
7314 // query_nodes.add( new PhylogenyNode( "D" ) );
7315 // if ( !s0.match( query_nodes ) ) {
7319 // query_nodes = new HashSet<PhylogenyNode>();
7320 // query_nodes.add( new PhylogenyNode( "X" ) );
7321 // query_nodes.add( new PhylogenyNode( "Y" ) );
7322 // query_nodes.add( new PhylogenyNode( "E" ) );
7323 // query_nodes.add( new PhylogenyNode( "F" ) );
7324 // query_nodes.add( new PhylogenyNode( "G" ) );
7325 // if ( !s0.match( query_nodes ) ) {
7329 // query_nodes = new HashSet<PhylogenyNode>();
7330 // query_nodes.add( new PhylogenyNode( "X" ) );
7331 // query_nodes.add( new PhylogenyNode( "Y" ) );
7332 // query_nodes.add( new PhylogenyNode( "F" ) );
7333 // query_nodes.add( new PhylogenyNode( "G" ) );
7334 // if ( !s0.match( query_nodes ) ) {
7338 query_nodes = new HashSet<PhylogenyNode>();
7339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7342 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7343 if ( s0.match( query_nodes ) ) {
7347 query_nodes = new HashSet<PhylogenyNode>();
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7351 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7352 if ( s0.match( query_nodes ) ) {
7355 ///////////////////////////
7357 query_nodes = new HashSet<PhylogenyNode>();
7358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7359 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7360 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7361 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7362 if ( s0.match( query_nodes ) ) {
7366 query_nodes = new HashSet<PhylogenyNode>();
7367 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7368 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7369 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7370 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7371 if ( s0.match( query_nodes ) ) {
7375 query_nodes = new HashSet<PhylogenyNode>();
7376 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7377 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7378 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7380 if ( s0.match( query_nodes ) ) {
7384 query_nodes = new HashSet<PhylogenyNode>();
7385 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7386 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7387 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7388 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7389 if ( s0.match( query_nodes ) ) {
7393 query_nodes = new HashSet<PhylogenyNode>();
7394 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7395 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7396 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7397 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7398 if ( s0.match( query_nodes ) ) {
7402 query_nodes = new HashSet<PhylogenyNode>();
7403 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7404 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7405 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7406 if ( s0.match( query_nodes ) ) {
7410 query_nodes = new HashSet<PhylogenyNode>();
7411 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7412 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7413 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7414 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7416 if ( s0.match( query_nodes ) ) {
7420 query_nodes = new HashSet<PhylogenyNode>();
7421 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7422 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7423 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7424 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7425 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7426 if ( s0.match( query_nodes ) ) {
7430 query_nodes = new HashSet<PhylogenyNode>();
7431 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7432 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7433 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7434 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7435 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7436 if ( s0.match( query_nodes ) ) {
7440 query_nodes = new HashSet<PhylogenyNode>();
7441 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7442 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7443 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7444 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7445 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7446 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7447 if ( s0.match( query_nodes ) ) {
7451 catch ( final Exception e ) {
7452 e.printStackTrace();
7458 private static boolean testSplitStrict() {
7460 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7461 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7462 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7463 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7464 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7465 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7466 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7467 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7468 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7469 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7470 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7471 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7472 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7473 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7474 if ( s0.match( query_nodes ) ) {
7477 query_nodes = new HashSet<PhylogenyNode>();
7478 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7479 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7480 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7481 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7482 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7485 if ( !s0.match( query_nodes ) ) {
7489 query_nodes = new HashSet<PhylogenyNode>();
7490 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7491 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7493 if ( !s0.match( query_nodes ) ) {
7497 query_nodes = new HashSet<PhylogenyNode>();
7498 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7499 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7500 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7501 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7502 if ( !s0.match( query_nodes ) ) {
7506 query_nodes = new HashSet<PhylogenyNode>();
7507 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7508 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7509 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7510 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7511 if ( !s0.match( query_nodes ) ) {
7515 query_nodes = new HashSet<PhylogenyNode>();
7516 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7517 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7518 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7519 if ( !s0.match( query_nodes ) ) {
7523 query_nodes = new HashSet<PhylogenyNode>();
7524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7525 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7526 if ( !s0.match( query_nodes ) ) {
7530 query_nodes = new HashSet<PhylogenyNode>();
7531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7533 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7534 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7535 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7536 if ( !s0.match( query_nodes ) ) {
7540 query_nodes = new HashSet<PhylogenyNode>();
7541 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7542 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7543 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7544 if ( !s0.match( query_nodes ) ) {
7548 query_nodes = new HashSet<PhylogenyNode>();
7549 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7550 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7551 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7552 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7553 if ( !s0.match( query_nodes ) ) {
7557 query_nodes = new HashSet<PhylogenyNode>();
7558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7560 if ( s0.match( query_nodes ) ) {
7564 query_nodes = new HashSet<PhylogenyNode>();
7565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7569 if ( s0.match( query_nodes ) ) {
7573 query_nodes = new HashSet<PhylogenyNode>();
7574 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7575 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7578 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7579 if ( s0.match( query_nodes ) ) {
7583 query_nodes = new HashSet<PhylogenyNode>();
7584 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7587 if ( s0.match( query_nodes ) ) {
7591 query_nodes = new HashSet<PhylogenyNode>();
7592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7594 if ( s0.match( query_nodes ) ) {
7598 query_nodes = new HashSet<PhylogenyNode>();
7599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7601 if ( s0.match( query_nodes ) ) {
7605 query_nodes = new HashSet<PhylogenyNode>();
7606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7608 if ( s0.match( query_nodes ) ) {
7612 query_nodes = new HashSet<PhylogenyNode>();
7613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7615 if ( s0.match( query_nodes ) ) {
7619 query_nodes = new HashSet<PhylogenyNode>();
7620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7622 if ( s0.match( query_nodes ) ) {
7626 query_nodes = new HashSet<PhylogenyNode>();
7627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7629 if ( s0.match( query_nodes ) ) {
7633 query_nodes = new HashSet<PhylogenyNode>();
7634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7637 if ( s0.match( query_nodes ) ) {
7641 query_nodes = new HashSet<PhylogenyNode>();
7642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7645 if ( s0.match( query_nodes ) ) {
7649 query_nodes = new HashSet<PhylogenyNode>();
7650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7653 if ( s0.match( query_nodes ) ) {
7657 query_nodes = new HashSet<PhylogenyNode>();
7658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7662 if ( s0.match( query_nodes ) ) {
7666 catch ( final Exception e ) {
7667 e.printStackTrace();
7673 private static boolean testSubtreeDeletion() {
7675 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7676 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7677 t1.deleteSubtree( t1.getNode( "A" ), false );
7678 if ( t1.getNumberOfExternalNodes() != 5 ) {
7681 t1.toNewHampshireX();
7682 t1.deleteSubtree( t1.getNode( "E" ), false );
7683 if ( t1.getNumberOfExternalNodes() != 4 ) {
7686 t1.toNewHampshireX();
7687 t1.deleteSubtree( t1.getNode( "F" ), false );
7688 if ( t1.getNumberOfExternalNodes() != 3 ) {
7691 t1.toNewHampshireX();
7692 t1.deleteSubtree( t1.getNode( "D" ), false );
7693 t1.toNewHampshireX();
7694 if ( t1.getNumberOfExternalNodes() != 3 ) {
7697 t1.deleteSubtree( t1.getNode( "def" ), false );
7698 t1.toNewHampshireX();
7699 if ( t1.getNumberOfExternalNodes() != 2 ) {
7702 t1.deleteSubtree( t1.getNode( "B" ), false );
7703 t1.toNewHampshireX();
7704 if ( t1.getNumberOfExternalNodes() != 1 ) {
7707 t1.deleteSubtree( t1.getNode( "C" ), false );
7708 t1.toNewHampshireX();
7709 if ( t1.getNumberOfExternalNodes() != 1 ) {
7712 t1.deleteSubtree( t1.getNode( "abc" ), false );
7713 t1.toNewHampshireX();
7714 if ( t1.getNumberOfExternalNodes() != 1 ) {
7717 t1.deleteSubtree( t1.getNode( "r" ), false );
7718 if ( t1.getNumberOfExternalNodes() != 0 ) {
7721 if ( !t1.isEmpty() ) {
7724 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7725 t2.deleteSubtree( t2.getNode( "A" ), false );
7726 t2.toNewHampshireX();
7727 if ( t2.getNumberOfExternalNodes() != 5 ) {
7730 t2.deleteSubtree( t2.getNode( "abc" ), false );
7731 t2.toNewHampshireX();
7732 if ( t2.getNumberOfExternalNodes() != 3 ) {
7735 t2.deleteSubtree( t2.getNode( "def" ), false );
7736 t2.toNewHampshireX();
7737 if ( t2.getNumberOfExternalNodes() != 1 ) {
7741 catch ( final Exception e ) {
7742 e.printStackTrace( System.out );
7748 private static boolean testSupportCount() {
7750 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7751 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7752 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7753 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7754 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7755 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7756 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7758 SupportCount.count( t0_1, phylogenies_1, true, false );
7759 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7760 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7761 + "(((((A,B),C),D),E),((F,G),X))"
7762 + "(((((A,Y),B),C),D),((F,G),E))"
7763 + "(((((A,B),C),D),E),(F,G))"
7764 + "(((((A,B),C),D),E),(F,G))"
7765 + "(((((A,B),C),D),E),(F,G))"
7766 + "(((((A,B),C),D),E),(F,G),Z)"
7767 + "(((((A,B),C),D),E),(F,G))"
7768 + "((((((A,B),C),D),E),F),G)"
7769 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7771 SupportCount.count( t0_2, phylogenies_2, true, false );
7772 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7773 while ( it.hasNext() ) {
7774 final PhylogenyNode n = it.next();
7775 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7779 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7780 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7781 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7782 SupportCount.count( t0_3, phylogenies_3, true, false );
7783 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7784 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7787 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7790 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7793 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7796 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7799 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7802 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7805 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7808 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7811 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7814 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7815 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7816 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7817 SupportCount.count( t0_4, phylogenies_4, true, false );
7818 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7819 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7822 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7825 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7828 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7831 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7834 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7837 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7840 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7843 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7846 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7849 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7850 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7851 double d = SupportCount.compare( b1, a, true, true, true );
7852 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7855 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7856 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7857 d = SupportCount.compare( b2, a, true, true, true );
7858 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7861 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7862 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7863 d = SupportCount.compare( b3, a, true, true, true );
7864 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7867 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7868 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7869 d = SupportCount.compare( b4, a, true, true, false );
7870 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7874 catch ( final Exception e ) {
7875 e.printStackTrace( System.out );
7881 private static boolean testSupportTransfer() {
7883 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7884 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)",
7885 new NHXParser() )[ 0 ];
7886 final Phylogeny p2 = factory
7887 .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 ];
7888 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7891 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7894 support_transfer.moveBranchLengthsToBootstrap( p1 );
7895 support_transfer.transferSupportValues( p1, p2 );
7896 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7899 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7902 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7905 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7908 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7911 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7914 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7917 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7921 catch ( final Exception e ) {
7922 e.printStackTrace( System.out );
7928 private static boolean testUniprotTaxonomySearch() {
7930 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7932 if ( results.size() != 1 ) {
7935 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7938 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7941 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7944 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7947 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7951 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7952 if ( results.size() != 1 ) {
7955 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7958 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7961 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7964 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7967 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7971 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7972 if ( results.size() != 1 ) {
7975 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7978 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7981 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7984 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7987 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7991 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7992 if ( results.size() != 1 ) {
7995 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7998 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8001 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8004 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8007 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8010 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
8013 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
8016 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
8017 .equals( "Nematostella vectensis" ) ) {
8018 System.out.println( results.get( 0 ).getLineage() );
8022 catch ( final IOException e ) {
8023 System.out.println();
8024 System.out.println( "the following might be due to absence internet connection:" );
8025 e.printStackTrace( System.out );
8028 catch ( final Exception e ) {
8034 private static boolean testEmblEntryRetrieval() {
8035 //The format for GenBank Accession numbers are:
8036 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
8037 //Protein: 3 letters + 5 numerals
8038 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
8039 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
8042 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
8045 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
8048 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
8051 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
8054 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
8057 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
8060 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
8063 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
8066 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
8069 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
8072 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
8075 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8081 private static boolean testUniprotEntryRetrieval() {
8082 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8085 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8088 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8091 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8094 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8097 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8100 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8103 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8106 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8109 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8112 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8115 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8118 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8122 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8123 if ( !entry.getAccession().equals( "P12345" ) ) {
8126 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8129 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8132 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8135 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8139 catch ( final IOException e ) {
8140 System.out.println();
8141 System.out.println( "the following might be due to absence internet connection:" );
8142 e.printStackTrace( System.out );
8145 catch ( final Exception e ) {
8151 private static boolean testWabiTxSearch() {
8154 result = TxSearch.searchSimple( "nematostella" );
8155 result = TxSearch.getTxId( "nematostella" );
8156 if ( !result.equals( "45350" ) ) {
8159 result = TxSearch.getTxName( "45350" );
8160 if ( !result.equals( "Nematostella" ) ) {
8163 result = TxSearch.getTxId( "nematostella vectensis" );
8164 if ( !result.equals( "45351" ) ) {
8167 result = TxSearch.getTxName( "45351" );
8168 if ( !result.equals( "Nematostella vectensis" ) ) {
8171 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8172 if ( !result.equals( "536089" ) ) {
8175 result = TxSearch.getTxName( "536089" );
8176 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8179 final List<String> queries = new ArrayList<String>();
8180 queries.add( "Campylobacter coli" );
8181 queries.add( "Escherichia coli" );
8182 queries.add( "Arabidopsis" );
8183 queries.add( "Trichoplax" );
8184 queries.add( "Samanea saman" );
8185 queries.add( "Kluyveromyces marxianus" );
8186 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8187 queries.add( "Bornavirus parrot/PDD/2008" );
8188 final List<RANKS> ranks = new ArrayList<RANKS>();
8189 ranks.add( RANKS.SUPERKINGDOM );
8190 ranks.add( RANKS.KINGDOM );
8191 ranks.add( RANKS.FAMILY );
8192 ranks.add( RANKS.GENUS );
8193 ranks.add( RANKS.TRIBE );
8194 result = TxSearch.searchLineage( queries, ranks );
8195 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8196 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8198 catch ( final Exception e ) {
8199 System.out.println();
8200 System.out.println( "the following might be due to absence internet connection:" );
8201 e.printStackTrace( System.out );
8207 private static boolean testAminoAcidSequence() {
8209 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8210 if ( aa1.getLength() != 13 ) {
8213 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8216 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8219 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8222 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8223 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8226 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8227 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8230 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8231 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8235 catch ( final Exception e ) {
8236 e.printStackTrace();
8242 private static boolean testCreateBalancedPhylogeny() {
8244 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8245 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8248 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8251 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8252 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8255 if ( p1.getNumberOfExternalNodes() != 100 ) {
8259 catch ( final Exception e ) {
8260 e.printStackTrace();
8266 private static boolean testFastaParser() {
8268 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8271 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8274 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8275 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8278 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8281 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8284 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8287 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8290 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8294 catch ( final Exception e ) {
8295 e.printStackTrace();
8301 private static boolean testGeneralMsaParser() {
8303 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8304 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8305 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8306 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8307 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8308 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8309 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8310 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8311 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8314 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8317 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8320 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8323 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8326 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8329 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8332 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8335 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8338 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8341 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8344 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8347 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8348 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8351 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8354 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8357 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8358 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8361 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8364 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8367 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8368 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8371 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8374 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8378 catch ( final Exception e ) {
8379 e.printStackTrace();
8385 private static boolean testMafft( final String path ) {
8387 final List<String> opts = new ArrayList<String>();
8388 opts.add( "--maxiterate" );
8390 opts.add( "--localpair" );
8391 opts.add( "--quiet" );
8393 final MsaInferrer mafft = Mafft.createInstance( path );
8394 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8395 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8398 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8402 catch ( final Exception e ) {
8403 e.printStackTrace( System.out );
8409 private static boolean testNextNodeWithCollapsing() {
8411 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8413 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8414 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8415 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8416 t0.getNode( "cd" ).setCollapse( true );
8417 t0.getNode( "cde" ).setCollapse( true );
8418 n = t0.getFirstExternalNode();
8419 while ( n != null ) {
8421 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8423 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8426 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8429 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8432 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8435 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8438 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8442 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8443 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8444 t1.getNode( "ab" ).setCollapse( true );
8445 t1.getNode( "cd" ).setCollapse( true );
8446 t1.getNode( "cde" ).setCollapse( true );
8447 n = t1.getNode( "ab" );
8448 ext = new ArrayList<PhylogenyNode>();
8449 while ( n != null ) {
8451 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8453 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8456 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8459 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8462 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8465 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8471 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8472 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8473 t2.getNode( "ab" ).setCollapse( true );
8474 t2.getNode( "cd" ).setCollapse( true );
8475 t2.getNode( "cde" ).setCollapse( true );
8476 t2.getNode( "c" ).setCollapse( true );
8477 t2.getNode( "d" ).setCollapse( true );
8478 t2.getNode( "e" ).setCollapse( true );
8479 t2.getNode( "gh" ).setCollapse( true );
8480 n = t2.getNode( "ab" );
8481 ext = new ArrayList<PhylogenyNode>();
8482 while ( n != null ) {
8484 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8486 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8489 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8492 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8495 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8501 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8502 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8503 t3.getNode( "ab" ).setCollapse( true );
8504 t3.getNode( "cd" ).setCollapse( true );
8505 t3.getNode( "cde" ).setCollapse( true );
8506 t3.getNode( "c" ).setCollapse( true );
8507 t3.getNode( "d" ).setCollapse( true );
8508 t3.getNode( "e" ).setCollapse( true );
8509 t3.getNode( "gh" ).setCollapse( true );
8510 t3.getNode( "fgh" ).setCollapse( true );
8511 n = t3.getNode( "ab" );
8512 ext = new ArrayList<PhylogenyNode>();
8513 while ( n != null ) {
8515 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8517 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8520 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8523 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8529 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8530 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8531 t4.getNode( "ab" ).setCollapse( true );
8532 t4.getNode( "cd" ).setCollapse( true );
8533 t4.getNode( "cde" ).setCollapse( true );
8534 t4.getNode( "c" ).setCollapse( true );
8535 t4.getNode( "d" ).setCollapse( true );
8536 t4.getNode( "e" ).setCollapse( true );
8537 t4.getNode( "gh" ).setCollapse( true );
8538 t4.getNode( "fgh" ).setCollapse( true );
8539 t4.getNode( "abcdefgh" ).setCollapse( true );
8540 n = t4.getNode( "abcdefgh" );
8541 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8546 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8547 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8549 n = t5.getFirstExternalNode();
8550 while ( n != null ) {
8552 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8554 if ( ext.size() != 8 ) {
8557 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8560 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8563 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8566 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8569 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8572 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8575 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8578 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8583 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8584 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8586 t6.getNode( "ab" ).setCollapse( true );
8587 n = t6.getNode( "ab" );
8588 while ( n != null ) {
8590 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8592 if ( ext.size() != 7 ) {
8595 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8598 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8601 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8604 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8607 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8610 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8613 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8618 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8619 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8621 t7.getNode( "cd" ).setCollapse( true );
8622 n = t7.getNode( "a" );
8623 while ( n != null ) {
8625 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8627 if ( ext.size() != 7 ) {
8630 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8633 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8636 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8639 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8642 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8645 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8648 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8653 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8654 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8656 t8.getNode( "cd" ).setCollapse( true );
8657 t8.getNode( "c" ).setCollapse( true );
8658 t8.getNode( "d" ).setCollapse( true );
8659 n = t8.getNode( "a" );
8660 while ( n != null ) {
8662 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8664 if ( ext.size() != 7 ) {
8667 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8670 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8673 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8674 System.out.println( "2 fail" );
8677 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8680 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8683 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8686 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8691 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8692 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8694 t9.getNode( "gh" ).setCollapse( true );
8695 n = t9.getNode( "a" );
8696 while ( n != null ) {
8698 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8700 if ( ext.size() != 7 ) {
8703 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8706 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8709 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8712 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8715 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8718 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8721 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8726 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8727 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8729 t10.getNode( "gh" ).setCollapse( true );
8730 t10.getNode( "g" ).setCollapse( true );
8731 t10.getNode( "h" ).setCollapse( true );
8732 n = t10.getNode( "a" );
8733 while ( n != null ) {
8735 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8737 if ( ext.size() != 7 ) {
8740 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8743 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8746 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8749 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8752 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8755 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8758 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8763 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8764 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8766 t11.getNode( "gh" ).setCollapse( true );
8767 t11.getNode( "fgh" ).setCollapse( true );
8768 n = t11.getNode( "a" );
8769 while ( n != null ) {
8771 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8773 if ( ext.size() != 6 ) {
8776 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8779 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8782 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8785 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8788 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8791 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8796 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8797 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8799 t12.getNode( "gh" ).setCollapse( true );
8800 t12.getNode( "fgh" ).setCollapse( true );
8801 t12.getNode( "g" ).setCollapse( true );
8802 t12.getNode( "h" ).setCollapse( true );
8803 t12.getNode( "f" ).setCollapse( true );
8804 n = t12.getNode( "a" );
8805 while ( n != null ) {
8807 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8809 if ( ext.size() != 6 ) {
8812 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8815 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8818 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8821 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8824 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8827 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8832 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8833 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8835 t13.getNode( "ab" ).setCollapse( true );
8836 t13.getNode( "b" ).setCollapse( true );
8837 t13.getNode( "fgh" ).setCollapse( true );
8838 t13.getNode( "gh" ).setCollapse( true );
8839 n = t13.getNode( "ab" );
8840 while ( n != null ) {
8842 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8844 if ( ext.size() != 5 ) {
8847 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8850 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8853 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8856 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8859 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8864 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8865 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8867 t14.getNode( "ab" ).setCollapse( true );
8868 t14.getNode( "a" ).setCollapse( true );
8869 t14.getNode( "fgh" ).setCollapse( true );
8870 t14.getNode( "gh" ).setCollapse( true );
8871 n = t14.getNode( "ab" );
8872 while ( n != null ) {
8874 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8876 if ( ext.size() != 5 ) {
8879 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8882 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8885 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8888 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8891 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8896 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" );
8897 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8899 t15.getNode( "ab" ).setCollapse( true );
8900 t15.getNode( "a" ).setCollapse( true );
8901 t15.getNode( "fgh" ).setCollapse( true );
8902 t15.getNode( "gh" ).setCollapse( true );
8903 n = t15.getNode( "ab" );
8904 while ( n != null ) {
8906 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8908 if ( ext.size() != 6 ) {
8911 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8914 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8917 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8920 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8923 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8926 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8931 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" );
8932 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8934 t16.getNode( "ab" ).setCollapse( true );
8935 t16.getNode( "a" ).setCollapse( true );
8936 t16.getNode( "fgh" ).setCollapse( true );
8937 t16.getNode( "gh" ).setCollapse( true );
8938 t16.getNode( "cd" ).setCollapse( true );
8939 t16.getNode( "cde" ).setCollapse( true );
8940 t16.getNode( "d" ).setCollapse( true );
8941 t16.getNode( "x" ).setCollapse( true );
8942 n = t16.getNode( "ab" );
8943 while ( n != null ) {
8945 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8947 if ( ext.size() != 4 ) {
8950 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8953 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8956 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8959 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8963 catch ( final Exception e ) {
8964 e.printStackTrace( System.out );
8970 private static boolean testMsaQualityMethod() {
8972 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8973 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8974 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8975 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8976 final List<Sequence> l = new ArrayList<Sequence>();
8981 final Msa msa = BasicMsa.createInstance( l );
8982 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8985 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8988 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8991 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8995 catch ( final Exception e ) {
8996 e.printStackTrace( System.out );
9002 private static boolean testSequenceIdParsing() {
9004 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
9005 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9006 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9008 System.out.println( "value =" + id.getValue() );
9009 System.out.println( "provider=" + id.getProvider() );
9014 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
9015 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9016 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9018 System.out.println( "value =" + id.getValue() );
9019 System.out.println( "provider=" + id.getProvider() );
9024 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
9025 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9026 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9028 System.out.println( "value =" + id.getValue() );
9029 System.out.println( "provider=" + id.getProvider() );
9034 id = SequenceIdParser.parse( "gb_AAA96518_1" );
9035 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9036 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
9038 System.out.println( "value =" + id.getValue() );
9039 System.out.println( "provider=" + id.getProvider() );
9044 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
9045 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9046 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
9048 System.out.println( "value =" + id.getValue() );
9049 System.out.println( "provider=" + id.getProvider() );
9054 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
9055 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9056 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
9058 System.out.println( "value =" + id.getValue() );
9059 System.out.println( "provider=" + id.getProvider() );
9064 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9065 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9066 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
9068 System.out.println( "value =" + id.getValue() );
9069 System.out.println( "provider=" + id.getProvider() );
9074 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9075 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9076 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9078 System.out.println( "value =" + id.getValue() );
9079 System.out.println( "provider=" + id.getProvider() );
9084 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9085 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9086 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9088 System.out.println( "value =" + id.getValue() );
9089 System.out.println( "provider=" + id.getProvider() );
9094 id = SequenceIdParser.parse( "P4A123" );
9095 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9096 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9098 System.out.println( "value =" + id.getValue() );
9099 System.out.println( "provider=" + id.getProvider() );
9104 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
9105 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9106 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9108 System.out.println( "value =" + id.getValue() );
9109 System.out.println( "provider=" + id.getProvider() );
9114 id = SequenceIdParser.parse( "XP_12345" );
9116 System.out.println( "value =" + id.getValue() );
9117 System.out.println( "provider=" + id.getProvider() );
9120 // lcl_91970_unknown_
9122 catch ( final Exception e ) {
9123 e.printStackTrace( System.out );