2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.nhx.NHXParser2;
56 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
57 import org.forester.io.parsers.tol.TolParser;
58 import org.forester.io.parsers.util.ParserUtils;
59 import org.forester.io.writers.PhylogenyWriter;
60 import org.forester.msa.BasicMsa;
61 import org.forester.msa.Mafft;
62 import org.forester.msa.Msa;
63 import org.forester.msa.MsaInferrer;
64 import org.forester.msa.MsaMethods;
65 import org.forester.pccx.TestPccx;
66 import org.forester.phylogeny.Phylogeny;
67 import org.forester.phylogeny.PhylogenyBranch;
68 import org.forester.phylogeny.PhylogenyMethods;
69 import org.forester.phylogeny.PhylogenyNode;
70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
71 import org.forester.phylogeny.data.BinaryCharacters;
72 import org.forester.phylogeny.data.BranchWidth;
73 import org.forester.phylogeny.data.Confidence;
74 import org.forester.phylogeny.data.Distribution;
75 import org.forester.phylogeny.data.DomainArchitecture;
76 import org.forester.phylogeny.data.Event;
77 import org.forester.phylogeny.data.Identifier;
78 import org.forester.phylogeny.data.PhylogenyData;
79 import org.forester.phylogeny.data.PhylogenyDataUtil;
80 import org.forester.phylogeny.data.Polygon;
81 import org.forester.phylogeny.data.PropertiesMap;
82 import org.forester.phylogeny.data.Property;
83 import org.forester.phylogeny.data.Property.AppliesTo;
84 import org.forester.phylogeny.data.ProteinDomain;
85 import org.forester.phylogeny.data.Taxonomy;
86 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
87 import org.forester.phylogeny.factories.PhylogenyFactory;
88 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
89 import org.forester.protein.Protein;
90 import org.forester.rio.TestRIO;
91 import org.forester.sdi.SDI;
92 import org.forester.sdi.SDIR;
93 import org.forester.sdi.TestGSDI;
94 import org.forester.sequence.BasicSequence;
95 import org.forester.sequence.Sequence;
96 import org.forester.surfacing.TestSurfacing;
97 import org.forester.tools.ConfidenceAssessor;
98 import org.forester.tools.SupportCount;
99 import org.forester.tools.TreeSplitMatrix;
100 import org.forester.util.AsciiHistogram;
101 import org.forester.util.BasicDescriptiveStatistics;
102 import org.forester.util.BasicTable;
103 import org.forester.util.BasicTableParser;
104 import org.forester.util.DescriptiveStatistics;
105 import org.forester.util.ForesterConstants;
106 import org.forester.util.ForesterUtil;
107 import org.forester.util.GeneralTable;
108 import org.forester.util.SequenceIdParser;
109 import org.forester.ws.seqdb.SequenceDatabaseEntry;
110 import org.forester.ws.seqdb.SequenceDbWsTools;
111 import org.forester.ws.seqdb.UniProtTaxonomy;
112 import org.forester.ws.wabi.TxSearch;
113 import org.forester.ws.wabi.TxSearch.RANKS;
114 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
115 import org.forester.ws.wabi.TxSearch.TAX_RANK;
117 @SuppressWarnings( "unused")
118 public final class Test {
120 private final static double ZERO_DIFF = 1.0E-9;
121 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
122 + ForesterUtil.getFileSeparator() + "test_data"
123 + ForesterUtil.getFileSeparator();
124 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
125 + ForesterUtil.getFileSeparator() + "resources"
126 + ForesterUtil.getFileSeparator();
127 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
128 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
129 + ForesterConstants.PHYLO_XML_VERSION + "/"
130 + ForesterConstants.PHYLO_XML_XSD;
131 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
132 + ForesterConstants.PHYLO_XML_VERSION + "/"
133 + ForesterConstants.PHYLO_XML_XSD;
135 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
136 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
140 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
141 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
144 public static boolean isEqual( final double a, final double b ) {
145 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
148 public static void main( final String[] args ) {
149 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
150 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
152 Locale.setDefault( Locale.US );
153 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
156 System.out.print( "[Test if directory with files for testing exists/is readable: " );
157 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
158 System.out.println( "OK.]" );
161 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
162 System.out.println( "Testing aborted." );
165 System.out.print( "[Test if resources directory exists/is readable: " );
166 if ( testDir( PATH_TO_RESOURCES ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
171 System.out.println( "Testing aborted." );
174 final long start_time = new Date().getTime();
175 System.out.print( "Sequence id parsing: " );
176 if ( testSequenceIdParsing() ) {
177 System.out.println( "OK." );
181 System.out.println( "failed." );
184 System.out.print( "Hmmscan output parser: " );
185 if ( testHmmscanOutputParser() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Basic node methods: " );
194 if ( Test.testBasicNodeMethods() ) {
195 System.out.println( "OK." );
199 System.out.println( "failed." );
202 System.out.print( "Taxonomy code extraction: " );
203 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
204 System.out.println( "OK." );
208 System.out.println( "failed." );
211 System.out.print( "Taxonomy extraction (general): " );
212 if ( Test.testTaxonomyExtraction() ) {
213 System.out.println( "OK." );
217 System.out.println( "failed." );
220 System.out.print( "Basic node construction and parsing of NHX (node level): " );
221 if ( Test.testNHXNodeParsing() ) {
222 System.out.println( "OK." );
226 System.out.println( "failed." );
229 System.out.print( "NHX parsing iterating: " );
230 if ( Test.testNHParsingIter() ) {
231 System.out.println( "OK." );
235 System.out.println( "failed." );
238 System.out.print( "NH parsing: " );
239 if ( Test.testNHParsing() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
248 System.out.print( "Conversion to NHX (node level): " );
249 if ( Test.testNHXconversion() ) {
250 System.out.println( "OK." );
254 System.out.println( "failed." );
257 System.out.print( "NHX parsing: " );
258 if ( Test.testNHXParsing() ) {
259 System.out.println( "OK." );
263 System.out.println( "failed." );
266 System.out.print( "NHX parsing with quotes: " );
267 if ( Test.testNHXParsingQuotes() ) {
268 System.out.println( "OK." );
272 System.out.println( "failed." );
275 System.out.print( "NHX parsing (MrBayes): " );
276 if ( Test.testNHXParsingMB() ) {
277 System.out.println( "OK." );
281 System.out.println( "failed." );
284 System.out.print( "Nexus characters parsing: " );
285 if ( Test.testNexusCharactersParsing() ) {
286 System.out.println( "OK." );
290 System.out.println( "failed." );
293 System.out.print( "Nexus tree parsing: " );
294 if ( Test.testNexusTreeParsing() ) {
295 System.out.println( "OK." );
299 System.out.println( "failed." );
302 System.out.print( "Nexus tree parsing (translating): " );
303 if ( Test.testNexusTreeParsingTranslating() ) {
304 System.out.println( "OK." );
308 System.out.println( "failed." );
311 System.out.print( "Nexus matrix parsing: " );
312 if ( Test.testNexusMatrixParsing() ) {
313 System.out.println( "OK." );
317 System.out.println( "failed." );
320 System.out.print( "Basic phyloXML parsing: " );
321 if ( Test.testBasicPhyloXMLparsing() ) {
322 System.out.println( "OK." );
326 System.out.println( "failed." );
329 System.out.print( "Basic phyloXML parsing (validating against schema): " );
330 if ( testBasicPhyloXMLparsingValidating() ) {
331 System.out.println( "OK." );
335 System.out.println( "failed." );
338 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
339 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
340 System.out.println( "OK." );
344 System.out.println( "failed." );
347 System.out.print( "phyloXML Distribution Element: " );
348 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
349 System.out.println( "OK." );
353 System.out.println( "failed." );
356 System.out.print( "Tol XML parsing: " );
357 if ( Test.testBasicTolXMLparsing() ) {
358 System.out.println( "OK." );
362 System.out.println( "failed." );
365 System.out.print( "Copying of node data: " );
366 if ( Test.testCopyOfNodeData() ) {
367 System.out.println( "OK." );
371 System.out.println( "failed." );
374 System.out.print( "Basic tree methods: " );
375 if ( Test.testBasicTreeMethods() ) {
376 System.out.println( "OK." );
380 System.out.println( "failed." );
383 System.out.print( "Postorder Iterator: " );
384 if ( Test.testPostOrderIterator() ) {
385 System.out.println( "OK." );
389 System.out.println( "failed." );
392 System.out.print( "Preorder Iterator: " );
393 if ( Test.testPreOrderIterator() ) {
394 System.out.println( "OK." );
398 System.out.println( "failed." );
401 System.out.print( "Levelorder Iterator: " );
402 if ( Test.testLevelOrderIterator() ) {
403 System.out.println( "OK." );
407 System.out.println( "failed." );
410 System.out.print( "Re-id methods: " );
411 if ( Test.testReIdMethods() ) {
412 System.out.println( "OK." );
416 System.out.println( "failed." );
419 System.out.print( "Methods on last external nodes: " );
420 if ( Test.testLastExternalNodeMethods() ) {
421 System.out.println( "OK." );
425 System.out.println( "failed." );
428 System.out.print( "Methods on external nodes: " );
429 if ( Test.testExternalNodeRelatedMethods() ) {
430 System.out.println( "OK." );
434 System.out.println( "failed." );
437 System.out.print( "Deletion of external nodes: " );
438 if ( Test.testDeletionOfExternalNodes() ) {
439 System.out.println( "OK." );
443 System.out.println( "failed." );
446 System.out.print( "Subtree deletion: " );
447 if ( Test.testSubtreeDeletion() ) {
448 System.out.println( "OK." );
452 System.out.println( "failed." );
455 System.out.print( "Phylogeny branch: " );
456 if ( Test.testPhylogenyBranch() ) {
457 System.out.println( "OK." );
461 System.out.println( "failed." );
464 System.out.print( "Rerooting: " );
465 if ( Test.testRerooting() ) {
466 System.out.println( "OK." );
470 System.out.println( "failed." );
473 System.out.print( "Mipoint rooting: " );
474 if ( Test.testMidpointrooting() ) {
475 System.out.println( "OK." );
479 System.out.println( "failed." );
482 System.out.print( "Node removal: " );
483 if ( Test.testNodeRemoval() ) {
484 System.out.println( "OK." );
488 System.out.println( "failed." );
491 System.out.print( "Support count: " );
492 if ( Test.testSupportCount() ) {
493 System.out.println( "OK." );
497 System.out.println( "failed." );
500 System.out.print( "Support transfer: " );
501 if ( Test.testSupportTransfer() ) {
502 System.out.println( "OK." );
506 System.out.println( "failed." );
509 System.out.print( "Finding of LCA: " );
510 if ( Test.testGetLCA() ) {
511 System.out.println( "OK." );
515 System.out.println( "failed." );
518 System.out.print( "Finding of LCA 2: " );
519 if ( Test.testGetLCA2() ) {
520 System.out.println( "OK." );
524 System.out.println( "failed." );
527 System.out.print( "Calculation of distance between nodes: " );
528 if ( Test.testGetDistance() ) {
529 System.out.println( "OK." );
533 System.out.println( "failed." );
536 System.out.print( "Descriptive statistics: " );
537 if ( Test.testDescriptiveStatistics() ) {
538 System.out.println( "OK." );
542 System.out.println( "failed." );
545 System.out.print( "Data objects and methods: " );
546 if ( Test.testDataObjects() ) {
547 System.out.println( "OK." );
551 System.out.println( "failed." );
554 System.out.print( "Properties map: " );
555 if ( Test.testPropertiesMap() ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "SDIse: " );
564 if ( Test.testSDIse() ) {
565 System.out.println( "OK." );
569 System.out.println( "failed." );
572 System.out.print( "SDIunrooted: " );
573 if ( Test.testSDIunrooted() ) {
574 System.out.println( "OK." );
578 System.out.println( "failed." );
581 System.out.print( "GSDI: " );
582 if ( TestGSDI.test() ) {
583 System.out.println( "OK." );
587 System.out.println( "failed." );
590 System.out.print( "RIO: " );
591 if ( TestRIO.test() ) {
592 System.out.println( "OK." );
596 System.out.println( "failed." );
599 System.out.print( "Phylogeny reconstruction:" );
600 System.out.println();
601 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
602 System.out.println( "OK." );
606 System.out.println( "failed." );
609 System.out.print( "Analysis of domain architectures: " );
610 System.out.println();
611 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
612 System.out.println( "OK." );
616 System.out.println( "failed." );
619 System.out.print( "GO: " );
620 System.out.println();
621 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
622 System.out.println( "OK." );
626 System.out.println( "failed." );
629 System.out.print( "Modeling tools: " );
630 if ( TestPccx.test() ) {
631 System.out.println( "OK." );
635 System.out.println( "failed." );
638 System.out.print( "Split Matrix strict: " );
639 if ( Test.testSplitStrict() ) {
640 System.out.println( "OK." );
644 System.out.println( "failed." );
647 System.out.print( "Split Matrix: " );
648 if ( Test.testSplit() ) {
649 System.out.println( "OK." );
653 System.out.println( "failed." );
656 System.out.print( "Confidence Assessor: " );
657 if ( Test.testConfidenceAssessor() ) {
658 System.out.println( "OK." );
662 System.out.println( "failed." );
665 System.out.print( "Basic table: " );
666 if ( Test.testBasicTable() ) {
667 System.out.println( "OK." );
671 System.out.println( "failed." );
674 System.out.print( "General table: " );
675 if ( Test.testGeneralTable() ) {
676 System.out.println( "OK." );
680 System.out.println( "failed." );
683 System.out.print( "Amino acid sequence: " );
684 if ( Test.testAminoAcidSequence() ) {
685 System.out.println( "OK." );
689 System.out.println( "failed." );
692 System.out.print( "General MSA parser: " );
693 if ( Test.testGeneralMsaParser() ) {
694 System.out.println( "OK." );
698 System.out.println( "failed." );
701 System.out.print( "Fasta parser for msa: " );
702 if ( Test.testFastaParser() ) {
703 System.out.println( "OK." );
707 System.out.println( "failed." );
710 System.out.print( "Creation of balanced phylogeny: " );
711 if ( Test.testCreateBalancedPhylogeny() ) {
712 System.out.println( "OK." );
716 System.out.println( "failed." );
719 System.out.print( "EMBL Entry Retrieval: " );
720 if ( Test.testEmblEntryRetrieval() ) {
721 System.out.println( "OK." );
725 System.out.println( "failed." );
728 System.out.print( "Uniprot Entry Retrieval: " );
729 if ( Test.testUniprotEntryRetrieval() ) {
730 System.out.println( "OK." );
734 System.out.println( "failed." );
737 System.out.print( "Uniprot Taxonomy Search: " );
738 if ( Test.testUniprotTaxonomySearch() ) {
739 System.out.println( "OK." );
743 System.out.println( "failed." );
748 final String os = ForesterUtil.OS_NAME.toLowerCase();
749 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
750 path = "/usr/local/bin/mafft";
752 else if ( os.indexOf( "win" ) >= 0 ) {
753 path = "C:\\Program Files\\mafft-win\\mafft.bat";
756 path = "/home/czmasek/bin/mafft";
758 if ( !MsaInferrer.isInstalled( path ) ) {
761 if ( !MsaInferrer.isInstalled( path ) ) {
762 path = "/usr/local/bin/mafft";
764 if ( MsaInferrer.isInstalled( path ) ) {
765 System.out.print( "MAFFT (external program): " );
766 if ( Test.testMafft( path ) ) {
767 System.out.println( "OK." );
771 System.out.println( "failed [will not count towards failed tests]" );
775 System.out.print( "Next nodes with collapsed: " );
776 if ( Test.testNextNodeWithCollapsing() ) {
777 System.out.println( "OK." );
781 System.out.println( "failed." );
784 System.out.print( "Simple MSA quality: " );
785 if ( Test.testMsaQualityMethod() ) {
786 System.out.println( "OK." );
790 System.out.println( "failed." );
793 System.out.println();
794 final Runtime rt = java.lang.Runtime.getRuntime();
795 final long free_memory = rt.freeMemory() / 1000000;
796 final long total_memory = rt.totalMemory() / 1000000;
797 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
798 + free_memory + "MB, total memory: " + total_memory + "MB)" );
799 System.out.println();
800 System.out.println( "Successful tests: " + succeeded );
801 System.out.println( "Failed tests: " + failed );
802 System.out.println();
804 System.out.println( "OK." );
807 System.out.println( "Not OK." );
811 private static boolean testExtractTaxonomyCodeFromNodeName() {
813 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
816 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
819 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
822 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
823 .equals( "MOUSE" ) ) {
826 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
827 .equals( "MOUSE" ) ) {
830 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
831 .equals( "MOUSE" ) ) {
834 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
837 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
840 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
844 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
848 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
852 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
855 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
858 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
861 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
865 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
866 .equals( "MOUSE" ) ) {
869 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
870 .equals( "MOUSE" ) ) {
874 catch ( final Exception e ) {
875 e.printStackTrace( System.out );
881 private static boolean testBasicNodeMethods() {
883 if ( PhylogenyNode.getNodeCount() != 0 ) {
886 final PhylogenyNode n1 = new PhylogenyNode();
887 final PhylogenyNode n2 = PhylogenyNode
888 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
889 final PhylogenyNode n3 = PhylogenyNode
890 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
891 final PhylogenyNode n4 = PhylogenyNode
892 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
893 if ( n1.isHasAssignedEvent() ) {
896 if ( PhylogenyNode.getNodeCount() != 4 ) {
899 if ( n3.getIndicator() != 0 ) {
902 if ( n3.getNumberOfExternalNodes() != 1 ) {
905 if ( !n3.isExternal() ) {
908 if ( !n3.isRoot() ) {
911 if ( !n4.getName().equals( "n4" ) ) {
915 catch ( final Exception e ) {
916 e.printStackTrace( System.out );
922 private static boolean testBasicPhyloXMLparsing() {
924 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
925 final PhyloXmlParser xml_parser = new PhyloXmlParser();
926 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
928 if ( xml_parser.getErrorCount() > 0 ) {
929 System.out.println( xml_parser.getErrorMessages().toString() );
932 if ( phylogenies_0.length != 4 ) {
935 final Phylogeny t1 = phylogenies_0[ 0 ];
936 final Phylogeny t2 = phylogenies_0[ 1 ];
937 final Phylogeny t3 = phylogenies_0[ 2 ];
938 final Phylogeny t4 = phylogenies_0[ 3 ];
939 if ( t1.getNumberOfExternalNodes() != 1 ) {
942 if ( !t1.isRooted() ) {
945 if ( t1.isRerootable() ) {
948 if ( !t1.getType().equals( "gene_tree" ) ) {
951 if ( t2.getNumberOfExternalNodes() != 2 ) {
954 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
957 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
960 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
963 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
966 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
969 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
972 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
973 .startsWith( "actgtgggggt" ) ) {
976 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
977 .startsWith( "ctgtgatgcat" ) ) {
980 if ( t3.getNumberOfExternalNodes() != 4 ) {
983 if ( !t1.getName().equals( "t1" ) ) {
986 if ( !t2.getName().equals( "t2" ) ) {
989 if ( !t3.getName().equals( "t3" ) ) {
992 if ( !t4.getName().equals( "t4" ) ) {
995 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
998 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1001 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1004 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1005 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1008 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1011 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1014 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1017 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1018 .equals( "apoptosis" ) ) {
1021 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1022 .equals( "GO:0006915" ) ) {
1025 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1026 .equals( "UniProtKB" ) ) {
1029 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1030 .equals( "experimental" ) ) {
1033 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1034 .equals( "function" ) ) {
1037 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1038 .getValue() != 1 ) {
1041 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1042 .getType().equals( "ml" ) ) {
1045 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1046 .equals( "apoptosis" ) ) {
1049 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1050 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1053 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1054 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1057 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1058 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1061 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1062 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1065 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1066 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1069 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1070 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1073 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1074 .equals( "GO:0005829" ) ) {
1077 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1078 .equals( "intracellular organelle" ) ) {
1081 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1084 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1085 .equals( "UniProt link" ) ) ) {
1088 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1092 catch ( final Exception e ) {
1093 e.printStackTrace( System.out );
1099 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1101 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1102 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1103 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1104 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1107 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1109 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1111 if ( xml_parser.getErrorCount() > 0 ) {
1112 System.out.println( xml_parser.getErrorMessages().toString() );
1115 if ( phylogenies_0.length != 4 ) {
1118 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1119 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1120 if ( phylogenies_t1.length != 1 ) {
1123 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1124 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1127 if ( !t1_rt.isRooted() ) {
1130 if ( t1_rt.isRerootable() ) {
1133 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1136 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1137 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1138 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1139 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1142 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1145 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1148 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1151 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1152 .startsWith( "actgtgggggt" ) ) {
1155 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1156 .startsWith( "ctgtgatgcat" ) ) {
1159 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1160 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1161 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1162 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1163 if ( phylogenies_1.length != 1 ) {
1166 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1167 if ( !t3_rt.getName().equals( "t3" ) ) {
1170 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1173 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1176 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1179 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1182 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1183 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1186 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1189 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1192 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1193 .equals( "UniProtKB" ) ) {
1196 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1197 .equals( "apoptosis" ) ) {
1200 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1201 .equals( "GO:0006915" ) ) {
1204 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1205 .equals( "UniProtKB" ) ) {
1208 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1209 .equals( "experimental" ) ) {
1212 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1213 .equals( "function" ) ) {
1216 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1217 .getValue() != 1 ) {
1220 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1221 .getType().equals( "ml" ) ) {
1224 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1225 .equals( "apoptosis" ) ) {
1228 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1229 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1232 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1233 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1236 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1237 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1240 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1241 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1244 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1245 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1249 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1253 .equals( "GO:0005829" ) ) {
1256 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1257 .equals( "intracellular organelle" ) ) {
1260 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1264 .equals( "UniProt link" ) ) ) {
1267 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1270 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1273 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1274 .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." ) ) ) {
1277 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1280 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1283 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1286 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1289 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1290 .equals( "ncbi" ) ) {
1293 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1296 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1297 .getName().equals( "B" ) ) {
1300 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1301 .getFrom() != 21 ) {
1304 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1307 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1308 .getLength() != 24 ) {
1311 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1312 .getConfidence() != 2144 ) {
1315 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1316 .equals( "pfam" ) ) {
1319 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1322 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1325 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1328 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1331 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1332 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1335 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1338 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1341 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1344 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1347 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1350 if ( taxbb.getSynonyms().size() != 2 ) {
1353 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1356 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1359 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1362 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1365 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1368 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1369 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1373 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1376 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1379 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1382 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1385 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1388 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1391 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1395 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1398 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1399 .equalsIgnoreCase( "435" ) ) {
1402 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1405 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1406 .equalsIgnoreCase( "443.7" ) ) {
1409 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1412 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1415 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1416 .equalsIgnoreCase( "433" ) ) {
1420 catch ( final Exception e ) {
1421 e.printStackTrace( System.out );
1427 private static boolean testBasicPhyloXMLparsingValidating() {
1429 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1430 PhyloXmlParser xml_parser = null;
1432 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1434 catch ( final Exception e ) {
1435 // Do nothing -- means were not running from jar.
1437 if ( xml_parser == null ) {
1438 xml_parser = new PhyloXmlParser();
1439 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1440 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1443 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1446 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1448 if ( xml_parser.getErrorCount() > 0 ) {
1449 System.out.println( xml_parser.getErrorMessages().toString() );
1452 if ( phylogenies_0.length != 4 ) {
1455 final Phylogeny t1 = phylogenies_0[ 0 ];
1456 final Phylogeny t2 = phylogenies_0[ 1 ];
1457 final Phylogeny t3 = phylogenies_0[ 2 ];
1458 final Phylogeny t4 = phylogenies_0[ 3 ];
1459 if ( !t1.getName().equals( "t1" ) ) {
1462 if ( !t2.getName().equals( "t2" ) ) {
1465 if ( !t3.getName().equals( "t3" ) ) {
1468 if ( !t4.getName().equals( "t4" ) ) {
1471 if ( t1.getNumberOfExternalNodes() != 1 ) {
1474 if ( t2.getNumberOfExternalNodes() != 2 ) {
1477 if ( t3.getNumberOfExternalNodes() != 4 ) {
1480 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1481 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1482 if ( xml_parser.getErrorCount() > 0 ) {
1483 System.out.println( "errors:" );
1484 System.out.println( xml_parser.getErrorMessages().toString() );
1487 if ( phylogenies_1.length != 4 ) {
1490 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1492 if ( xml_parser.getErrorCount() > 0 ) {
1493 System.out.println( "errors:" );
1494 System.out.println( xml_parser.getErrorMessages().toString() );
1497 if ( phylogenies_2.length != 1 ) {
1500 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1503 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1505 if ( xml_parser.getErrorCount() > 0 ) {
1506 System.out.println( xml_parser.getErrorMessages().toString() );
1509 if ( phylogenies_3.length != 2 ) {
1512 final Phylogeny a = phylogenies_3[ 0 ];
1513 if ( !a.getName().equals( "tree 4" ) ) {
1516 if ( a.getNumberOfExternalNodes() != 3 ) {
1519 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1522 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1525 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1527 if ( xml_parser.getErrorCount() > 0 ) {
1528 System.out.println( xml_parser.getErrorMessages().toString() );
1531 if ( phylogenies_4.length != 1 ) {
1534 final Phylogeny s = phylogenies_4[ 0 ];
1535 if ( s.getNumberOfExternalNodes() != 6 ) {
1538 s.getNode( "first" );
1540 s.getNode( "\"<a'b&c'd\">\"" );
1541 s.getNode( "'''\"" );
1542 s.getNode( "\"\"\"" );
1543 s.getNode( "dick & doof" );
1545 catch ( final Exception e ) {
1546 e.printStackTrace( System.out );
1552 private static boolean testBasicTable() {
1554 final BasicTable<String> t0 = new BasicTable<String>();
1555 if ( t0.getNumberOfColumns() != 0 ) {
1558 if ( t0.getNumberOfRows() != 0 ) {
1561 t0.setValue( 3, 2, "23" );
1562 t0.setValue( 10, 1, "error" );
1563 t0.setValue( 10, 1, "110" );
1564 t0.setValue( 9, 1, "19" );
1565 t0.setValue( 1, 10, "101" );
1566 t0.setValue( 10, 10, "1010" );
1567 t0.setValue( 100, 10, "10100" );
1568 t0.setValue( 0, 0, "00" );
1569 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1572 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1575 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1578 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1581 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1584 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1587 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1590 if ( t0.getNumberOfColumns() != 101 ) {
1593 if ( t0.getNumberOfRows() != 11 ) {
1596 if ( t0.getValueAsString( 49, 4 ) != null ) {
1599 final String l = ForesterUtil.getLineSeparator();
1600 final StringBuffer source = new StringBuffer();
1601 source.append( "" + l );
1602 source.append( "# 1 1 1 1 1 1 1 1" + l );
1603 source.append( " 00 01 02 03" + l );
1604 source.append( " 10 11 12 13 " + l );
1605 source.append( "20 21 22 23 " + l );
1606 source.append( " 30 31 32 33" + l );
1607 source.append( "40 41 42 43" + l );
1608 source.append( " # 1 1 1 1 1 " + l );
1609 source.append( "50 51 52 53 54" + l );
1610 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1611 if ( t1.getNumberOfColumns() != 5 ) {
1614 if ( t1.getNumberOfRows() != 6 ) {
1617 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1620 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1623 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1626 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1629 final StringBuffer source1 = new StringBuffer();
1630 source1.append( "" + l );
1631 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1632 source1.append( " 00; 01 ;02;03" + l );
1633 source1.append( " 10; 11; 12; 13 " + l );
1634 source1.append( "20; 21; 22; 23 " + l );
1635 source1.append( " 30; 31; 32; 33" + l );
1636 source1.append( "40;41;42;43" + l );
1637 source1.append( " # 1 1 1 1 1 " + l );
1638 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1639 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1640 if ( t2.getNumberOfColumns() != 5 ) {
1643 if ( t2.getNumberOfRows() != 6 ) {
1646 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1649 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1652 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1655 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1658 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1661 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1664 final StringBuffer source2 = new StringBuffer();
1665 source2.append( "" + l );
1666 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1667 source2.append( " 00; 01 ;02;03" + l );
1668 source2.append( " 10; 11; 12; 13 " + l );
1669 source2.append( "20; 21; 22; 23 " + l );
1670 source2.append( " " + l );
1671 source2.append( " 30; 31; 32; 33" + l );
1672 source2.append( "40;41;42;43" + l );
1673 source2.append( " comment: 1 1 1 1 1 " + l );
1674 source2.append( ";;;50 ; 52; 53;;54 " + l );
1675 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1681 if ( tl.size() != 2 ) {
1684 final BasicTable<String> t3 = tl.get( 0 );
1685 final BasicTable<String> t4 = tl.get( 1 );
1686 if ( t3.getNumberOfColumns() != 4 ) {
1689 if ( t3.getNumberOfRows() != 3 ) {
1692 if ( t4.getNumberOfColumns() != 4 ) {
1695 if ( t4.getNumberOfRows() != 3 ) {
1698 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1701 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1705 catch ( final Exception e ) {
1706 e.printStackTrace( System.out );
1712 private static boolean testBasicTolXMLparsing() {
1714 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1715 final TolParser parser = new TolParser();
1716 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1717 if ( parser.getErrorCount() > 0 ) {
1718 System.out.println( parser.getErrorMessages().toString() );
1721 if ( phylogenies_0.length != 1 ) {
1724 final Phylogeny t1 = phylogenies_0[ 0 ];
1725 if ( t1.getNumberOfExternalNodes() != 5 ) {
1728 if ( !t1.isRooted() ) {
1731 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1734 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1737 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1740 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1743 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1744 if ( parser.getErrorCount() > 0 ) {
1745 System.out.println( parser.getErrorMessages().toString() );
1748 if ( phylogenies_1.length != 1 ) {
1751 final Phylogeny t2 = phylogenies_1[ 0 ];
1752 if ( t2.getNumberOfExternalNodes() != 664 ) {
1755 if ( !t2.isRooted() ) {
1758 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1761 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1764 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1767 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1770 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1773 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1774 .equals( "Aquifex" ) ) {
1777 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1778 if ( parser.getErrorCount() > 0 ) {
1779 System.out.println( parser.getErrorMessages().toString() );
1782 if ( phylogenies_2.length != 1 ) {
1785 final Phylogeny t3 = phylogenies_2[ 0 ];
1786 if ( t3.getNumberOfExternalNodes() != 184 ) {
1789 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1792 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1795 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1798 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1799 if ( parser.getErrorCount() > 0 ) {
1800 System.out.println( parser.getErrorMessages().toString() );
1803 if ( phylogenies_3.length != 1 ) {
1806 final Phylogeny t4 = phylogenies_3[ 0 ];
1807 if ( t4.getNumberOfExternalNodes() != 1 ) {
1810 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1813 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1816 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1819 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1820 if ( parser.getErrorCount() > 0 ) {
1821 System.out.println( parser.getErrorMessages().toString() );
1824 if ( phylogenies_4.length != 1 ) {
1827 final Phylogeny t5 = phylogenies_4[ 0 ];
1828 if ( t5.getNumberOfExternalNodes() != 13 ) {
1831 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1834 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1837 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1841 catch ( final Exception e ) {
1842 e.printStackTrace( System.out );
1848 private static boolean testBasicTreeMethods() {
1850 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1851 final Phylogeny t1 = factory.create();
1852 if ( !t1.isEmpty() ) {
1855 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1856 if ( t2.getNumberOfExternalNodes() != 4 ) {
1859 if ( t2.getHeight() != 8.5 ) {
1862 if ( !t2.isCompletelyBinary() ) {
1865 if ( t2.isEmpty() ) {
1868 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1869 if ( t3.getNumberOfExternalNodes() != 5 ) {
1872 if ( t3.getHeight() != 11 ) {
1875 if ( t3.isCompletelyBinary() ) {
1878 final PhylogenyNode n = t3.getNode( "ABC" );
1879 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 ];
1880 if ( t4.getNumberOfExternalNodes() != 9 ) {
1883 if ( t4.getHeight() != 11 ) {
1886 if ( t4.isCompletelyBinary() ) {
1889 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)" );
1890 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1891 if ( t5.getNumberOfExternalNodes() != 8 ) {
1894 if ( t5.getHeight() != 15 ) {
1897 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)" );
1898 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1899 if ( t6.getHeight() != 15 ) {
1902 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)" );
1903 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1904 if ( t7.getHeight() != 15 ) {
1907 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)" );
1908 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1909 if ( t8.getNumberOfExternalNodes() != 10 ) {
1912 if ( t8.getHeight() != 15 ) {
1915 final char[] a9 = new char[] {};
1916 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1917 if ( t9.getHeight() != 0 ) {
1920 final char[] a10 = new char[] { 'a', ':', '6' };
1921 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1922 if ( t10.getHeight() != 6 ) {
1926 catch ( final Exception e ) {
1927 e.printStackTrace( System.out );
1933 private static boolean testConfidenceAssessor() {
1935 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1936 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1937 final Phylogeny[] ev0 = factory
1938 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1940 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1941 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1944 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1947 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1948 final Phylogeny[] ev1 = factory
1949 .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)));",
1951 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1952 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1955 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1958 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1959 final Phylogeny[] ev_b = factory
1960 .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",
1962 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1963 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1966 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1970 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1971 final Phylogeny[] ev1x = 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)));",
1974 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1975 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1978 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1981 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1982 final Phylogeny[] ev_bx = factory
1983 .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",
1985 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1986 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1989 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1993 final Phylogeny[] t2 = factory
1994 .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);",
1996 final Phylogeny[] ev2 = factory
1997 .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);",
1999 for( final Phylogeny target : t2 ) {
2000 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2003 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2004 new NHXParser() )[ 0 ];
2005 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2006 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2007 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2010 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2013 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2017 catch ( final Exception e ) {
2018 e.printStackTrace();
2024 private static boolean testCopyOfNodeData() {
2026 final PhylogenyNode n1 = PhylogenyNode
2027 .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]" );
2028 final PhylogenyNode n2 = n1.copyNodeData();
2029 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2033 catch ( final Exception e ) {
2034 e.printStackTrace();
2040 private static boolean testDataObjects() {
2042 final Confidence s0 = new Confidence();
2043 final Confidence s1 = new Confidence();
2044 if ( !s0.isEqual( s1 ) ) {
2047 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2048 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2049 if ( s2.isEqual( s1 ) ) {
2052 if ( !s2.isEqual( s3 ) ) {
2055 final Confidence s4 = ( Confidence ) s3.copy();
2056 if ( !s4.isEqual( s3 ) ) {
2063 final Taxonomy t1 = new Taxonomy();
2064 final Taxonomy t2 = new Taxonomy();
2065 final Taxonomy t3 = new Taxonomy();
2066 final Taxonomy t4 = new Taxonomy();
2067 final Taxonomy t5 = new Taxonomy();
2068 t1.setIdentifier( new Identifier( "ecoli" ) );
2069 t1.setTaxonomyCode( "ECOLI" );
2070 t1.setScientificName( "E. coli" );
2071 t1.setCommonName( "coli" );
2072 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2073 if ( !t1.isEqual( t0 ) ) {
2076 t2.setIdentifier( new Identifier( "ecoli" ) );
2077 t2.setTaxonomyCode( "OTHER" );
2078 t2.setScientificName( "what" );
2079 t2.setCommonName( "something" );
2080 if ( !t1.isEqual( t2 ) ) {
2083 t2.setIdentifier( new Identifier( "nemve" ) );
2084 if ( t1.isEqual( t2 ) ) {
2087 t1.setIdentifier( null );
2088 t3.setTaxonomyCode( "ECOLI" );
2089 t3.setScientificName( "what" );
2090 t3.setCommonName( "something" );
2091 if ( !t1.isEqual( t3 ) ) {
2094 t1.setIdentifier( null );
2095 t1.setTaxonomyCode( "" );
2096 t4.setScientificName( "E. ColI" );
2097 t4.setCommonName( "something" );
2098 if ( !t1.isEqual( t4 ) ) {
2101 t4.setScientificName( "B. subtilis" );
2102 t4.setCommonName( "something" );
2103 if ( t1.isEqual( t4 ) ) {
2106 t1.setIdentifier( null );
2107 t1.setTaxonomyCode( "" );
2108 t1.setScientificName( "" );
2109 t5.setCommonName( "COLI" );
2110 if ( !t1.isEqual( t5 ) ) {
2113 t5.setCommonName( "vibrio" );
2114 if ( t1.isEqual( t5 ) ) {
2119 final Identifier id0 = new Identifier( "123", "pfam" );
2120 final Identifier id1 = ( Identifier ) id0.copy();
2121 if ( !id1.isEqual( id1 ) ) {
2124 if ( !id1.isEqual( id0 ) ) {
2127 if ( !id0.isEqual( id1 ) ) {
2134 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2135 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2136 if ( !pd1.isEqual( pd1 ) ) {
2139 if ( !pd1.isEqual( pd0 ) ) {
2144 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2145 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2146 if ( !pd3.isEqual( pd3 ) ) {
2149 if ( !pd2.isEqual( pd3 ) ) {
2152 if ( !pd0.isEqual( pd3 ) ) {
2157 // DomainArchitecture
2158 // ------------------
2159 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2160 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2161 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2162 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2163 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2164 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2169 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2170 if ( ds0.getNumberOfDomains() != 4 ) {
2173 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2174 if ( !ds0.isEqual( ds0 ) ) {
2177 if ( !ds0.isEqual( ds1 ) ) {
2180 if ( ds1.getNumberOfDomains() != 4 ) {
2183 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2188 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2189 if ( ds0.isEqual( ds2 ) ) {
2195 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2196 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2197 System.out.println( ds3.toNHX() );
2200 if ( ds3.getNumberOfDomains() != 3 ) {
2205 final Event e1 = new Event( Event.EventType.fusion );
2206 if ( e1.isDuplication() ) {
2209 if ( !e1.isFusion() ) {
2212 if ( !e1.asText().toString().equals( "fusion" ) ) {
2215 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2218 final Event e11 = new Event( Event.EventType.fusion );
2219 if ( !e11.isEqual( e1 ) ) {
2222 if ( !e11.toNHX().toString().equals( "" ) ) {
2225 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2226 if ( e2.isDuplication() ) {
2229 if ( !e2.isSpeciationOrDuplication() ) {
2232 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2235 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2238 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2241 if ( e11.isEqual( e2 ) ) {
2244 final Event e2c = ( Event ) e2.copy();
2245 if ( !e2c.isEqual( e2 ) ) {
2248 Event e3 = new Event( 1, 2, 3 );
2249 if ( e3.isDuplication() ) {
2252 if ( e3.isSpeciation() ) {
2255 if ( e3.isGeneLoss() ) {
2258 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2261 final Event e3c = ( Event ) e3.copy();
2262 final Event e3cc = ( Event ) e3c.copy();
2263 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2267 if ( !e3c.isEqual( e3cc ) ) {
2270 Event e4 = new Event( 1, 2, 3 );
2271 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2274 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2277 final Event e4c = ( Event ) e4.copy();
2279 final Event e4cc = ( Event ) e4c.copy();
2280 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2283 if ( !e4c.isEqual( e4cc ) ) {
2286 final Event e5 = new Event();
2287 if ( !e5.isUnassigned() ) {
2290 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2293 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2296 final Event e6 = new Event( 1, 0, 0 );
2297 if ( !e6.asText().toString().equals( "duplication" ) ) {
2300 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2303 final Event e7 = new Event( 0, 1, 0 );
2304 if ( !e7.asText().toString().equals( "speciation" ) ) {
2307 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2310 final Event e8 = new Event( 0, 0, 1 );
2311 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2314 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2318 catch ( final Exception e ) {
2319 e.printStackTrace( System.out );
2325 private static boolean testDeletionOfExternalNodes() {
2327 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2328 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2329 final PhylogenyWriter w = new PhylogenyWriter();
2330 if ( t0.isEmpty() ) {
2333 if ( t0.getNumberOfExternalNodes() != 1 ) {
2336 t0.deleteSubtree( t0.getNode( "A" ), false );
2337 if ( t0.getNumberOfExternalNodes() != 0 ) {
2340 if ( !t0.isEmpty() ) {
2343 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2344 if ( t1.getNumberOfExternalNodes() != 2 ) {
2347 t1.deleteSubtree( t1.getNode( "A" ), false );
2348 if ( t1.getNumberOfExternalNodes() != 1 ) {
2351 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2354 t1.deleteSubtree( t1.getNode( "B" ), false );
2355 if ( t1.getNumberOfExternalNodes() != 1 ) {
2358 t1.deleteSubtree( t1.getNode( "r" ), false );
2359 if ( !t1.isEmpty() ) {
2362 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2363 if ( t2.getNumberOfExternalNodes() != 3 ) {
2366 t2.deleteSubtree( t2.getNode( "B" ), false );
2367 if ( t2.getNumberOfExternalNodes() != 2 ) {
2370 t2.toNewHampshireX();
2371 PhylogenyNode n = t2.getNode( "A" );
2372 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2375 t2.deleteSubtree( t2.getNode( "A" ), false );
2376 if ( t2.getNumberOfExternalNodes() != 2 ) {
2379 t2.deleteSubtree( t2.getNode( "C" ), true );
2380 if ( t2.getNumberOfExternalNodes() != 1 ) {
2383 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2384 if ( t3.getNumberOfExternalNodes() != 4 ) {
2387 t3.deleteSubtree( t3.getNode( "B" ), true );
2388 if ( t3.getNumberOfExternalNodes() != 3 ) {
2391 n = t3.getNode( "A" );
2392 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2395 n = n.getNextExternalNode();
2396 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2399 t3.deleteSubtree( t3.getNode( "A" ), true );
2400 if ( t3.getNumberOfExternalNodes() != 2 ) {
2403 n = t3.getNode( "C" );
2404 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2407 t3.deleteSubtree( t3.getNode( "C" ), true );
2408 if ( t3.getNumberOfExternalNodes() != 1 ) {
2411 t3.deleteSubtree( t3.getNode( "D" ), true );
2412 if ( t3.getNumberOfExternalNodes() != 0 ) {
2415 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2416 if ( t4.getNumberOfExternalNodes() != 6 ) {
2419 t4.deleteSubtree( t4.getNode( "B2" ), true );
2420 if ( t4.getNumberOfExternalNodes() != 5 ) {
2423 String s = w.toNewHampshire( t4, false, true ).toString();
2424 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2427 t4.deleteSubtree( t4.getNode( "B11" ), true );
2428 if ( t4.getNumberOfExternalNodes() != 4 ) {
2431 t4.deleteSubtree( t4.getNode( "C" ), true );
2432 if ( t4.getNumberOfExternalNodes() != 3 ) {
2435 n = t4.getNode( "A" );
2436 n = n.getNextExternalNode();
2437 if ( !n.getName().equals( "B12" ) ) {
2440 n = n.getNextExternalNode();
2441 if ( !n.getName().equals( "D" ) ) {
2444 s = w.toNewHampshire( t4, false, true ).toString();
2445 if ( !s.equals( "((A,B12),D);" ) ) {
2448 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2449 t5.deleteSubtree( t5.getNode( "A" ), true );
2450 if ( t5.getNumberOfExternalNodes() != 5 ) {
2453 s = w.toNewHampshire( t5, false, true ).toString();
2454 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2457 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2458 t6.deleteSubtree( t6.getNode( "B11" ), true );
2459 if ( t6.getNumberOfExternalNodes() != 5 ) {
2462 s = w.toNewHampshire( t6, false, false ).toString();
2463 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2466 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2467 t7.deleteSubtree( t7.getNode( "B12" ), true );
2468 if ( t7.getNumberOfExternalNodes() != 5 ) {
2471 s = w.toNewHampshire( t7, false, true ).toString();
2472 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2475 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2476 t8.deleteSubtree( t8.getNode( "B2" ), true );
2477 if ( t8.getNumberOfExternalNodes() != 5 ) {
2480 s = w.toNewHampshire( t8, false, false ).toString();
2481 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2484 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2485 t9.deleteSubtree( t9.getNode( "C" ), true );
2486 if ( t9.getNumberOfExternalNodes() != 5 ) {
2489 s = w.toNewHampshire( t9, false, true ).toString();
2490 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2493 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2494 t10.deleteSubtree( t10.getNode( "D" ), true );
2495 if ( t10.getNumberOfExternalNodes() != 5 ) {
2498 s = w.toNewHampshire( t10, false, true ).toString();
2499 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2502 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2503 t11.deleteSubtree( t11.getNode( "A" ), true );
2504 if ( t11.getNumberOfExternalNodes() != 2 ) {
2507 s = w.toNewHampshire( t11, false, true ).toString();
2508 if ( !s.equals( "(B,C);" ) ) {
2511 t11.deleteSubtree( t11.getNode( "C" ), true );
2512 if ( t11.getNumberOfExternalNodes() != 1 ) {
2515 s = w.toNewHampshire( t11, false, false ).toString();
2516 if ( !s.equals( "B;" ) ) {
2519 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2520 t12.deleteSubtree( t12.getNode( "B2" ), true );
2521 if ( t12.getNumberOfExternalNodes() != 8 ) {
2524 s = w.toNewHampshire( t12, false, true ).toString();
2525 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2528 t12.deleteSubtree( t12.getNode( "B3" ), true );
2529 if ( t12.getNumberOfExternalNodes() != 7 ) {
2532 s = w.toNewHampshire( t12, false, true ).toString();
2533 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2536 t12.deleteSubtree( t12.getNode( "C3" ), true );
2537 if ( t12.getNumberOfExternalNodes() != 6 ) {
2540 s = w.toNewHampshire( t12, false, true ).toString();
2541 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2544 t12.deleteSubtree( t12.getNode( "A1" ), true );
2545 if ( t12.getNumberOfExternalNodes() != 5 ) {
2548 s = w.toNewHampshire( t12, false, true ).toString();
2549 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2552 t12.deleteSubtree( t12.getNode( "B1" ), true );
2553 if ( t12.getNumberOfExternalNodes() != 4 ) {
2556 s = w.toNewHampshire( t12, false, true ).toString();
2557 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2560 t12.deleteSubtree( t12.getNode( "A3" ), true );
2561 if ( t12.getNumberOfExternalNodes() != 3 ) {
2564 s = w.toNewHampshire( t12, false, true ).toString();
2565 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2568 t12.deleteSubtree( t12.getNode( "A2" ), true );
2569 if ( t12.getNumberOfExternalNodes() != 2 ) {
2572 s = w.toNewHampshire( t12, false, true ).toString();
2573 if ( !s.equals( "(C1,C2);" ) ) {
2576 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2577 t13.deleteSubtree( t13.getNode( "D" ), true );
2578 if ( t13.getNumberOfExternalNodes() != 4 ) {
2581 s = w.toNewHampshire( t13, false, true ).toString();
2582 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2585 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2586 t14.deleteSubtree( t14.getNode( "E" ), true );
2587 if ( t14.getNumberOfExternalNodes() != 5 ) {
2590 s = w.toNewHampshire( t14, false, true ).toString();
2591 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2594 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2595 t15.deleteSubtree( t15.getNode( "B2" ), true );
2596 if ( t15.getNumberOfExternalNodes() != 11 ) {
2599 t15.deleteSubtree( t15.getNode( "B1" ), true );
2600 if ( t15.getNumberOfExternalNodes() != 10 ) {
2603 t15.deleteSubtree( t15.getNode( "B3" ), true );
2604 if ( t15.getNumberOfExternalNodes() != 9 ) {
2607 t15.deleteSubtree( t15.getNode( "B4" ), true );
2608 if ( t15.getNumberOfExternalNodes() != 8 ) {
2611 t15.deleteSubtree( t15.getNode( "A1" ), true );
2612 if ( t15.getNumberOfExternalNodes() != 7 ) {
2615 t15.deleteSubtree( t15.getNode( "C4" ), true );
2616 if ( t15.getNumberOfExternalNodes() != 6 ) {
2620 catch ( final Exception e ) {
2621 e.printStackTrace( System.out );
2627 private static boolean testDescriptiveStatistics() {
2629 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2630 dss1.addValue( 82 );
2631 dss1.addValue( 78 );
2632 dss1.addValue( 70 );
2633 dss1.addValue( 58 );
2634 dss1.addValue( 42 );
2635 if ( dss1.getN() != 5 ) {
2638 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2641 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2644 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2647 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2650 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2653 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2656 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2659 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2662 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2665 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2668 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2671 dss1.addValue( 123 );
2672 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2675 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2678 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2681 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2682 dss2.addValue( -1.85 );
2683 dss2.addValue( 57.5 );
2684 dss2.addValue( 92.78 );
2685 dss2.addValue( 57.78 );
2686 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2689 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2692 final double[] a = dss2.getDataAsDoubleArray();
2693 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2696 dss2.addValue( -100 );
2697 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2700 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2703 final double[] ds = new double[ 14 ];
2718 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2719 if ( bins.length != 4 ) {
2722 if ( bins[ 0 ] != 2 ) {
2725 if ( bins[ 1 ] != 3 ) {
2728 if ( bins[ 2 ] != 4 ) {
2731 if ( bins[ 3 ] != 5 ) {
2734 final double[] ds1 = new double[ 9 ];
2744 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2745 if ( bins1.length != 4 ) {
2748 if ( bins1[ 0 ] != 2 ) {
2751 if ( bins1[ 1 ] != 3 ) {
2754 if ( bins1[ 2 ] != 0 ) {
2757 if ( bins1[ 3 ] != 4 ) {
2760 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2761 if ( bins1_1.length != 3 ) {
2764 if ( bins1_1[ 0 ] != 3 ) {
2767 if ( bins1_1[ 1 ] != 2 ) {
2770 if ( bins1_1[ 2 ] != 4 ) {
2773 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2774 if ( bins1_2.length != 3 ) {
2777 if ( bins1_2[ 0 ] != 2 ) {
2780 if ( bins1_2[ 1 ] != 2 ) {
2783 if ( bins1_2[ 2 ] != 2 ) {
2786 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2800 dss3.addValue( 10 );
2801 dss3.addValue( 10 );
2802 dss3.addValue( 10 );
2803 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2804 histo.toStringBuffer( 10, '=', 40, 5 );
2805 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2807 catch ( final Exception e ) {
2808 e.printStackTrace( System.out );
2814 private static boolean testDir( final String file ) {
2816 final File f = new File( file );
2817 if ( !f.exists() ) {
2820 if ( !f.isDirectory() ) {
2823 if ( !f.canRead() ) {
2827 catch ( final Exception e ) {
2833 private static boolean testExternalNodeRelatedMethods() {
2835 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2836 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2837 PhylogenyNode n = t1.getNode( "A" );
2838 n = n.getNextExternalNode();
2839 if ( !n.getName().equals( "B" ) ) {
2842 n = n.getNextExternalNode();
2843 if ( !n.getName().equals( "C" ) ) {
2846 n = n.getNextExternalNode();
2847 if ( !n.getName().equals( "D" ) ) {
2850 n = t1.getNode( "B" );
2851 while ( !n.isLastExternalNode() ) {
2852 n = n.getNextExternalNode();
2854 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2855 n = t2.getNode( "A" );
2856 n = n.getNextExternalNode();
2857 if ( !n.getName().equals( "B" ) ) {
2860 n = n.getNextExternalNode();
2861 if ( !n.getName().equals( "C" ) ) {
2864 n = n.getNextExternalNode();
2865 if ( !n.getName().equals( "D" ) ) {
2868 n = t2.getNode( "B" );
2869 while ( !n.isLastExternalNode() ) {
2870 n = n.getNextExternalNode();
2872 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2873 n = t3.getNode( "A" );
2874 n = n.getNextExternalNode();
2875 if ( !n.getName().equals( "B" ) ) {
2878 n = n.getNextExternalNode();
2879 if ( !n.getName().equals( "C" ) ) {
2882 n = n.getNextExternalNode();
2883 if ( !n.getName().equals( "D" ) ) {
2886 n = n.getNextExternalNode();
2887 if ( !n.getName().equals( "E" ) ) {
2890 n = n.getNextExternalNode();
2891 if ( !n.getName().equals( "F" ) ) {
2894 n = n.getNextExternalNode();
2895 if ( !n.getName().equals( "G" ) ) {
2898 n = n.getNextExternalNode();
2899 if ( !n.getName().equals( "H" ) ) {
2902 n = t3.getNode( "B" );
2903 while ( !n.isLastExternalNode() ) {
2904 n = n.getNextExternalNode();
2906 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2907 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2908 final PhylogenyNode node = iter.next();
2910 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2911 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2912 final PhylogenyNode node = iter.next();
2914 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2915 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2916 if ( !iter.next().getName().equals( "A" ) ) {
2919 if ( !iter.next().getName().equals( "B" ) ) {
2922 if ( !iter.next().getName().equals( "C" ) ) {
2925 if ( !iter.next().getName().equals( "D" ) ) {
2928 if ( !iter.next().getName().equals( "E" ) ) {
2931 if ( !iter.next().getName().equals( "F" ) ) {
2934 if ( iter.hasNext() ) {
2938 catch ( final Exception e ) {
2939 e.printStackTrace( System.out );
2945 private static boolean testGeneralTable() {
2947 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2948 t0.setValue( 3, 2, "23" );
2949 t0.setValue( 10, 1, "error" );
2950 t0.setValue( 10, 1, "110" );
2951 t0.setValue( 9, 1, "19" );
2952 t0.setValue( 1, 10, "101" );
2953 t0.setValue( 10, 10, "1010" );
2954 t0.setValue( 100, 10, "10100" );
2955 t0.setValue( 0, 0, "00" );
2956 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2959 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2962 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2965 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2968 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2971 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2974 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2977 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2980 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2983 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2984 t1.setValue( "3", "2", "23" );
2985 t1.setValue( "10", "1", "error" );
2986 t1.setValue( "10", "1", "110" );
2987 t1.setValue( "9", "1", "19" );
2988 t1.setValue( "1", "10", "101" );
2989 t1.setValue( "10", "10", "1010" );
2990 t1.setValue( "100", "10", "10100" );
2991 t1.setValue( "0", "0", "00" );
2992 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2993 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2996 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2999 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3002 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3005 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3008 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3011 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3014 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3017 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3020 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3024 catch ( final Exception e ) {
3025 e.printStackTrace( System.out );
3031 private static boolean testGetDistance() {
3033 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3034 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",
3035 new NHXParser() )[ 0 ];
3036 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3039 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3042 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3045 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3048 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3051 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3054 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3057 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3060 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3063 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3066 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3069 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3072 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3075 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3078 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3081 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3084 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3087 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3090 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3093 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3096 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3099 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3102 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3105 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3108 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3111 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3114 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3117 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3120 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3123 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3126 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3129 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",
3130 new NHXParser() )[ 0 ];
3131 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3134 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3137 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3140 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3143 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3146 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3149 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3152 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3155 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3158 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3161 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3165 catch ( final Exception e ) {
3166 e.printStackTrace( System.out );
3172 private static boolean testGetLCA() {
3174 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3175 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3176 new NHXParser() )[ 0 ];
3177 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3178 if ( !A.getName().equals( "A" ) ) {
3181 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3182 if ( !gh.getName().equals( "gh" ) ) {
3185 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3186 if ( !ab.getName().equals( "ab" ) ) {
3189 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3190 if ( !ab2.getName().equals( "ab" ) ) {
3193 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3194 if ( !gh2.getName().equals( "gh" ) ) {
3197 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3198 if ( !gh3.getName().equals( "gh" ) ) {
3201 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3202 if ( !abc.getName().equals( "abc" ) ) {
3205 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3206 if ( !abc2.getName().equals( "abc" ) ) {
3209 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3210 if ( !abcd.getName().equals( "abcd" ) ) {
3213 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3214 if ( !abcd2.getName().equals( "abcd" ) ) {
3217 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3218 if ( !abcdef.getName().equals( "abcdef" ) ) {
3221 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3222 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3225 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3226 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3229 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3230 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3233 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3234 if ( !abcde.getName().equals( "abcde" ) ) {
3237 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3238 if ( !abcde2.getName().equals( "abcde" ) ) {
3241 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3242 if ( !r.getName().equals( "abcdefgh" ) ) {
3245 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3246 if ( !r2.getName().equals( "abcdefgh" ) ) {
3249 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3250 if ( !r3.getName().equals( "abcdefgh" ) ) {
3253 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3254 if ( !abcde3.getName().equals( "abcde" ) ) {
3257 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3258 if ( !abcde4.getName().equals( "abcde" ) ) {
3261 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3262 if ( !ab3.getName().equals( "ab" ) ) {
3265 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3266 if ( !ab4.getName().equals( "ab" ) ) {
3269 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3270 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3271 if ( !cd.getName().equals( "cd" ) ) {
3274 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3275 if ( !cd2.getName().equals( "cd" ) ) {
3278 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3279 if ( !cde.getName().equals( "cde" ) ) {
3282 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3283 if ( !cde2.getName().equals( "cde" ) ) {
3286 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3287 if ( !cdef.getName().equals( "cdef" ) ) {
3290 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3291 if ( !cdef2.getName().equals( "cdef" ) ) {
3294 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3295 if ( !cdef3.getName().equals( "cdef" ) ) {
3298 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3299 if ( !rt.getName().equals( "r" ) ) {
3302 final Phylogeny p3 = factory
3303 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3304 new NHXParser() )[ 0 ];
3305 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3306 if ( !bc_3.getName().equals( "bc" ) ) {
3309 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3310 if ( !ac_3.getName().equals( "abc" ) ) {
3313 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3314 if ( !ad_3.getName().equals( "abcde" ) ) {
3317 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3318 if ( !af_3.getName().equals( "abcdef" ) ) {
3321 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3322 if ( !ag_3.getName().equals( "" ) ) {
3325 if ( !ag_3.isRoot() ) {
3328 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3329 if ( !al_3.getName().equals( "" ) ) {
3332 if ( !al_3.isRoot() ) {
3335 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3336 if ( !kl_3.getName().equals( "" ) ) {
3339 if ( !kl_3.isRoot() ) {
3342 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3343 if ( !fl_3.getName().equals( "" ) ) {
3346 if ( !fl_3.isRoot() ) {
3349 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3350 if ( !gk_3.getName().equals( "ghijk" ) ) {
3353 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3354 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3355 if ( !r_4.getName().equals( "r" ) ) {
3358 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3359 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3360 if ( !r_5.getName().equals( "root" ) ) {
3363 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3364 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3365 if ( !r_6.getName().equals( "rot" ) ) {
3368 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3369 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3370 if ( !r_7.getName().equals( "rott" ) ) {
3374 catch ( final Exception e ) {
3375 e.printStackTrace( System.out );
3381 private static boolean testGetLCA2() {
3383 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3384 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3385 PhylogenyMethods.preOrderReId( p_a );
3386 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3387 p_a.getNode( "a" ) );
3388 if ( !p_a_1.getName().equals( "a" ) ) {
3391 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3392 PhylogenyMethods.preOrderReId( p_b );
3393 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3394 p_b.getNode( "a" ) );
3395 if ( !p_b_1.getName().equals( "b" ) ) {
3398 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3399 p_b.getNode( "b" ) );
3400 if ( !p_b_2.getName().equals( "b" ) ) {
3403 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3404 PhylogenyMethods.preOrderReId( p_c );
3405 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3406 p_c.getNode( "a" ) );
3407 if ( !p_c_1.getName().equals( "b" ) ) {
3410 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3411 p_c.getNode( "c" ) );
3412 if ( !p_c_2.getName().equals( "c" ) ) {
3413 System.out.println( p_c_2.getName() );
3417 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3418 p_c.getNode( "b" ) );
3419 if ( !p_c_3.getName().equals( "b" ) ) {
3422 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3423 p_c.getNode( "a" ) );
3424 if ( !p_c_4.getName().equals( "c" ) ) {
3427 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3428 new NHXParser() )[ 0 ];
3429 PhylogenyMethods.preOrderReId( p1 );
3430 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3431 p1.getNode( "A" ) );
3432 if ( !A.getName().equals( "A" ) ) {
3435 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3436 p1.getNode( "gh" ) );
3437 if ( !gh.getName().equals( "gh" ) ) {
3440 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3441 p1.getNode( "B" ) );
3442 if ( !ab.getName().equals( "ab" ) ) {
3445 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3446 p1.getNode( "A" ) );
3447 if ( !ab2.getName().equals( "ab" ) ) {
3450 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3451 p1.getNode( "G" ) );
3452 if ( !gh2.getName().equals( "gh" ) ) {
3455 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3456 p1.getNode( "H" ) );
3457 if ( !gh3.getName().equals( "gh" ) ) {
3460 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3461 p1.getNode( "A" ) );
3462 if ( !abc.getName().equals( "abc" ) ) {
3465 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3466 p1.getNode( "C" ) );
3467 if ( !abc2.getName().equals( "abc" ) ) {
3470 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3471 p1.getNode( "D" ) );
3472 if ( !abcd.getName().equals( "abcd" ) ) {
3475 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3476 p1.getNode( "A" ) );
3477 if ( !abcd2.getName().equals( "abcd" ) ) {
3480 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3481 p1.getNode( "F" ) );
3482 if ( !abcdef.getName().equals( "abcdef" ) ) {
3485 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3486 p1.getNode( "A" ) );
3487 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3490 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3491 p1.getNode( "F" ) );
3492 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3495 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3496 p1.getNode( "ab" ) );
3497 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3500 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3501 p1.getNode( "E" ) );
3502 if ( !abcde.getName().equals( "abcde" ) ) {
3505 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3506 p1.getNode( "A" ) );
3507 if ( !abcde2.getName().equals( "abcde" ) ) {
3510 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3511 p1.getNode( "abcdefgh" ) );
3512 if ( !r.getName().equals( "abcdefgh" ) ) {
3515 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3516 p1.getNode( "H" ) );
3517 if ( !r2.getName().equals( "abcdefgh" ) ) {
3520 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3521 p1.getNode( "A" ) );
3522 if ( !r3.getName().equals( "abcdefgh" ) ) {
3525 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3526 p1.getNode( "abcde" ) );
3527 if ( !abcde3.getName().equals( "abcde" ) ) {
3530 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3531 p1.getNode( "E" ) );
3532 if ( !abcde4.getName().equals( "abcde" ) ) {
3535 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3536 p1.getNode( "B" ) );
3537 if ( !ab3.getName().equals( "ab" ) ) {
3540 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3541 p1.getNode( "ab" ) );
3542 if ( !ab4.getName().equals( "ab" ) ) {
3545 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3546 PhylogenyMethods.preOrderReId( p2 );
3547 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3548 p2.getNode( "d" ) );
3549 if ( !cd.getName().equals( "cd" ) ) {
3552 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3553 p2.getNode( "c" ) );
3554 if ( !cd2.getName().equals( "cd" ) ) {
3557 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3558 p2.getNode( "e" ) );
3559 if ( !cde.getName().equals( "cde" ) ) {
3562 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3563 p2.getNode( "c" ) );
3564 if ( !cde2.getName().equals( "cde" ) ) {
3567 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3568 p2.getNode( "f" ) );
3569 if ( !cdef.getName().equals( "cdef" ) ) {
3572 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3573 p2.getNode( "f" ) );
3574 if ( !cdef2.getName().equals( "cdef" ) ) {
3577 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3578 p2.getNode( "d" ) );
3579 if ( !cdef3.getName().equals( "cdef" ) ) {
3582 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3583 p2.getNode( "a" ) );
3584 if ( !rt.getName().equals( "r" ) ) {
3587 final Phylogeny p3 = factory
3588 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3589 new NHXParser() )[ 0 ];
3590 PhylogenyMethods.preOrderReId( p3 );
3591 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3592 p3.getNode( "c" ) );
3593 if ( !bc_3.getName().equals( "bc" ) ) {
3596 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3597 p3.getNode( "c" ) );
3598 if ( !ac_3.getName().equals( "abc" ) ) {
3601 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3602 p3.getNode( "d" ) );
3603 if ( !ad_3.getName().equals( "abcde" ) ) {
3606 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3607 p3.getNode( "f" ) );
3608 if ( !af_3.getName().equals( "abcdef" ) ) {
3611 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3612 p3.getNode( "g" ) );
3613 if ( !ag_3.getName().equals( "" ) ) {
3616 if ( !ag_3.isRoot() ) {
3619 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3620 p3.getNode( "l" ) );
3621 if ( !al_3.getName().equals( "" ) ) {
3624 if ( !al_3.isRoot() ) {
3627 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3628 p3.getNode( "l" ) );
3629 if ( !kl_3.getName().equals( "" ) ) {
3632 if ( !kl_3.isRoot() ) {
3635 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3636 p3.getNode( "l" ) );
3637 if ( !fl_3.getName().equals( "" ) ) {
3640 if ( !fl_3.isRoot() ) {
3643 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3644 p3.getNode( "k" ) );
3645 if ( !gk_3.getName().equals( "ghijk" ) ) {
3648 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3649 PhylogenyMethods.preOrderReId( p4 );
3650 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3651 p4.getNode( "c" ) );
3652 if ( !r_4.getName().equals( "r" ) ) {
3655 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3656 PhylogenyMethods.preOrderReId( p5 );
3657 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3658 p5.getNode( "c" ) );
3659 if ( !r_5.getName().equals( "root" ) ) {
3662 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3663 PhylogenyMethods.preOrderReId( p6 );
3664 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3665 p6.getNode( "a" ) );
3666 if ( !r_6.getName().equals( "rot" ) ) {
3669 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3670 PhylogenyMethods.preOrderReId( p7 );
3671 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3672 p7.getNode( "e" ) );
3673 if ( !r_7.getName().equals( "rott" ) ) {
3676 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3677 p7.getNode( "a" ) );
3678 if ( !r_71.getName().equals( "rott" ) ) {
3681 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3682 p7.getNode( "rott" ) );
3683 if ( !r_72.getName().equals( "rott" ) ) {
3686 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3687 p7.getNode( "a" ) );
3688 if ( !r_73.getName().equals( "rott" ) ) {
3691 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3692 p7.getNode( "rott" ) );
3693 if ( !r_74.getName().equals( "rott" ) ) {
3696 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3697 p7.getNode( "e" ) );
3698 if ( !r_75.getName().equals( "e" ) ) {
3702 catch ( final Exception e ) {
3703 e.printStackTrace( System.out );
3709 private static boolean testHmmscanOutputParser() {
3710 final String test_dir = Test.PATH_TO_TEST_DATA;
3712 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3713 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3715 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3716 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3717 final List<Protein> proteins = parser2.parse();
3718 if ( parser2.getProteinsEncountered() != 4 ) {
3721 if ( proteins.size() != 4 ) {
3724 if ( parser2.getDomainsEncountered() != 69 ) {
3727 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3730 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3733 final Protein p1 = proteins.get( 0 );
3734 if ( p1.getNumberOfProteinDomains() != 15 ) {
3737 if ( p1.getLength() != 850 ) {
3740 final Protein p2 = proteins.get( 1 );
3741 if ( p2.getNumberOfProteinDomains() != 51 ) {
3744 if ( p2.getLength() != 1291 ) {
3747 final Protein p3 = proteins.get( 2 );
3748 if ( p3.getNumberOfProteinDomains() != 2 ) {
3751 final Protein p4 = proteins.get( 3 );
3752 if ( p4.getNumberOfProteinDomains() != 1 ) {
3755 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3758 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3761 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3764 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3767 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3770 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3773 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3776 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3779 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3783 catch ( final Exception e ) {
3784 e.printStackTrace( System.out );
3790 private static boolean testLastExternalNodeMethods() {
3792 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3793 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3794 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3795 final PhylogenyNode n1 = t0.getNode( "A" );
3796 if ( n1.isLastExternalNode() ) {
3799 final PhylogenyNode n2 = t0.getNode( "B" );
3800 if ( n2.isLastExternalNode() ) {
3803 final PhylogenyNode n3 = t0.getNode( "C" );
3804 if ( n3.isLastExternalNode() ) {
3807 final PhylogenyNode n4 = t0.getNode( "D" );
3808 if ( !n4.isLastExternalNode() ) {
3812 catch ( final Exception e ) {
3813 e.printStackTrace( System.out );
3819 private static boolean testLevelOrderIterator() {
3821 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3822 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3823 PhylogenyNodeIterator it0;
3824 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3827 for( it0.reset(); it0.hasNext(); ) {
3830 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3831 if ( !it.next().getName().equals( "r" ) ) {
3834 if ( !it.next().getName().equals( "ab" ) ) {
3837 if ( !it.next().getName().equals( "cd" ) ) {
3840 if ( !it.next().getName().equals( "A" ) ) {
3843 if ( !it.next().getName().equals( "B" ) ) {
3846 if ( !it.next().getName().equals( "C" ) ) {
3849 if ( !it.next().getName().equals( "D" ) ) {
3852 if ( it.hasNext() ) {
3855 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",
3856 new NHXParser() )[ 0 ];
3857 PhylogenyNodeIterator it2;
3858 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3861 for( it2.reset(); it2.hasNext(); ) {
3864 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3865 if ( !it3.next().getName().equals( "r" ) ) {
3868 if ( !it3.next().getName().equals( "abc" ) ) {
3871 if ( !it3.next().getName().equals( "defg" ) ) {
3874 if ( !it3.next().getName().equals( "A" ) ) {
3877 if ( !it3.next().getName().equals( "B" ) ) {
3880 if ( !it3.next().getName().equals( "C" ) ) {
3883 if ( !it3.next().getName().equals( "D" ) ) {
3886 if ( !it3.next().getName().equals( "E" ) ) {
3889 if ( !it3.next().getName().equals( "F" ) ) {
3892 if ( !it3.next().getName().equals( "G" ) ) {
3895 if ( !it3.next().getName().equals( "1" ) ) {
3898 if ( !it3.next().getName().equals( "2" ) ) {
3901 if ( !it3.next().getName().equals( "3" ) ) {
3904 if ( !it3.next().getName().equals( "4" ) ) {
3907 if ( !it3.next().getName().equals( "5" ) ) {
3910 if ( !it3.next().getName().equals( "6" ) ) {
3913 if ( !it3.next().getName().equals( "f1" ) ) {
3916 if ( !it3.next().getName().equals( "f2" ) ) {
3919 if ( !it3.next().getName().equals( "f3" ) ) {
3922 if ( !it3.next().getName().equals( "a" ) ) {
3925 if ( !it3.next().getName().equals( "b" ) ) {
3928 if ( !it3.next().getName().equals( "f21" ) ) {
3931 if ( !it3.next().getName().equals( "X" ) ) {
3934 if ( !it3.next().getName().equals( "Y" ) ) {
3937 if ( !it3.next().getName().equals( "Z" ) ) {
3940 if ( it3.hasNext() ) {
3943 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3944 PhylogenyNodeIterator it4;
3945 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3948 for( it4.reset(); it4.hasNext(); ) {
3951 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3952 if ( !it5.next().getName().equals( "r" ) ) {
3955 if ( !it5.next().getName().equals( "A" ) ) {
3958 if ( !it5.next().getName().equals( "B" ) ) {
3961 if ( !it5.next().getName().equals( "C" ) ) {
3964 if ( !it5.next().getName().equals( "D" ) ) {
3967 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3968 PhylogenyNodeIterator it6;
3969 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3972 for( it6.reset(); it6.hasNext(); ) {
3975 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3976 if ( !it7.next().getName().equals( "A" ) ) {
3979 if ( it.hasNext() ) {
3983 catch ( final Exception e ) {
3984 e.printStackTrace( System.out );
3990 private static boolean testNodeRemoval() {
3992 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3993 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3994 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
3995 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
3998 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
3999 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
4000 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4003 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4004 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4005 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4009 catch ( final Exception e ) {
4010 e.printStackTrace( System.out );
4016 private static boolean testMidpointrooting() {
4018 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4019 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4020 PhylogenyMethods.midpointRoot( t0 );
4021 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4024 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4027 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4031 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",
4032 new NHXParser() )[ 0 ];
4033 if ( !t1.isRooted() ) {
4036 PhylogenyMethods.midpointRoot( t1 );
4037 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4040 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4043 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4046 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4049 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4052 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4055 t1.reRoot( t1.getNode( "A" ) );
4056 PhylogenyMethods.midpointRoot( t1 );
4057 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4060 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4063 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4066 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4069 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4073 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4077 catch ( final Exception e ) {
4078 e.printStackTrace( System.out );
4084 private static boolean testNexusCharactersParsing() {
4086 final NexusCharactersParser parser = new NexusCharactersParser();
4087 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4089 String[] labels = parser.getCharStateLabels();
4090 if ( labels.length != 7 ) {
4093 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4096 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4099 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4102 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4105 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4108 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4111 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4114 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4116 labels = parser.getCharStateLabels();
4117 if ( labels.length != 7 ) {
4120 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4123 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4126 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4129 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4132 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4135 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4138 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4142 catch ( final Exception e ) {
4143 e.printStackTrace( System.out );
4149 private static boolean testNexusMatrixParsing() {
4151 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4152 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4154 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4155 if ( m.getNumberOfCharacters() != 9 ) {
4158 if ( m.getNumberOfIdentifiers() != 5 ) {
4161 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4164 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4167 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4170 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4173 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4176 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4179 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4182 // if ( labels.length != 7 ) {
4185 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4188 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4191 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4194 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4197 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4200 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4203 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4206 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4208 // labels = parser.getCharStateLabels();
4209 // if ( labels.length != 7 ) {
4212 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4215 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4218 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4221 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4224 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4227 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4230 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4234 catch ( final Exception e ) {
4235 e.printStackTrace( System.out );
4241 private static boolean testNexusTreeParsing() {
4243 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4244 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4245 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4246 if ( phylogenies.length != 1 ) {
4249 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4252 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4256 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4257 if ( phylogenies.length != 1 ) {
4260 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4263 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4267 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4268 if ( phylogenies.length != 1 ) {
4271 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4274 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4277 if ( phylogenies[ 0 ].isRooted() ) {
4281 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4282 if ( phylogenies.length != 18 ) {
4285 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4288 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4291 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4294 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4297 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4300 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4303 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4306 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4309 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4312 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4315 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4318 if ( phylogenies[ 8 ].isRooted() ) {
4321 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4324 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4327 if ( !phylogenies[ 9 ].isRooted() ) {
4330 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4333 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4336 if ( !phylogenies[ 10 ].isRooted() ) {
4339 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4342 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4345 if ( phylogenies[ 11 ].isRooted() ) {
4348 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4351 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4354 if ( !phylogenies[ 12 ].isRooted() ) {
4357 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4360 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4363 if ( !phylogenies[ 13 ].isRooted() ) {
4366 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4369 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4372 if ( !phylogenies[ 14 ].isRooted() ) {
4375 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4378 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4381 if ( phylogenies[ 15 ].isRooted() ) {
4384 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4387 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4390 if ( !phylogenies[ 16 ].isRooted() ) {
4393 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4396 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4399 if ( phylogenies[ 17 ].isRooted() ) {
4402 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4406 catch ( final Exception e ) {
4407 e.printStackTrace( System.out );
4413 private static boolean testNexusTreeParsingTranslating() {
4415 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4416 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4417 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4418 if ( phylogenies.length != 1 ) {
4421 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4424 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4427 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4430 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4433 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4434 .equals( "Aranaeus" ) ) {
4438 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4439 if ( phylogenies.length != 3 ) {
4442 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4445 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4448 if ( phylogenies[ 0 ].isRooted() ) {
4451 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4454 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4457 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4458 .equals( "Aranaeus" ) ) {
4461 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4464 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4467 if ( phylogenies[ 1 ].isRooted() ) {
4470 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4473 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4476 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4477 .equals( "Aranaeus" ) ) {
4480 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4483 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4486 if ( !phylogenies[ 2 ].isRooted() ) {
4489 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4492 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4495 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4496 .equals( "Aranaeus" ) ) {
4500 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4501 if ( phylogenies.length != 3 ) {
4504 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4507 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4510 if ( phylogenies[ 0 ].isRooted() ) {
4513 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4516 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4519 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4520 .equals( "Aranaeus" ) ) {
4523 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4526 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4529 if ( phylogenies[ 1 ].isRooted() ) {
4532 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4535 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4538 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4539 .equals( "Aranaeus" ) ) {
4542 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4545 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4548 if ( !phylogenies[ 2 ].isRooted() ) {
4551 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4554 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4557 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4558 .equals( "Aranaeus" ) ) {
4562 catch ( final Exception e ) {
4563 e.printStackTrace( System.out );
4569 private static boolean testNHParsing() {
4571 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4572 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser2() )[ 0 ];
4573 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4576 final NHXParser nhxp = new NHXParser();
4577 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4578 nhxp.setReplaceUnderscores( true );
4579 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4580 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4583 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4586 final Phylogeny p1b = factory
4587 .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 ",
4588 new NHXParser() )[ 0 ];
4589 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4592 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4595 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser2() )[ 0 ];
4596 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser2() )[ 0 ];
4597 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser2() )[ 0 ];
4598 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser2() )[ 0 ];
4599 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser2() );
4600 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser2() );
4601 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser2() );
4602 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser2() );
4603 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser2() );
4604 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser2() );
4605 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4606 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4607 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4609 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4612 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4615 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4618 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4621 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser2() );
4622 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser2() );
4623 final String p16_S = "((A,B),C)";
4624 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser2() );
4625 if ( p16.length != 1 ) {
4628 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4631 final String p17_S = "(C,(A,B))";
4632 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser2() );
4633 if ( p17.length != 1 ) {
4636 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4639 final String p18_S = "((A,B),(C,D))";
4640 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser2() );
4641 if ( p18.length != 1 ) {
4644 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4647 final String p19_S = "(((A,B),C),D)";
4648 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser2() );
4649 if ( p19.length != 1 ) {
4652 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4655 final String p20_S = "(A,(B,(C,D)))";
4656 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser2() );
4657 if ( p20.length != 1 ) {
4660 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4663 final String p21_S = "(A,(B,(C,(D,E))))";
4664 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser2() );
4665 if ( p21.length != 1 ) {
4668 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4671 final String p22_S = "((((A,B),C),D),E)";
4672 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser2() );
4673 if ( p22.length != 1 ) {
4676 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4679 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4680 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser2() );
4681 if ( p23.length != 1 ) {
4682 System.out.println( "xl=" + p23.length );
4686 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4689 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4690 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser2() );
4691 if ( p24.length != 1 ) {
4694 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4697 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4698 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4699 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser2() );
4700 if ( p241.length != 2 ) {
4703 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4706 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4709 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4710 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4711 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4712 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4713 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4714 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4715 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4716 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4717 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser2() );
4718 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4721 final String p26_S = "(A,B)ab";
4722 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser2() );
4723 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4726 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4727 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser2() );
4728 if ( p27s.length != 1 ) {
4729 System.out.println( "xxl=" + p27s.length );
4733 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4734 System.out.println( p27s[ 0 ].toNewHampshireX() );
4738 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4740 if ( p27.length != 1 ) {
4741 System.out.println( "yl=" + p27.length );
4745 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4746 System.out.println( p27[ 0 ].toNewHampshireX() );
4750 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4751 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4752 final String p28_S3 = "(A,B)ab";
4753 final String p28_S4 = "((((A,B),C),D),;E;)";
4754 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4756 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4759 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4762 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4765 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4768 if ( p28.length != 4 ) {
4771 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";
4772 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser2() );
4773 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4776 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";
4777 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser2() );
4778 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4781 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4782 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser2() );
4783 if ( ( p32.length != 0 ) ) {
4786 final String p33_S = "A";
4787 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser2() );
4788 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4791 final String p34_S = "B;";
4792 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser2() );
4793 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4796 final String p35_S = "B:0.2";
4797 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser2() );
4798 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4801 final String p36_S = "(A)";
4802 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser2() );
4803 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4806 final String p37_S = "((A))";
4807 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser2() );
4808 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4811 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4812 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser2() );
4813 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4816 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4817 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser2() );
4818 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4821 final String p40_S = "(A,B,C)";
4822 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser2() );
4823 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4826 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4827 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser2() );
4828 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4831 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4832 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser2() );
4833 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4836 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)";
4837 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser2() );
4838 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4841 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)))";
4842 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser2() );
4843 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4846 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4847 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser2() );
4848 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4851 final String p46_S = "";
4852 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser2() );
4853 if ( p46.length != 0 ) {
4856 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser2() )[ 0 ];
4857 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4860 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser2() )[ 0 ];
4861 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4864 final Phylogeny p49 = factory
4865 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4866 new NHXParser2() )[ 0 ];
4867 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4870 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser2() )[ 0 ];
4871 if ( p50.getNode( "A" ) == null ) {
4874 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4875 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4878 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4881 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4882 .equals( "((A,B)88:2.0,C);" ) ) {
4885 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser2() )[ 0 ];
4886 if ( p51.getNode( "A(A" ) == null ) {
4889 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser2() )[ 0 ];
4890 if ( p52.getNode( "A(A" ) == null ) {
4893 final Phylogeny p53 = factory
4894 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4895 new NHXParser2() )[ 0 ];
4896 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4900 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser2() )[ 0 ];
4901 if ( p54.getNode( "A" ) == null ) {
4904 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4905 .equals( "((A,B)[88],C);" ) ) {
4909 catch ( final Exception e ) {
4910 e.printStackTrace( System.out );
4916 private static boolean testNHParsingIter() {
4918 String p0_str = "(A,B);";
4919 NHXParser2 p = new NHXParser2();
4920 p.setSource( p0_str );
4921 if ( !p.hasNext() ) {
4924 Phylogeny p0 = p.next();
4925 if ( !p0.toNewHampshire().equals( p0_str ) ) {
4926 System.out.println( p0.toNewHampshire() );
4929 if ( p.hasNext() ) {
4932 if ( p.next() != null ) {
4936 String p00_str = "(A,B)root;";
4937 p.setSource( p00_str );
4938 Phylogeny p00 = p.next();
4939 if ( !p00.toNewHampshire().equals( p00_str ) ) {
4940 System.out.println( p00.toNewHampshire() );
4944 String p000_str = "A;";
4945 p.setSource( p000_str );
4946 Phylogeny p000 = p.next();
4947 if ( !p000.toNewHampshire().equals( p000_str ) ) {
4948 System.out.println( p000.toNewHampshire() );
4952 String p0000_str = "A";
4953 p.setSource( p0000_str );
4954 Phylogeny p0000 = p.next();
4955 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
4956 System.out.println( p0000.toNewHampshire() );
4960 p.setSource( "(A)" );
4961 Phylogeny p00000 = p.next();
4962 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
4963 System.out.println( p00000.toNewHampshire() );
4967 String p1_str = "(A,B)(C,D)(E,F)(G,H)";
4968 p.setSource( p1_str );
4969 if ( !p.hasNext() ) {
4972 Phylogeny p1_0 = p.next();
4973 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
4974 System.out.println( p1_0.toNewHampshire() );
4977 if ( !p.hasNext() ) {
4980 Phylogeny p1_1 = p.next();
4981 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
4982 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
4985 if ( !p.hasNext() ) {
4988 Phylogeny p1_2 = p.next();
4989 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
4990 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
4993 if ( !p.hasNext() ) {
4996 Phylogeny p1_3 = p.next();
4997 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
4998 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
5001 if ( p.hasNext() ) {
5004 if ( p.next() != null ) {
5008 String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
5009 p.setSource( p2_str );
5010 if ( !p.hasNext() ) {
5013 Phylogeny p2_0 = p.next();
5014 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5015 System.out.println( p2_0.toNewHampshire() );
5018 if ( !p.hasNext() ) {
5021 Phylogeny p2_1 = p.next();
5022 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5023 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5026 if ( !p.hasNext() ) {
5029 Phylogeny p2_2 = p.next();
5030 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5031 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5034 if ( !p.hasNext() ) {
5037 Phylogeny p2_3 = p.next();
5038 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5039 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5042 if ( !p.hasNext() ) {
5045 Phylogeny p2_4 = p.next();
5046 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5047 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5050 if ( p.hasNext() ) {
5053 if ( p.next() != null ) {
5058 if ( !p.hasNext() ) {
5062 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5063 System.out.println( p2_0.toNewHampshire() );
5066 if ( !p.hasNext() ) {
5070 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5071 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5074 if ( !p.hasNext() ) {
5078 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5079 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5082 if ( !p.hasNext() ) {
5086 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5087 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5090 if ( !p.hasNext() ) {
5094 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5095 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5098 if ( p.hasNext() ) {
5101 if ( p.next() != null ) {
5105 String p3_str = "((A,B),C)abc";
5106 p.setSource( p3_str );
5107 if ( !p.hasNext() ) {
5110 Phylogeny p3_0 = p.next();
5111 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
5114 if ( p.hasNext() ) {
5117 if ( p.next() != null ) {
5121 String p4_str = "((A,B)ab,C)abc";
5122 p.setSource( p4_str );
5123 if ( !p.hasNext() ) {
5126 Phylogeny p4_0 = p.next();
5127 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
5130 if ( p.hasNext() ) {
5133 if ( p.next() != null ) {
5137 String p5_str = "(((A,B)ab,C)abc,D)abcd";
5138 p.setSource( p5_str );
5139 if ( !p.hasNext() ) {
5142 Phylogeny p5_0 = p.next();
5143 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
5146 if ( p.hasNext() ) {
5149 if ( p.next() != null ) {
5153 String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5154 p.setSource( p6_str );
5155 if ( !p.hasNext() ) {
5158 Phylogeny p6_0 = p.next();
5159 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5162 if ( p.hasNext() ) {
5165 if ( p.next() != null ) {
5169 if ( !p.hasNext() ) {
5173 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5176 if ( p.hasNext() ) {
5179 if ( p.next() != null ) {
5183 String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5184 p.setSource( p7_str );
5185 if ( !p.hasNext() ) {
5188 Phylogeny p7_0 = p.next();
5189 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5192 if ( p.hasNext() ) {
5195 if ( p.next() != null ) {
5199 if ( !p.hasNext() ) {
5203 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5206 if ( p.hasNext() ) {
5209 if ( p.next() != null ) {
5213 String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
5214 p.setSource( p8_str );
5215 if ( !p.hasNext() ) {
5218 Phylogeny p8_0 = p.next();
5219 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5222 if ( !p.hasNext() ) {
5225 if ( !p.hasNext() ) {
5228 Phylogeny p8_1 = p.next();
5229 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5232 if ( p.hasNext() ) {
5235 if ( p.next() != null ) {
5239 if ( !p.hasNext() ) {
5243 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5246 if ( !p.hasNext() ) {
5250 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5253 if ( p.hasNext() ) {
5256 if ( p.next() != null ) {
5262 if ( p.hasNext() ) {
5266 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
5267 if ( !p.hasNext() ) {
5270 Phylogeny p_27 = p.next();
5271 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5272 System.out.println( p_27.toNewHampshireX() );
5276 if ( p.hasNext() ) {
5279 if ( p.next() != null ) {
5283 if ( !p.hasNext() ) {
5287 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5288 System.out.println( p_27.toNewHampshireX() );
5292 if ( p.hasNext() ) {
5295 if ( p.next() != null ) {
5299 catch ( final Exception e ) {
5300 e.printStackTrace( System.out );
5306 private static boolean testNHXconversion() {
5308 final PhylogenyNode n1 = new PhylogenyNode();
5309 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5310 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5311 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5312 final PhylogenyNode n5 = PhylogenyNode
5313 .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]" );
5314 final PhylogenyNode n6 = PhylogenyNode
5315 .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]" );
5316 if ( !n1.toNewHampshireX().equals( "" ) ) {
5319 if ( !n2.toNewHampshireX().equals( "" ) ) {
5322 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
5325 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
5328 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56:W=2.0:C=10.20.30]" ) ) {
5331 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100:W=2.0:C=0.0.0]" ) ) {
5335 catch ( final Exception e ) {
5336 e.printStackTrace( System.out );
5342 private static boolean testTaxonomyExtraction() {
5344 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5345 NHXParser.TAXONOMY_EXTRACTION.YES );
5346 if ( n0.getNodeData().isHasTaxonomy() ) {
5349 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
5350 NHXParser.TAXONOMY_EXTRACTION.YES );
5351 if ( n1.getNodeData().isHasTaxonomy() ) {
5352 System.out.println( n1.toString() );
5355 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
5356 NHXParser.TAXONOMY_EXTRACTION.YES );
5357 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5358 System.out.println( n2.toString() );
5361 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
5362 NHXParser.TAXONOMY_EXTRACTION.YES );
5363 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5364 System.out.println( n3.toString() );
5367 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
5368 NHXParser.TAXONOMY_EXTRACTION.YES );
5369 if ( n4.getNodeData().isHasTaxonomy() ) {
5370 System.out.println( n4.toString() );
5373 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
5374 NHXParser.TAXONOMY_EXTRACTION.YES );
5375 if ( n5.getNodeData().isHasTaxonomy() ) {
5376 System.out.println( n5.toString() );
5379 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
5380 NHXParser.TAXONOMY_EXTRACTION.YES );
5381 if ( n6.getNodeData().isHasTaxonomy() ) {
5382 System.out.println( n6.toString() );
5385 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
5386 NHXParser.TAXONOMY_EXTRACTION.YES );
5387 if ( n7.getNodeData().isHasTaxonomy() ) {
5388 System.out.println( n7.toString() );
5391 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
5392 NHXParser.TAXONOMY_EXTRACTION.YES );
5393 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5394 System.out.println( n8.toString() );
5397 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
5398 NHXParser.TAXONOMY_EXTRACTION.YES );
5399 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5400 System.out.println( n9.toString() );
5403 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
5404 NHXParser.TAXONOMY_EXTRACTION.YES );
5405 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
5406 System.out.println( n10.toString() );
5409 final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
5410 NHXParser.TAXONOMY_EXTRACTION.YES );
5411 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
5412 System.out.println( n11.toString() );
5415 final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
5416 NHXParser.TAXONOMY_EXTRACTION.YES );
5417 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
5418 System.out.println( n12.toString() );
5421 final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
5422 NHXParser.TAXONOMY_EXTRACTION.YES );
5423 if ( n13.getNodeData().isHasTaxonomy() ) {
5424 System.out.println( n13.toString() );
5427 final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
5428 NHXParser.TAXONOMY_EXTRACTION.YES );
5429 if ( n14.getNodeData().isHasTaxonomy() ) {
5430 System.out.println( n14.toString() );
5433 final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
5434 NHXParser.TAXONOMY_EXTRACTION.YES );
5435 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
5436 System.out.println( n15.toString() );
5439 final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
5440 NHXParser.TAXONOMY_EXTRACTION.YES );
5441 if ( n16.getNodeData().isHasTaxonomy() ) {
5442 System.out.println( n16.toString() );
5445 final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
5446 NHXParser.TAXONOMY_EXTRACTION.YES );
5447 if ( n17.getNodeData().isHasTaxonomy() ) {
5448 System.out.println( n17.toString() );
5452 catch ( final Exception e ) {
5453 e.printStackTrace( System.out );
5459 private static boolean testNHXNodeParsing() {
5461 final PhylogenyNode n1 = new PhylogenyNode();
5462 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5463 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5464 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5465 final PhylogenyNode n5 = PhylogenyNode
5466 .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]" );
5467 if ( !n3.getName().equals( "n3" ) ) {
5470 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5473 if ( n3.isDuplication() ) {
5476 if ( n3.isHasAssignedEvent() ) {
5479 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
5482 if ( !n4.getName().equals( "n4" ) ) {
5485 if ( n4.getDistanceToParent() != 0.01 ) {
5488 if ( !n5.getName().equals( "n5" ) ) {
5491 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
5494 if ( n5.getDistanceToParent() != 0.1 ) {
5497 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
5500 if ( !n5.isDuplication() ) {
5503 if ( !n5.isHasAssignedEvent() ) {
5506 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
5509 final PhylogenyNode n8 = PhylogenyNode
5510 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5511 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
5514 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
5517 final PhylogenyNode n9 = PhylogenyNode
5518 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5519 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
5522 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
5525 final PhylogenyNode n10 = PhylogenyNode
5526 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5527 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
5530 final PhylogenyNode n20 = PhylogenyNode
5531 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5532 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
5535 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
5538 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
5539 NHXParser.TAXONOMY_EXTRACTION.YES );
5540 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
5543 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
5546 final PhylogenyNode n20xx = PhylogenyNode
5547 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5548 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
5551 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
5554 final PhylogenyNode n20xxx = PhylogenyNode
5555 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5556 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
5559 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
5562 final PhylogenyNode n20xxxx = PhylogenyNode
5563 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5564 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
5567 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
5570 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
5571 NHXParser.TAXONOMY_EXTRACTION.YES );
5572 if ( !n21.getName().equals( "n21_PIG" ) ) {
5575 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
5578 final PhylogenyNode n21x = PhylogenyNode
5579 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5580 if ( !n21x.getName().equals( "n21_PIG" ) ) {
5583 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
5586 final PhylogenyNode n22 = PhylogenyNode
5587 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5588 if ( !n22.getName().equals( "n22/PIG" ) ) {
5591 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
5594 final PhylogenyNode n23 = PhylogenyNode
5595 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5596 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
5599 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
5602 final PhylogenyNode a = PhylogenyNode
5603 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5604 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
5607 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
5610 final PhylogenyNode b = PhylogenyNode
5611 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5612 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
5615 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
5618 final PhylogenyNode c = PhylogenyNode
5619 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
5620 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5621 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
5624 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
5627 final PhylogenyNode c1 = PhylogenyNode
5628 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
5629 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5630 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
5633 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
5636 final PhylogenyNode c2 = PhylogenyNode
5637 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
5638 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5639 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5642 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5645 final PhylogenyNode d = PhylogenyNode
5646 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5647 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5650 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5653 final PhylogenyNode e = PhylogenyNode
5654 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5655 if ( !e.getName().equals( "n10_RAT1" ) ) {
5658 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5661 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5662 NHXParser.TAXONOMY_EXTRACTION.YES );
5663 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5666 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5669 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5670 NHXParser.TAXONOMY_EXTRACTION.YES );
5671 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5674 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5677 final PhylogenyNode n11 = PhylogenyNode
5678 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5679 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5680 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5683 if ( n11.getDistanceToParent() != 0.4 ) {
5686 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5689 final PhylogenyNode n12 = PhylogenyNode
5690 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5691 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5692 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5695 if ( n12.getDistanceToParent() != 0.4 ) {
5698 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5701 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5702 NHXParser.TAXONOMY_EXTRACTION.YES );
5703 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5706 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5709 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5710 NHXParser.TAXONOMY_EXTRACTION.YES );
5711 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5714 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5717 if ( n1.getName().compareTo( "" ) != 0 ) {
5720 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5723 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5726 if ( n2.getName().compareTo( "" ) != 0 ) {
5729 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5732 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5735 final PhylogenyNode n00 = PhylogenyNode
5736 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1:W=2:C=0.0.0]" );
5737 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5740 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5743 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5744 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5747 final PhylogenyNode n13 = PhylogenyNode
5748 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5749 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5752 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5755 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5758 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5761 final PhylogenyNode n14 = PhylogenyNode
5762 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5763 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5766 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5769 final PhylogenyNode n15 = PhylogenyNode
5770 .createInstanceFromNhxString( "something_wicked[123]",
5771 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5772 if ( !n15.getName().equals( "something_wicked" ) ) {
5775 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5778 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5781 final PhylogenyNode n16 = PhylogenyNode
5782 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5783 if ( !n16.getName().equals( "something_wicked2" ) ) {
5786 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5789 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5792 final PhylogenyNode n17 = PhylogenyNode
5793 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5794 if ( !n17.getName().equals( "something_wicked3" ) ) {
5797 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5800 final PhylogenyNode n18 = PhylogenyNode
5801 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5802 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5805 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5808 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5811 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
5812 NHXParser.TAXONOMY_EXTRACTION.YES );
5813 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
5816 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5819 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
5820 NHXParser.TAXONOMY_EXTRACTION.YES );
5821 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
5824 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5827 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
5828 NHXParser.TAXONOMY_EXTRACTION.YES );
5829 if ( n31.getNodeData().isHasTaxonomy() ) {
5832 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5833 NHXParser.TAXONOMY_EXTRACTION.YES );
5834 if ( n32.getNodeData().isHasTaxonomy() ) {
5838 catch ( final Exception e ) {
5839 e.printStackTrace( System.out );
5845 private static boolean testNHXParsing() {
5847 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5848 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5849 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5852 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]";
5853 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5854 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5857 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]";
5858 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5859 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5862 final Phylogeny[] p3 = factory
5863 .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]",
5865 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5868 final Phylogeny[] p4 = factory
5869 .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(]",
5871 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5874 final Phylogeny[] p5 = factory
5875 .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(((]",
5877 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5880 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)";
5881 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)";
5882 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5883 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5886 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)))";
5887 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)))";
5888 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5889 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5892 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]) ))[,,, ])))))))";
5893 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5894 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5895 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5898 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5899 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5902 final Phylogeny p10 = factory
5903 .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]",
5904 new NHXParser() )[ 0 ];
5905 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5909 catch ( final Exception e ) {
5910 e.printStackTrace( System.out );
5916 private static boolean testNHXParsingQuotes() {
5918 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5919 final NHXParser p = new NHXParser();
5920 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5921 if ( phylogenies_0.length != 5 ) {
5924 final Phylogeny phy = phylogenies_0[ 4 ];
5925 if ( phy.getNumberOfExternalNodes() != 7 ) {
5928 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5931 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5934 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5935 .getScientificName().equals( "hsapiens" ) ) {
5938 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5941 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5944 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5947 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5950 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5953 final NHXParser p1p = new NHXParser();
5954 p1p.setIgnoreQuotes( true );
5955 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5956 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5959 final NHXParser p2p = new NHXParser();
5960 p1p.setIgnoreQuotes( false );
5961 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5962 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5965 final NHXParser p3p = new NHXParser();
5966 p3p.setIgnoreQuotes( false );
5967 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5968 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5971 final NHXParser p4p = new NHXParser();
5972 p4p.setIgnoreQuotes( false );
5973 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5974 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5977 final Phylogeny p10 = factory
5978 .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]",
5979 new NHXParser() )[ 0 ];
5980 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]";
5981 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5984 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5985 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5989 final Phylogeny p12 = factory
5990 .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]",
5991 new NHXParser() )[ 0 ];
5992 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]";
5993 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5996 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5997 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
6000 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;";
6001 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
6004 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
6005 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
6009 catch ( final Exception e ) {
6010 e.printStackTrace( System.out );
6016 private static boolean testNHXParsingMB() {
6018 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6019 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
6020 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6021 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6022 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6023 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6024 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6025 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6026 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6027 + "7.369400000000000e-02}])", new NHXParser2() )[ 0 ];
6028 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
6031 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
6034 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
6035 0.1100000000000000e+00 ) ) {
6038 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
6041 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
6044 final Phylogeny p2 = factory
6045 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
6046 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6047 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6048 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6049 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6050 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6051 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6052 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6053 + "7.369400000000000e-02}])",
6054 new NHXParser2() )[ 0 ];
6055 if ( p2.getNode( "1" ) == null ) {
6058 if ( p2.getNode( "2" ) == null ) {
6062 catch ( final Exception e ) {
6063 e.printStackTrace( System.out );
6070 private static boolean testPhylogenyBranch() {
6072 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
6073 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
6074 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
6075 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
6076 if ( !a1b1.equals( a1b1 ) ) {
6079 if ( !a1b1.equals( b1a1 ) ) {
6082 if ( !b1a1.equals( a1b1 ) ) {
6085 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
6086 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
6087 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
6088 if ( a1_b1.equals( b1_a1 ) ) {
6091 if ( a1_b1.equals( a1_b1_ ) ) {
6094 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
6095 if ( !a1_b1.equals( b1_a1_ ) ) {
6098 if ( a1_b1_.equals( b1_a1_ ) ) {
6101 if ( !a1_b1_.equals( b1_a1 ) ) {
6105 catch ( final Exception e ) {
6106 e.printStackTrace( System.out );
6112 private static boolean testPhyloXMLparsingOfDistributionElement() {
6114 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6115 PhyloXmlParser xml_parser = null;
6117 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
6119 catch ( final Exception e ) {
6120 // Do nothing -- means were not running from jar.
6122 if ( xml_parser == null ) {
6123 xml_parser = new PhyloXmlParser();
6124 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
6125 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
6128 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
6131 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
6133 if ( xml_parser.getErrorCount() > 0 ) {
6134 System.out.println( xml_parser.getErrorMessages().toString() );
6137 if ( phylogenies_0.length != 1 ) {
6140 final Phylogeny t1 = phylogenies_0[ 0 ];
6141 PhylogenyNode n = null;
6142 Distribution d = null;
6143 n = t1.getNode( "root node" );
6144 if ( !n.getNodeData().isHasDistribution() ) {
6147 if ( n.getNodeData().getDistributions().size() != 1 ) {
6150 d = n.getNodeData().getDistribution();
6151 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6154 if ( d.getPoints().size() != 1 ) {
6157 if ( d.getPolygons() != null ) {
6160 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6163 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6166 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6169 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6172 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6175 n = t1.getNode( "node a" );
6176 if ( !n.getNodeData().isHasDistribution() ) {
6179 if ( n.getNodeData().getDistributions().size() != 2 ) {
6182 d = n.getNodeData().getDistribution( 1 );
6183 if ( !d.getDesc().equals( "San Diego" ) ) {
6186 if ( d.getPoints().size() != 1 ) {
6189 if ( d.getPolygons() != null ) {
6192 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6195 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6198 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6201 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6204 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6207 n = t1.getNode( "node bb" );
6208 if ( !n.getNodeData().isHasDistribution() ) {
6211 if ( n.getNodeData().getDistributions().size() != 1 ) {
6214 d = n.getNodeData().getDistribution( 0 );
6215 if ( d.getPoints().size() != 3 ) {
6218 if ( d.getPolygons().size() != 2 ) {
6221 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6224 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6227 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6230 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6233 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6236 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6239 Polygon p = d.getPolygons().get( 0 );
6240 if ( p.getPoints().size() != 3 ) {
6243 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6246 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6249 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6252 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6255 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6258 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6261 p = d.getPolygons().get( 1 );
6262 if ( p.getPoints().size() != 3 ) {
6265 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6268 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6271 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6275 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
6276 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
6277 if ( rt.length != 1 ) {
6280 final Phylogeny t1_rt = rt[ 0 ];
6281 n = t1_rt.getNode( "root node" );
6282 if ( !n.getNodeData().isHasDistribution() ) {
6285 if ( n.getNodeData().getDistributions().size() != 1 ) {
6288 d = n.getNodeData().getDistribution();
6289 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6292 if ( d.getPoints().size() != 1 ) {
6295 if ( d.getPolygons() != null ) {
6298 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6301 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6304 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6307 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6310 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6313 n = t1_rt.getNode( "node a" );
6314 if ( !n.getNodeData().isHasDistribution() ) {
6317 if ( n.getNodeData().getDistributions().size() != 2 ) {
6320 d = n.getNodeData().getDistribution( 1 );
6321 if ( !d.getDesc().equals( "San Diego" ) ) {
6324 if ( d.getPoints().size() != 1 ) {
6327 if ( d.getPolygons() != null ) {
6330 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6333 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6336 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6339 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6342 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6345 n = t1_rt.getNode( "node bb" );
6346 if ( !n.getNodeData().isHasDistribution() ) {
6349 if ( n.getNodeData().getDistributions().size() != 1 ) {
6352 d = n.getNodeData().getDistribution( 0 );
6353 if ( d.getPoints().size() != 3 ) {
6356 if ( d.getPolygons().size() != 2 ) {
6359 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6362 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6365 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6368 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6371 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6374 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6377 p = d.getPolygons().get( 0 );
6378 if ( p.getPoints().size() != 3 ) {
6381 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6384 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6387 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6390 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6393 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6396 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6399 p = d.getPolygons().get( 1 );
6400 if ( p.getPoints().size() != 3 ) {
6403 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6406 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6409 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6413 catch ( final Exception e ) {
6414 e.printStackTrace( System.out );
6420 private static boolean testPostOrderIterator() {
6422 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6423 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6424 PhylogenyNodeIterator it0;
6425 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
6428 for( it0.reset(); it0.hasNext(); ) {
6431 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6432 final PhylogenyNodeIterator it = t1.iteratorPostorder();
6433 if ( !it.next().getName().equals( "A" ) ) {
6436 if ( !it.next().getName().equals( "B" ) ) {
6439 if ( !it.next().getName().equals( "ab" ) ) {
6442 if ( !it.next().getName().equals( "C" ) ) {
6445 if ( !it.next().getName().equals( "D" ) ) {
6448 if ( !it.next().getName().equals( "cd" ) ) {
6451 if ( !it.next().getName().equals( "abcd" ) ) {
6454 if ( !it.next().getName().equals( "E" ) ) {
6457 if ( !it.next().getName().equals( "F" ) ) {
6460 if ( !it.next().getName().equals( "ef" ) ) {
6463 if ( !it.next().getName().equals( "G" ) ) {
6466 if ( !it.next().getName().equals( "H" ) ) {
6469 if ( !it.next().getName().equals( "gh" ) ) {
6472 if ( !it.next().getName().equals( "efgh" ) ) {
6475 if ( !it.next().getName().equals( "r" ) ) {
6478 if ( it.hasNext() ) {
6482 catch ( final Exception e ) {
6483 e.printStackTrace( System.out );
6489 private static boolean testPreOrderIterator() {
6491 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6492 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6493 PhylogenyNodeIterator it0;
6494 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
6497 for( it0.reset(); it0.hasNext(); ) {
6500 PhylogenyNodeIterator it = t0.iteratorPreorder();
6501 if ( !it.next().getName().equals( "r" ) ) {
6504 if ( !it.next().getName().equals( "ab" ) ) {
6507 if ( !it.next().getName().equals( "A" ) ) {
6510 if ( !it.next().getName().equals( "B" ) ) {
6513 if ( !it.next().getName().equals( "cd" ) ) {
6516 if ( !it.next().getName().equals( "C" ) ) {
6519 if ( !it.next().getName().equals( "D" ) ) {
6522 if ( it.hasNext() ) {
6525 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6526 it = t1.iteratorPreorder();
6527 if ( !it.next().getName().equals( "r" ) ) {
6530 if ( !it.next().getName().equals( "abcd" ) ) {
6533 if ( !it.next().getName().equals( "ab" ) ) {
6536 if ( !it.next().getName().equals( "A" ) ) {
6539 if ( !it.next().getName().equals( "B" ) ) {
6542 if ( !it.next().getName().equals( "cd" ) ) {
6545 if ( !it.next().getName().equals( "C" ) ) {
6548 if ( !it.next().getName().equals( "D" ) ) {
6551 if ( !it.next().getName().equals( "efgh" ) ) {
6554 if ( !it.next().getName().equals( "ef" ) ) {
6557 if ( !it.next().getName().equals( "E" ) ) {
6560 if ( !it.next().getName().equals( "F" ) ) {
6563 if ( !it.next().getName().equals( "gh" ) ) {
6566 if ( !it.next().getName().equals( "G" ) ) {
6569 if ( !it.next().getName().equals( "H" ) ) {
6572 if ( it.hasNext() ) {
6576 catch ( final Exception e ) {
6577 e.printStackTrace( System.out );
6583 private static boolean testPropertiesMap() {
6585 final PropertiesMap pm = new PropertiesMap();
6586 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6587 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6588 final Property p2 = new Property( "something:else",
6590 "improbable:research",
6593 pm.addProperty( p0 );
6594 pm.addProperty( p1 );
6595 pm.addProperty( p2 );
6596 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
6599 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
6602 if ( pm.getProperties().size() != 3 ) {
6605 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
6608 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6611 if ( pm.getProperties().size() != 3 ) {
6614 pm.removeProperty( "dimensions:diameter" );
6615 if ( pm.getProperties().size() != 2 ) {
6618 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
6621 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6625 catch ( final Exception e ) {
6626 e.printStackTrace( System.out );
6632 private static boolean testReIdMethods() {
6634 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6635 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6636 final int count = PhylogenyNode.getNodeCount();
6638 if ( p.getNode( "r" ).getId() != count ) {
6641 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6644 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6647 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6650 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6653 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6656 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6659 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6662 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6665 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6668 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6671 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6674 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6677 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6680 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6684 catch ( final Exception e ) {
6685 e.printStackTrace( System.out );
6691 private static boolean testRerooting() {
6693 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6694 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",
6695 new NHXParser() )[ 0 ];
6696 if ( !t1.isRooted() ) {
6699 t1.reRoot( t1.getNode( "D" ) );
6700 t1.reRoot( t1.getNode( "CD" ) );
6701 t1.reRoot( t1.getNode( "A" ) );
6702 t1.reRoot( t1.getNode( "B" ) );
6703 t1.reRoot( t1.getNode( "AB" ) );
6704 t1.reRoot( t1.getNode( "D" ) );
6705 t1.reRoot( t1.getNode( "C" ) );
6706 t1.reRoot( t1.getNode( "CD" ) );
6707 t1.reRoot( t1.getNode( "A" ) );
6708 t1.reRoot( t1.getNode( "B" ) );
6709 t1.reRoot( t1.getNode( "AB" ) );
6710 t1.reRoot( t1.getNode( "D" ) );
6711 t1.reRoot( t1.getNode( "D" ) );
6712 t1.reRoot( t1.getNode( "C" ) );
6713 t1.reRoot( t1.getNode( "A" ) );
6714 t1.reRoot( t1.getNode( "B" ) );
6715 t1.reRoot( t1.getNode( "AB" ) );
6716 t1.reRoot( t1.getNode( "C" ) );
6717 t1.reRoot( t1.getNode( "D" ) );
6718 t1.reRoot( t1.getNode( "CD" ) );
6719 t1.reRoot( t1.getNode( "D" ) );
6720 t1.reRoot( t1.getNode( "A" ) );
6721 t1.reRoot( t1.getNode( "B" ) );
6722 t1.reRoot( t1.getNode( "AB" ) );
6723 t1.reRoot( t1.getNode( "C" ) );
6724 t1.reRoot( t1.getNode( "D" ) );
6725 t1.reRoot( t1.getNode( "CD" ) );
6726 t1.reRoot( t1.getNode( "D" ) );
6727 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6730 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6733 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6736 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6739 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6742 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6745 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",
6746 new NHXParser() )[ 0 ];
6747 t2.reRoot( t2.getNode( "A" ) );
6748 t2.reRoot( t2.getNode( "D" ) );
6749 t2.reRoot( t2.getNode( "ABC" ) );
6750 t2.reRoot( t2.getNode( "A" ) );
6751 t2.reRoot( t2.getNode( "B" ) );
6752 t2.reRoot( t2.getNode( "D" ) );
6753 t2.reRoot( t2.getNode( "C" ) );
6754 t2.reRoot( t2.getNode( "ABC" ) );
6755 t2.reRoot( t2.getNode( "A" ) );
6756 t2.reRoot( t2.getNode( "B" ) );
6757 t2.reRoot( t2.getNode( "AB" ) );
6758 t2.reRoot( t2.getNode( "AB" ) );
6759 t2.reRoot( t2.getNode( "D" ) );
6760 t2.reRoot( t2.getNode( "C" ) );
6761 t2.reRoot( t2.getNode( "B" ) );
6762 t2.reRoot( t2.getNode( "AB" ) );
6763 t2.reRoot( t2.getNode( "D" ) );
6764 t2.reRoot( t2.getNode( "D" ) );
6765 t2.reRoot( t2.getNode( "ABC" ) );
6766 t2.reRoot( t2.getNode( "A" ) );
6767 t2.reRoot( t2.getNode( "B" ) );
6768 t2.reRoot( t2.getNode( "AB" ) );
6769 t2.reRoot( t2.getNode( "D" ) );
6770 t2.reRoot( t2.getNode( "C" ) );
6771 t2.reRoot( t2.getNode( "ABC" ) );
6772 t2.reRoot( t2.getNode( "A" ) );
6773 t2.reRoot( t2.getNode( "B" ) );
6774 t2.reRoot( t2.getNode( "AB" ) );
6775 t2.reRoot( t2.getNode( "D" ) );
6776 t2.reRoot( t2.getNode( "D" ) );
6777 t2.reRoot( t2.getNode( "C" ) );
6778 t2.reRoot( t2.getNode( "A" ) );
6779 t2.reRoot( t2.getNode( "B" ) );
6780 t2.reRoot( t2.getNode( "AB" ) );
6781 t2.reRoot( t2.getNode( "C" ) );
6782 t2.reRoot( t2.getNode( "D" ) );
6783 t2.reRoot( t2.getNode( "ABC" ) );
6784 t2.reRoot( t2.getNode( "D" ) );
6785 t2.reRoot( t2.getNode( "A" ) );
6786 t2.reRoot( t2.getNode( "B" ) );
6787 t2.reRoot( t2.getNode( "AB" ) );
6788 t2.reRoot( t2.getNode( "C" ) );
6789 t2.reRoot( t2.getNode( "D" ) );
6790 t2.reRoot( t2.getNode( "ABC" ) );
6791 t2.reRoot( t2.getNode( "D" ) );
6792 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6795 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6798 t2.reRoot( t2.getNode( "ABC" ) );
6799 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6802 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6805 t2.reRoot( t2.getNode( "AB" ) );
6806 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6809 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6812 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6815 t2.reRoot( t2.getNode( "AB" ) );
6816 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6819 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6822 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6825 t2.reRoot( t2.getNode( "D" ) );
6826 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6829 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6832 t2.reRoot( t2.getNode( "ABC" ) );
6833 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6836 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6839 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6840 new NHXParser() )[ 0 ];
6841 t3.reRoot( t3.getNode( "B" ) );
6842 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6845 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6848 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6851 t3.reRoot( t3.getNode( "B" ) );
6852 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6855 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6858 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6861 t3.reRoot( t3.getRoot() );
6862 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6865 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6868 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6872 catch ( final Exception e ) {
6873 e.printStackTrace( System.out );
6879 private static boolean testSDIse() {
6881 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6882 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6883 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6884 gene1.setRooted( true );
6885 species1.setRooted( true );
6886 final SDI sdi = new SDI( gene1, species1 );
6887 if ( !gene1.getRoot().isDuplication() ) {
6890 final Phylogeny species2 = factory
6891 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6892 new NHXParser() )[ 0 ];
6893 final Phylogeny gene2 = factory
6894 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6895 new NHXParser() )[ 0 ];
6896 species2.setRooted( true );
6897 gene2.setRooted( true );
6898 final SDI sdi2 = new SDI( gene2, species2 );
6899 if ( sdi2.getDuplicationsSum() != 0 ) {
6902 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6905 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6908 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6911 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6914 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6917 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6920 final Phylogeny species3 = factory
6921 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6922 new NHXParser() )[ 0 ];
6923 final Phylogeny gene3 = factory
6924 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6925 new NHXParser() )[ 0 ];
6926 species3.setRooted( true );
6927 gene3.setRooted( true );
6928 final SDI sdi3 = new SDI( gene3, species3 );
6929 if ( sdi3.getDuplicationsSum() != 1 ) {
6932 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6935 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6938 final Phylogeny species4 = factory
6939 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6940 new NHXParser() )[ 0 ];
6941 final Phylogeny gene4 = factory
6942 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6943 new NHXParser() )[ 0 ];
6944 species4.setRooted( true );
6945 gene4.setRooted( true );
6946 final SDI sdi4 = new SDI( gene4, species4 );
6947 if ( sdi4.getDuplicationsSum() != 1 ) {
6950 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6953 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6956 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6959 if ( species4.getNumberOfExternalNodes() != 6 ) {
6962 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6965 final Phylogeny species5 = factory
6966 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6967 new NHXParser() )[ 0 ];
6968 final Phylogeny gene5 = factory
6969 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6970 new NHXParser() )[ 0 ];
6971 species5.setRooted( true );
6972 gene5.setRooted( true );
6973 final SDI sdi5 = new SDI( gene5, species5 );
6974 if ( sdi5.getDuplicationsSum() != 2 ) {
6977 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6980 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6983 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6986 if ( species5.getNumberOfExternalNodes() != 6 ) {
6989 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6992 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6993 // Conjecture for Comparing Molecular Phylogenies"
6994 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6995 final Phylogeny species6 = factory
6996 .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,"
6997 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6998 new NHXParser() )[ 0 ];
6999 final Phylogeny gene6 = factory
7000 .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,"
7001 + "((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,"
7002 + "(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;",
7003 new NHXParser() )[ 0 ];
7004 species6.setRooted( true );
7005 gene6.setRooted( true );
7006 final SDI sdi6 = new SDI( gene6, species6 );
7007 if ( sdi6.getDuplicationsSum() != 3 ) {
7010 if ( !gene6.getNode( "r" ).isDuplication() ) {
7013 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
7016 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
7019 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
7022 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
7025 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
7028 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
7031 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
7034 sdi6.computeMappingCostL();
7035 if ( sdi6.computeMappingCostL() != 17 ) {
7038 if ( species6.getNumberOfExternalNodes() != 9 ) {
7041 if ( gene6.getNumberOfExternalNodes() != 9 ) {
7044 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
7045 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
7046 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
7047 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
7048 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
7049 species7.setRooted( true );
7050 final Phylogeny gene7_1 = Test
7051 .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])" );
7052 gene7_1.setRooted( true );
7053 final SDI sdi7 = new SDI( gene7_1, species7 );
7054 if ( sdi7.getDuplicationsSum() != 0 ) {
7057 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
7060 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
7063 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
7066 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
7069 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
7072 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
7075 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
7078 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
7081 final Phylogeny gene7_2 = Test
7082 .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])" );
7083 gene7_2.setRooted( true );
7084 final SDI sdi7_2 = new SDI( gene7_2, species7 );
7085 if ( sdi7_2.getDuplicationsSum() != 1 ) {
7088 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
7091 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
7094 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
7097 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
7100 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
7103 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
7106 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
7109 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
7112 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
7116 catch ( final Exception e ) {
7122 private static boolean testSDIunrooted() {
7124 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7125 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
7126 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
7127 final Iterator<PhylogenyBranch> iter = l.iterator();
7128 PhylogenyBranch br = iter.next();
7129 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
7132 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
7136 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7139 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7143 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
7146 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
7150 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7153 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7157 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7160 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7164 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7167 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7171 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7174 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7178 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7181 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7185 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7188 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7192 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7195 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7199 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7202 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7206 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
7209 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
7213 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7216 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7220 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
7223 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
7227 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
7230 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
7233 if ( iter.hasNext() ) {
7236 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
7237 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
7238 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
7240 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7243 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7247 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7250 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7254 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7257 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7260 if ( iter1.hasNext() ) {
7263 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
7264 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
7265 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
7267 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7270 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7274 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7277 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7281 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7284 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7287 if ( iter2.hasNext() ) {
7290 final Phylogeny species0 = factory
7291 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7292 new NHXParser() )[ 0 ];
7293 final Phylogeny gene1 = factory
7294 .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])",
7295 new NHXParser() )[ 0 ];
7296 species0.setRooted( true );
7297 gene1.setRooted( true );
7298 final SDIR sdi_unrooted = new SDIR();
7299 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
7300 if ( sdi_unrooted.getCount() != 1 ) {
7303 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
7306 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
7309 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
7312 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7315 final Phylogeny gene2 = factory
7316 .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])",
7317 new NHXParser() )[ 0 ];
7318 gene2.setRooted( true );
7319 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
7320 if ( sdi_unrooted.getCount() != 1 ) {
7323 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7326 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7329 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7332 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7335 final Phylogeny species6 = factory
7336 .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,"
7337 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7338 new NHXParser() )[ 0 ];
7339 final Phylogeny gene6 = factory
7340 .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],"
7341 + "(((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],"
7342 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7343 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7344 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7345 new NHXParser() )[ 0 ];
7346 species6.setRooted( true );
7347 gene6.setRooted( true );
7348 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7349 if ( sdi_unrooted.getCount() != 1 ) {
7352 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7355 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7358 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7361 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7364 if ( !p6[ 0 ].getRoot().isDuplication() ) {
7367 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7370 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7373 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
7376 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7379 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
7382 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
7385 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7389 final Phylogeny species7 = factory
7390 .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,"
7391 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7392 new NHXParser() )[ 0 ];
7393 final Phylogeny gene7 = factory
7394 .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],"
7395 + "(((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],"
7396 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7397 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7398 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7399 new NHXParser() )[ 0 ];
7400 species7.setRooted( true );
7401 gene7.setRooted( true );
7402 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
7403 if ( sdi_unrooted.getCount() != 1 ) {
7406 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7409 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7412 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7415 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
7418 if ( !p7[ 0 ].getRoot().isDuplication() ) {
7421 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7424 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7427 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
7430 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7433 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
7436 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
7439 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7443 final Phylogeny species8 = factory
7444 .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,"
7445 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7446 new NHXParser() )[ 0 ];
7447 final Phylogeny gene8 = factory
7448 .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],"
7449 + "(((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],"
7450 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7451 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7452 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7453 new NHXParser() )[ 0 ];
7454 species8.setRooted( true );
7455 gene8.setRooted( true );
7456 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
7457 if ( sdi_unrooted.getCount() != 1 ) {
7460 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7463 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7466 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7469 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7472 if ( !p8[ 0 ].getRoot().isDuplication() ) {
7475 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7478 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7481 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
7484 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7487 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
7490 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
7493 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7498 catch ( final Exception e ) {
7499 e.printStackTrace( System.out );
7505 private static boolean testSplit() {
7507 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7508 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7509 //Archaeopteryx.createApplication( p0 );
7510 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7511 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7512 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7513 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7514 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7515 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7516 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7517 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7518 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7519 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7520 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
7521 // System.out.println( s0.toString() );
7523 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7525 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7526 if ( s0.match( query_nodes ) ) {
7529 query_nodes = new HashSet<PhylogenyNode>();
7530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7533 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7534 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7535 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7536 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7537 if ( !s0.match( query_nodes ) ) {
7541 query_nodes = new HashSet<PhylogenyNode>();
7542 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7543 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7544 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7545 if ( !s0.match( query_nodes ) ) {
7549 query_nodes = new HashSet<PhylogenyNode>();
7550 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7551 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7552 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7553 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7554 if ( !s0.match( query_nodes ) ) {
7558 query_nodes = new HashSet<PhylogenyNode>();
7559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7560 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7561 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7562 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7563 if ( !s0.match( query_nodes ) ) {
7567 query_nodes = new HashSet<PhylogenyNode>();
7568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7569 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7570 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7571 if ( !s0.match( query_nodes ) ) {
7575 query_nodes = new HashSet<PhylogenyNode>();
7576 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7577 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7578 if ( !s0.match( query_nodes ) ) {
7582 query_nodes = new HashSet<PhylogenyNode>();
7583 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7584 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7588 if ( !s0.match( query_nodes ) ) {
7592 query_nodes = new HashSet<PhylogenyNode>();
7593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7594 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7595 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7596 if ( !s0.match( query_nodes ) ) {
7600 query_nodes = new HashSet<PhylogenyNode>();
7601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7602 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7603 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7604 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7605 if ( !s0.match( query_nodes ) ) {
7609 query_nodes = new HashSet<PhylogenyNode>();
7610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7612 if ( s0.match( query_nodes ) ) {
7616 query_nodes = new HashSet<PhylogenyNode>();
7617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7621 if ( s0.match( query_nodes ) ) {
7625 query_nodes = new HashSet<PhylogenyNode>();
7626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7631 if ( s0.match( query_nodes ) ) {
7635 query_nodes = new HashSet<PhylogenyNode>();
7636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7638 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7639 if ( s0.match( query_nodes ) ) {
7643 query_nodes = new HashSet<PhylogenyNode>();
7644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7646 if ( s0.match( query_nodes ) ) {
7650 query_nodes = new HashSet<PhylogenyNode>();
7651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7653 if ( s0.match( query_nodes ) ) {
7657 query_nodes = new HashSet<PhylogenyNode>();
7658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7659 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7660 if ( s0.match( query_nodes ) ) {
7664 query_nodes = new HashSet<PhylogenyNode>();
7665 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7667 if ( s0.match( query_nodes ) ) {
7671 query_nodes = new HashSet<PhylogenyNode>();
7672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7674 if ( s0.match( query_nodes ) ) {
7678 query_nodes = new HashSet<PhylogenyNode>();
7679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7681 if ( s0.match( query_nodes ) ) {
7685 query_nodes = new HashSet<PhylogenyNode>();
7686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7689 if ( s0.match( query_nodes ) ) {
7693 query_nodes = new HashSet<PhylogenyNode>();
7694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7697 if ( s0.match( query_nodes ) ) {
7701 query_nodes = new HashSet<PhylogenyNode>();
7702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7705 if ( s0.match( query_nodes ) ) {
7709 query_nodes = new HashSet<PhylogenyNode>();
7710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7714 if ( s0.match( query_nodes ) ) {
7718 // query_nodes = new HashSet<PhylogenyNode>();
7719 // query_nodes.add( new PhylogenyNode( "X" ) );
7720 // query_nodes.add( new PhylogenyNode( "Y" ) );
7721 // query_nodes.add( new PhylogenyNode( "A" ) );
7722 // query_nodes.add( new PhylogenyNode( "B" ) );
7723 // query_nodes.add( new PhylogenyNode( "C" ) );
7724 // query_nodes.add( new PhylogenyNode( "D" ) );
7725 // query_nodes.add( new PhylogenyNode( "E" ) );
7726 // query_nodes.add( new PhylogenyNode( "F" ) );
7727 // query_nodes.add( new PhylogenyNode( "G" ) );
7728 // if ( !s0.match( query_nodes ) ) {
7731 // query_nodes = new HashSet<PhylogenyNode>();
7732 // query_nodes.add( new PhylogenyNode( "X" ) );
7733 // query_nodes.add( new PhylogenyNode( "Y" ) );
7734 // query_nodes.add( new PhylogenyNode( "A" ) );
7735 // query_nodes.add( new PhylogenyNode( "B" ) );
7736 // query_nodes.add( new PhylogenyNode( "C" ) );
7737 // if ( !s0.match( query_nodes ) ) {
7741 // query_nodes = new HashSet<PhylogenyNode>();
7742 // query_nodes.add( new PhylogenyNode( "X" ) );
7743 // query_nodes.add( new PhylogenyNode( "Y" ) );
7744 // query_nodes.add( new PhylogenyNode( "D" ) );
7745 // query_nodes.add( new PhylogenyNode( "E" ) );
7746 // query_nodes.add( new PhylogenyNode( "F" ) );
7747 // query_nodes.add( new PhylogenyNode( "G" ) );
7748 // if ( !s0.match( query_nodes ) ) {
7752 // query_nodes = new HashSet<PhylogenyNode>();
7753 // query_nodes.add( new PhylogenyNode( "X" ) );
7754 // query_nodes.add( new PhylogenyNode( "Y" ) );
7755 // query_nodes.add( new PhylogenyNode( "A" ) );
7756 // query_nodes.add( new PhylogenyNode( "B" ) );
7757 // query_nodes.add( new PhylogenyNode( "C" ) );
7758 // query_nodes.add( new PhylogenyNode( "D" ) );
7759 // if ( !s0.match( query_nodes ) ) {
7763 // query_nodes = new HashSet<PhylogenyNode>();
7764 // query_nodes.add( new PhylogenyNode( "X" ) );
7765 // query_nodes.add( new PhylogenyNode( "Y" ) );
7766 // query_nodes.add( new PhylogenyNode( "E" ) );
7767 // query_nodes.add( new PhylogenyNode( "F" ) );
7768 // query_nodes.add( new PhylogenyNode( "G" ) );
7769 // if ( !s0.match( query_nodes ) ) {
7773 // query_nodes = new HashSet<PhylogenyNode>();
7774 // query_nodes.add( new PhylogenyNode( "X" ) );
7775 // query_nodes.add( new PhylogenyNode( "Y" ) );
7776 // query_nodes.add( new PhylogenyNode( "F" ) );
7777 // query_nodes.add( new PhylogenyNode( "G" ) );
7778 // if ( !s0.match( query_nodes ) ) {
7782 query_nodes = new HashSet<PhylogenyNode>();
7783 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7784 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7785 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7786 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7787 if ( s0.match( query_nodes ) ) {
7791 query_nodes = new HashSet<PhylogenyNode>();
7792 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7793 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7794 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7795 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7796 if ( s0.match( query_nodes ) ) {
7799 ///////////////////////////
7801 query_nodes = new HashSet<PhylogenyNode>();
7802 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7803 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7804 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7805 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7806 if ( s0.match( query_nodes ) ) {
7810 query_nodes = new HashSet<PhylogenyNode>();
7811 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7812 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7813 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7814 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7815 if ( s0.match( query_nodes ) ) {
7819 query_nodes = new HashSet<PhylogenyNode>();
7820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7821 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7822 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7823 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7824 if ( s0.match( query_nodes ) ) {
7828 query_nodes = new HashSet<PhylogenyNode>();
7829 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7830 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7831 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7832 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7833 if ( s0.match( query_nodes ) ) {
7837 query_nodes = new HashSet<PhylogenyNode>();
7838 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7839 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7840 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7841 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7842 if ( s0.match( query_nodes ) ) {
7846 query_nodes = new HashSet<PhylogenyNode>();
7847 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7848 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7849 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7850 if ( s0.match( query_nodes ) ) {
7854 query_nodes = new HashSet<PhylogenyNode>();
7855 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7856 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7857 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7858 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7860 if ( s0.match( query_nodes ) ) {
7864 query_nodes = new HashSet<PhylogenyNode>();
7865 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7866 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7867 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7868 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7869 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7870 if ( s0.match( query_nodes ) ) {
7874 query_nodes = new HashSet<PhylogenyNode>();
7875 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7876 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7877 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7880 if ( s0.match( query_nodes ) ) {
7884 query_nodes = new HashSet<PhylogenyNode>();
7885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7890 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7891 if ( s0.match( query_nodes ) ) {
7895 catch ( final Exception e ) {
7896 e.printStackTrace();
7902 private static boolean testSplitStrict() {
7904 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7905 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7906 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7907 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7908 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7909 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7910 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7911 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7912 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7913 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7914 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7915 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7917 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7918 if ( s0.match( query_nodes ) ) {
7921 query_nodes = new HashSet<PhylogenyNode>();
7922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7927 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7928 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7929 if ( !s0.match( query_nodes ) ) {
7933 query_nodes = new HashSet<PhylogenyNode>();
7934 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7935 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7936 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7937 if ( !s0.match( query_nodes ) ) {
7941 query_nodes = new HashSet<PhylogenyNode>();
7942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7943 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7944 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7945 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7946 if ( !s0.match( query_nodes ) ) {
7950 query_nodes = new HashSet<PhylogenyNode>();
7951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7952 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7953 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7955 if ( !s0.match( query_nodes ) ) {
7959 query_nodes = new HashSet<PhylogenyNode>();
7960 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7961 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7962 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7963 if ( !s0.match( query_nodes ) ) {
7967 query_nodes = new HashSet<PhylogenyNode>();
7968 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7969 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7970 if ( !s0.match( query_nodes ) ) {
7974 query_nodes = new HashSet<PhylogenyNode>();
7975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7977 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7978 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7979 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7980 if ( !s0.match( query_nodes ) ) {
7984 query_nodes = new HashSet<PhylogenyNode>();
7985 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7986 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7987 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7988 if ( !s0.match( query_nodes ) ) {
7992 query_nodes = new HashSet<PhylogenyNode>();
7993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7996 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7997 if ( !s0.match( query_nodes ) ) {
8001 query_nodes = new HashSet<PhylogenyNode>();
8002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8004 if ( s0.match( query_nodes ) ) {
8008 query_nodes = new HashSet<PhylogenyNode>();
8009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8010 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8011 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8013 if ( s0.match( query_nodes ) ) {
8017 query_nodes = new HashSet<PhylogenyNode>();
8018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8019 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8020 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8021 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8022 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8023 if ( s0.match( query_nodes ) ) {
8027 query_nodes = new HashSet<PhylogenyNode>();
8028 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8029 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8030 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8031 if ( s0.match( query_nodes ) ) {
8035 query_nodes = new HashSet<PhylogenyNode>();
8036 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8037 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8038 if ( s0.match( query_nodes ) ) {
8042 query_nodes = new HashSet<PhylogenyNode>();
8043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8045 if ( s0.match( query_nodes ) ) {
8049 query_nodes = new HashSet<PhylogenyNode>();
8050 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8052 if ( s0.match( query_nodes ) ) {
8056 query_nodes = new HashSet<PhylogenyNode>();
8057 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8059 if ( s0.match( query_nodes ) ) {
8063 query_nodes = new HashSet<PhylogenyNode>();
8064 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8065 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8066 if ( s0.match( query_nodes ) ) {
8070 query_nodes = new HashSet<PhylogenyNode>();
8071 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8072 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8073 if ( s0.match( query_nodes ) ) {
8077 query_nodes = new HashSet<PhylogenyNode>();
8078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8080 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8081 if ( s0.match( query_nodes ) ) {
8085 query_nodes = new HashSet<PhylogenyNode>();
8086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8089 if ( s0.match( query_nodes ) ) {
8093 query_nodes = new HashSet<PhylogenyNode>();
8094 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8097 if ( s0.match( query_nodes ) ) {
8101 query_nodes = new HashSet<PhylogenyNode>();
8102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8106 if ( s0.match( query_nodes ) ) {
8110 catch ( final Exception e ) {
8111 e.printStackTrace();
8117 private static boolean testSubtreeDeletion() {
8119 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8120 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8121 t1.deleteSubtree( t1.getNode( "A" ), false );
8122 if ( t1.getNumberOfExternalNodes() != 5 ) {
8125 t1.toNewHampshireX();
8126 t1.deleteSubtree( t1.getNode( "E" ), false );
8127 if ( t1.getNumberOfExternalNodes() != 4 ) {
8130 t1.toNewHampshireX();
8131 t1.deleteSubtree( t1.getNode( "F" ), false );
8132 if ( t1.getNumberOfExternalNodes() != 3 ) {
8135 t1.toNewHampshireX();
8136 t1.deleteSubtree( t1.getNode( "D" ), false );
8137 t1.toNewHampshireX();
8138 if ( t1.getNumberOfExternalNodes() != 3 ) {
8141 t1.deleteSubtree( t1.getNode( "def" ), false );
8142 t1.toNewHampshireX();
8143 if ( t1.getNumberOfExternalNodes() != 2 ) {
8146 t1.deleteSubtree( t1.getNode( "B" ), false );
8147 t1.toNewHampshireX();
8148 if ( t1.getNumberOfExternalNodes() != 1 ) {
8151 t1.deleteSubtree( t1.getNode( "C" ), false );
8152 t1.toNewHampshireX();
8153 if ( t1.getNumberOfExternalNodes() != 1 ) {
8156 t1.deleteSubtree( t1.getNode( "abc" ), false );
8157 t1.toNewHampshireX();
8158 if ( t1.getNumberOfExternalNodes() != 1 ) {
8161 t1.deleteSubtree( t1.getNode( "r" ), false );
8162 if ( t1.getNumberOfExternalNodes() != 0 ) {
8165 if ( !t1.isEmpty() ) {
8168 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8169 t2.deleteSubtree( t2.getNode( "A" ), false );
8170 t2.toNewHampshireX();
8171 if ( t2.getNumberOfExternalNodes() != 5 ) {
8174 t2.deleteSubtree( t2.getNode( "abc" ), false );
8175 t2.toNewHampshireX();
8176 if ( t2.getNumberOfExternalNodes() != 3 ) {
8179 t2.deleteSubtree( t2.getNode( "def" ), false );
8180 t2.toNewHampshireX();
8181 if ( t2.getNumberOfExternalNodes() != 1 ) {
8185 catch ( final Exception e ) {
8186 e.printStackTrace( System.out );
8192 private static boolean testSupportCount() {
8194 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8195 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
8196 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
8197 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
8198 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
8199 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
8200 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
8202 SupportCount.count( t0_1, phylogenies_1, true, false );
8203 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
8204 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
8205 + "(((((A,B),C),D),E),((F,G),X))"
8206 + "(((((A,Y),B),C),D),((F,G),E))"
8207 + "(((((A,B),C),D),E),(F,G))"
8208 + "(((((A,B),C),D),E),(F,G))"
8209 + "(((((A,B),C),D),E),(F,G))"
8210 + "(((((A,B),C),D),E),(F,G),Z)"
8211 + "(((((A,B),C),D),E),(F,G))"
8212 + "((((((A,B),C),D),E),F),G)"
8213 + "(((((X,Y),F,G),E),((A,B),C)),D)",
8215 SupportCount.count( t0_2, phylogenies_2, true, false );
8216 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
8217 while ( it.hasNext() ) {
8218 final PhylogenyNode n = it.next();
8219 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
8223 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
8224 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
8225 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
8226 SupportCount.count( t0_3, phylogenies_3, true, false );
8227 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
8228 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
8231 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
8234 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
8237 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
8240 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
8243 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
8246 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
8249 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
8252 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
8255 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
8258 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8259 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
8260 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
8261 SupportCount.count( t0_4, phylogenies_4, true, false );
8262 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
8263 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
8266 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
8269 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
8272 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
8275 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
8278 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
8281 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
8284 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
8287 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
8290 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
8293 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8294 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8295 double d = SupportCount.compare( b1, a, true, true, true );
8296 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
8299 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8300 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8301 d = SupportCount.compare( b2, a, true, true, true );
8302 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
8305 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8306 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
8307 d = SupportCount.compare( b3, a, true, true, true );
8308 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
8311 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
8312 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
8313 d = SupportCount.compare( b4, a, true, true, false );
8314 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
8318 catch ( final Exception e ) {
8319 e.printStackTrace( System.out );
8325 private static boolean testSupportTransfer() {
8327 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8328 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)",
8329 new NHXParser() )[ 0 ];
8330 final Phylogeny p2 = factory
8331 .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 ];
8332 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8335 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8338 support_transfer.moveBranchLengthsToBootstrap( p1 );
8339 support_transfer.transferSupportValues( p1, p2 );
8340 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8343 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8346 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8349 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8352 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
8355 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
8358 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
8361 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
8365 catch ( final Exception e ) {
8366 e.printStackTrace( System.out );
8372 private static boolean testUniprotTaxonomySearch() {
8374 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
8376 if ( results.size() != 1 ) {
8379 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8382 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8385 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8388 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8391 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8395 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
8396 if ( results.size() != 1 ) {
8399 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8402 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8405 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8408 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8411 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8415 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
8416 if ( results.size() != 1 ) {
8419 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8422 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8425 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8428 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8431 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8435 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
8436 if ( results.size() != 1 ) {
8439 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8442 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8445 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8448 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8451 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8454 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
8457 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
8460 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
8461 .equals( "Nematostella vectensis" ) ) {
8462 System.out.println( results.get( 0 ).getLineage() );
8466 catch ( final IOException e ) {
8467 System.out.println();
8468 System.out.println( "the following might be due to absence internet connection:" );
8469 e.printStackTrace( System.out );
8472 catch ( final Exception e ) {
8478 private static boolean testEmblEntryRetrieval() {
8479 //The format for GenBank Accession numbers are:
8480 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
8481 //Protein: 3 letters + 5 numerals
8482 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
8483 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
8486 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
8489 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
8492 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
8495 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
8498 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
8501 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
8504 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
8507 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
8510 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
8513 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
8516 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
8519 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8525 private static boolean testUniprotEntryRetrieval() {
8526 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8529 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8532 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8535 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8538 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8541 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8544 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8547 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8550 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8553 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8556 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8559 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8562 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8566 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8567 if ( !entry.getAccession().equals( "P12345" ) ) {
8570 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8573 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8576 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8579 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8583 catch ( final IOException e ) {
8584 System.out.println();
8585 System.out.println( "the following might be due to absence internet connection:" );
8586 e.printStackTrace( System.out );
8589 catch ( final Exception e ) {
8595 private static boolean testWabiTxSearch() {
8598 result = TxSearch.searchSimple( "nematostella" );
8599 result = TxSearch.getTxId( "nematostella" );
8600 if ( !result.equals( "45350" ) ) {
8603 result = TxSearch.getTxName( "45350" );
8604 if ( !result.equals( "Nematostella" ) ) {
8607 result = TxSearch.getTxId( "nematostella vectensis" );
8608 if ( !result.equals( "45351" ) ) {
8611 result = TxSearch.getTxName( "45351" );
8612 if ( !result.equals( "Nematostella vectensis" ) ) {
8615 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8616 if ( !result.equals( "536089" ) ) {
8619 result = TxSearch.getTxName( "536089" );
8620 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8623 final List<String> queries = new ArrayList<String>();
8624 queries.add( "Campylobacter coli" );
8625 queries.add( "Escherichia coli" );
8626 queries.add( "Arabidopsis" );
8627 queries.add( "Trichoplax" );
8628 queries.add( "Samanea saman" );
8629 queries.add( "Kluyveromyces marxianus" );
8630 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8631 queries.add( "Bornavirus parrot/PDD/2008" );
8632 final List<RANKS> ranks = new ArrayList<RANKS>();
8633 ranks.add( RANKS.SUPERKINGDOM );
8634 ranks.add( RANKS.KINGDOM );
8635 ranks.add( RANKS.FAMILY );
8636 ranks.add( RANKS.GENUS );
8637 ranks.add( RANKS.TRIBE );
8638 result = TxSearch.searchLineage( queries, ranks );
8639 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8640 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8642 catch ( final Exception e ) {
8643 System.out.println();
8644 System.out.println( "the following might be due to absence internet connection:" );
8645 e.printStackTrace( System.out );
8651 private static boolean testAminoAcidSequence() {
8653 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8654 if ( aa1.getLength() != 13 ) {
8657 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8660 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8663 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8666 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8667 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8670 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8671 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8674 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8675 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8679 catch ( final Exception e ) {
8680 e.printStackTrace();
8686 private static boolean testCreateBalancedPhylogeny() {
8688 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8689 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8692 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8695 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8696 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8699 if ( p1.getNumberOfExternalNodes() != 100 ) {
8703 catch ( final Exception e ) {
8704 e.printStackTrace();
8710 private static boolean testFastaParser() {
8712 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8715 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8718 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8719 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8722 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8725 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8728 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8731 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8734 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8738 catch ( final Exception e ) {
8739 e.printStackTrace();
8745 private static boolean testGeneralMsaParser() {
8747 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8748 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8749 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8750 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8751 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8752 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8753 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8754 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8755 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8758 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8761 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8764 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8767 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8770 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8773 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8776 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8779 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8782 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8785 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8788 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8791 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8792 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8795 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8798 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8801 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8802 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8805 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8808 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8811 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8812 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8815 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8818 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8822 catch ( final Exception e ) {
8823 e.printStackTrace();
8829 private static boolean testMafft( final String path ) {
8831 final List<String> opts = new ArrayList<String>();
8832 opts.add( "--maxiterate" );
8834 opts.add( "--localpair" );
8835 opts.add( "--quiet" );
8837 final MsaInferrer mafft = Mafft.createInstance( path );
8838 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8839 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8842 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8846 catch ( final Exception e ) {
8847 e.printStackTrace( System.out );
8853 private static boolean testNextNodeWithCollapsing() {
8855 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8857 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8858 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8859 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8860 t0.getNode( "cd" ).setCollapse( true );
8861 t0.getNode( "cde" ).setCollapse( true );
8862 n = t0.getFirstExternalNode();
8863 while ( n != null ) {
8865 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8867 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8870 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8873 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8876 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8879 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8882 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8886 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8887 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8888 t1.getNode( "ab" ).setCollapse( true );
8889 t1.getNode( "cd" ).setCollapse( true );
8890 t1.getNode( "cde" ).setCollapse( true );
8891 n = t1.getNode( "ab" );
8892 ext = new ArrayList<PhylogenyNode>();
8893 while ( n != null ) {
8895 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8897 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8900 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8903 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8906 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8909 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8915 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8916 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8917 t2.getNode( "ab" ).setCollapse( true );
8918 t2.getNode( "cd" ).setCollapse( true );
8919 t2.getNode( "cde" ).setCollapse( true );
8920 t2.getNode( "c" ).setCollapse( true );
8921 t2.getNode( "d" ).setCollapse( true );
8922 t2.getNode( "e" ).setCollapse( true );
8923 t2.getNode( "gh" ).setCollapse( true );
8924 n = t2.getNode( "ab" );
8925 ext = new ArrayList<PhylogenyNode>();
8926 while ( n != null ) {
8928 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8930 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8933 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8936 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8939 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8945 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8946 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8947 t3.getNode( "ab" ).setCollapse( true );
8948 t3.getNode( "cd" ).setCollapse( true );
8949 t3.getNode( "cde" ).setCollapse( true );
8950 t3.getNode( "c" ).setCollapse( true );
8951 t3.getNode( "d" ).setCollapse( true );
8952 t3.getNode( "e" ).setCollapse( true );
8953 t3.getNode( "gh" ).setCollapse( true );
8954 t3.getNode( "fgh" ).setCollapse( true );
8955 n = t3.getNode( "ab" );
8956 ext = new ArrayList<PhylogenyNode>();
8957 while ( n != null ) {
8959 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8961 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8964 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8967 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8973 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8974 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8975 t4.getNode( "ab" ).setCollapse( true );
8976 t4.getNode( "cd" ).setCollapse( true );
8977 t4.getNode( "cde" ).setCollapse( true );
8978 t4.getNode( "c" ).setCollapse( true );
8979 t4.getNode( "d" ).setCollapse( true );
8980 t4.getNode( "e" ).setCollapse( true );
8981 t4.getNode( "gh" ).setCollapse( true );
8982 t4.getNode( "fgh" ).setCollapse( true );
8983 t4.getNode( "abcdefgh" ).setCollapse( true );
8984 n = t4.getNode( "abcdefgh" );
8985 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8990 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8991 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8993 n = t5.getFirstExternalNode();
8994 while ( n != null ) {
8996 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8998 if ( ext.size() != 8 ) {
9001 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9004 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9007 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9010 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9013 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9016 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9019 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
9022 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
9027 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9028 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
9030 t6.getNode( "ab" ).setCollapse( true );
9031 n = t6.getNode( "ab" );
9032 while ( n != null ) {
9034 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9036 if ( ext.size() != 7 ) {
9039 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9042 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9045 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9048 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9051 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9054 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9057 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9062 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9063 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
9065 t7.getNode( "cd" ).setCollapse( true );
9066 n = t7.getNode( "a" );
9067 while ( n != null ) {
9069 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9071 if ( ext.size() != 7 ) {
9074 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9077 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9080 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9083 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9086 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9089 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9092 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9097 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9098 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
9100 t8.getNode( "cd" ).setCollapse( true );
9101 t8.getNode( "c" ).setCollapse( true );
9102 t8.getNode( "d" ).setCollapse( true );
9103 n = t8.getNode( "a" );
9104 while ( n != null ) {
9106 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9108 if ( ext.size() != 7 ) {
9111 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9114 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9117 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9118 System.out.println( "2 fail" );
9121 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9124 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9127 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9130 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9135 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9136 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
9138 t9.getNode( "gh" ).setCollapse( true );
9139 n = t9.getNode( "a" );
9140 while ( n != null ) {
9142 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9144 if ( ext.size() != 7 ) {
9147 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9150 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9153 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9156 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9159 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9162 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9165 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9170 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9171 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
9173 t10.getNode( "gh" ).setCollapse( true );
9174 t10.getNode( "g" ).setCollapse( true );
9175 t10.getNode( "h" ).setCollapse( true );
9176 n = t10.getNode( "a" );
9177 while ( n != null ) {
9179 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9181 if ( ext.size() != 7 ) {
9184 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9187 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9190 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9193 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9196 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9199 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9202 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9207 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9208 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
9210 t11.getNode( "gh" ).setCollapse( true );
9211 t11.getNode( "fgh" ).setCollapse( true );
9212 n = t11.getNode( "a" );
9213 while ( n != null ) {
9215 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9217 if ( ext.size() != 6 ) {
9220 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9223 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9226 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9229 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9232 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9235 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9240 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9241 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
9243 t12.getNode( "gh" ).setCollapse( true );
9244 t12.getNode( "fgh" ).setCollapse( true );
9245 t12.getNode( "g" ).setCollapse( true );
9246 t12.getNode( "h" ).setCollapse( true );
9247 t12.getNode( "f" ).setCollapse( true );
9248 n = t12.getNode( "a" );
9249 while ( n != null ) {
9251 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9253 if ( ext.size() != 6 ) {
9256 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9259 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9262 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9265 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9268 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9271 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9276 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9277 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
9279 t13.getNode( "ab" ).setCollapse( true );
9280 t13.getNode( "b" ).setCollapse( true );
9281 t13.getNode( "fgh" ).setCollapse( true );
9282 t13.getNode( "gh" ).setCollapse( true );
9283 n = t13.getNode( "ab" );
9284 while ( n != null ) {
9286 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9288 if ( ext.size() != 5 ) {
9291 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9294 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9297 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9300 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9303 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9308 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
9309 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
9311 t14.getNode( "ab" ).setCollapse( true );
9312 t14.getNode( "a" ).setCollapse( true );
9313 t14.getNode( "fgh" ).setCollapse( true );
9314 t14.getNode( "gh" ).setCollapse( true );
9315 n = t14.getNode( "ab" );
9316 while ( n != null ) {
9318 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9320 if ( ext.size() != 5 ) {
9323 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9326 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9329 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9332 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9335 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9340 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" );
9341 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9343 t15.getNode( "ab" ).setCollapse( true );
9344 t15.getNode( "a" ).setCollapse( true );
9345 t15.getNode( "fgh" ).setCollapse( true );
9346 t15.getNode( "gh" ).setCollapse( true );
9347 n = t15.getNode( "ab" );
9348 while ( n != null ) {
9350 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9352 if ( ext.size() != 6 ) {
9355 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9358 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9361 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9364 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9367 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
9370 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9375 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" );
9376 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
9378 t16.getNode( "ab" ).setCollapse( true );
9379 t16.getNode( "a" ).setCollapse( true );
9380 t16.getNode( "fgh" ).setCollapse( true );
9381 t16.getNode( "gh" ).setCollapse( true );
9382 t16.getNode( "cd" ).setCollapse( true );
9383 t16.getNode( "cde" ).setCollapse( true );
9384 t16.getNode( "d" ).setCollapse( true );
9385 t16.getNode( "x" ).setCollapse( true );
9386 n = t16.getNode( "ab" );
9387 while ( n != null ) {
9389 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9391 if ( ext.size() != 4 ) {
9394 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9397 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9400 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
9403 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
9407 catch ( final Exception e ) {
9408 e.printStackTrace( System.out );
9414 private static boolean testMsaQualityMethod() {
9416 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
9417 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
9418 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
9419 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
9420 final List<Sequence> l = new ArrayList<Sequence>();
9425 final Msa msa = BasicMsa.createInstance( l );
9426 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
9429 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
9432 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
9435 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
9439 catch ( final Exception e ) {
9440 e.printStackTrace( System.out );
9446 private static boolean testSequenceIdParsing() {
9448 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
9449 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9450 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9452 System.out.println( "value =" + id.getValue() );
9453 System.out.println( "provider=" + id.getProvider() );
9458 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
9459 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9460 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9462 System.out.println( "value =" + id.getValue() );
9463 System.out.println( "provider=" + id.getProvider() );
9468 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
9469 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9470 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9472 System.out.println( "value =" + id.getValue() );
9473 System.out.println( "provider=" + id.getProvider() );
9478 id = SequenceIdParser.parse( "gb_AAA96518_1" );
9479 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9480 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
9482 System.out.println( "value =" + id.getValue() );
9483 System.out.println( "provider=" + id.getProvider() );
9488 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
9489 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9490 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
9492 System.out.println( "value =" + id.getValue() );
9493 System.out.println( "provider=" + id.getProvider() );
9498 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
9499 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9500 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
9502 System.out.println( "value =" + id.getValue() );
9503 System.out.println( "provider=" + id.getProvider() );
9508 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9509 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9510 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
9512 System.out.println( "value =" + id.getValue() );
9513 System.out.println( "provider=" + id.getProvider() );
9518 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9519 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9520 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9522 System.out.println( "value =" + id.getValue() );
9523 System.out.println( "provider=" + id.getProvider() );
9528 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9529 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9530 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9532 System.out.println( "value =" + id.getValue() );
9533 System.out.println( "provider=" + id.getProvider() );
9538 id = SequenceIdParser.parse( "P4A123" );
9539 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9540 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9542 System.out.println( "value =" + id.getValue() );
9543 System.out.println( "provider=" + id.getProvider() );
9548 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
9549 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9550 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9552 System.out.println( "value =" + id.getValue() );
9553 System.out.println( "provider=" + id.getProvider() );
9558 id = SequenceIdParser.parse( "XP_12345" );
9560 System.out.println( "value =" + id.getValue() );
9561 System.out.println( "provider=" + id.getProvider() );
9564 // lcl_91970_unknown_
9566 catch ( final Exception e ) {
9567 e.printStackTrace( System.out );