2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
56 import org.forester.io.parsers.tol.TolParser;
57 import org.forester.io.parsers.util.ParserUtils;
58 import org.forester.io.writers.PhylogenyWriter;
59 import org.forester.msa.BasicMsa;
60 import org.forester.msa.Mafft;
61 import org.forester.msa.Msa;
62 import org.forester.msa.MsaInferrer;
63 import org.forester.msa.MsaMethods;
64 import org.forester.pccx.TestPccx;
65 import org.forester.phylogeny.Phylogeny;
66 import org.forester.phylogeny.PhylogenyBranch;
67 import org.forester.phylogeny.PhylogenyMethods;
68 import org.forester.phylogeny.PhylogenyNode;
69 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
70 import org.forester.phylogeny.data.BinaryCharacters;
71 import org.forester.phylogeny.data.BranchWidth;
72 import org.forester.phylogeny.data.Confidence;
73 import org.forester.phylogeny.data.Distribution;
74 import org.forester.phylogeny.data.DomainArchitecture;
75 import org.forester.phylogeny.data.Event;
76 import org.forester.phylogeny.data.Identifier;
77 import org.forester.phylogeny.data.PhylogenyData;
78 import org.forester.phylogeny.data.PhylogenyDataUtil;
79 import org.forester.phylogeny.data.Polygon;
80 import org.forester.phylogeny.data.PropertiesMap;
81 import org.forester.phylogeny.data.Property;
82 import org.forester.phylogeny.data.Property.AppliesTo;
83 import org.forester.phylogeny.data.ProteinDomain;
84 import org.forester.phylogeny.data.Taxonomy;
85 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
86 import org.forester.phylogeny.factories.PhylogenyFactory;
87 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
88 import org.forester.protein.Protein;
89 import org.forester.rio.TestRIO;
90 import org.forester.sdi.SDI;
91 import org.forester.sdi.SDIR;
92 import org.forester.sdi.SDIse;
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 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
142 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
145 public static boolean isEqual( final double a, final double b ) {
146 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
149 public static void main( final String[] args ) {
150 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
151 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
153 Locale.setDefault( Locale.US );
154 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
157 System.out.print( "[Test if directory with files for testing exists/is readable: " );
158 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
159 System.out.println( "OK.]" );
162 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
163 System.out.println( "Testing aborted." );
166 System.out.print( "[Test if resources directory exists/is readable: " );
167 if ( testDir( PATH_TO_RESOURCES ) ) {
168 System.out.println( "OK.]" );
171 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
172 System.out.println( "Testing aborted." );
175 final long start_time = new Date().getTime();
176 System.out.print( "Sequence id parsing: " );
177 if ( testSequenceIdParsing() ) {
178 System.out.println( "OK." );
182 System.out.println( "failed." );
185 System.out.print( "Hmmscan output parser: " );
186 if ( testHmmscanOutputParser() ) {
187 System.out.println( "OK." );
191 System.out.println( "failed." );
194 System.out.print( "Basic node methods: " );
195 if ( Test.testBasicNodeMethods() ) {
196 System.out.println( "OK." );
200 System.out.println( "failed." );
203 System.out.print( "Taxonomy extraction: " );
204 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
205 System.out.println( "OK." );
209 System.out.println( "failed." );
212 System.out.print( "Basic node construction and parsing of NHX (node level): " );
213 if ( Test.testNHXNodeParsing() ) {
214 System.out.println( "OK." );
218 System.out.println( "failed." );
221 System.out.print( "NH parsing: " );
222 if ( Test.testNHParsing() ) {
223 System.out.println( "OK." );
227 System.out.println( "failed." );
230 System.out.print( "Conversion to NHX (node level): " );
231 if ( Test.testNHXconversion() ) {
232 System.out.println( "OK." );
236 System.out.println( "failed." );
239 System.out.print( "NHX parsing: " );
240 if ( Test.testNHXParsing() ) {
241 System.out.println( "OK." );
245 System.out.println( "failed." );
248 System.out.print( "NHX parsing with quotes: " );
249 if ( Test.testNHXParsingQuotes() ) {
250 System.out.println( "OK." );
254 System.out.println( "failed." );
257 System.out.print( "NHX parsing (MrBayes): " );
258 if ( Test.testNHXParsingMB() ) {
259 System.out.println( "OK." );
263 System.out.println( "failed." );
266 System.out.print( "Nexus characters parsing: " );
267 if ( Test.testNexusCharactersParsing() ) {
268 System.out.println( "OK." );
272 System.out.println( "failed." );
275 System.out.print( "Nexus tree parsing: " );
276 if ( Test.testNexusTreeParsing() ) {
277 System.out.println( "OK." );
281 System.out.println( "failed." );
284 System.out.print( "Nexus tree parsing (translating): " );
285 if ( Test.testNexusTreeParsingTranslating() ) {
286 System.out.println( "OK." );
290 System.out.println( "failed." );
293 System.out.print( "Nexus matrix parsing: " );
294 if ( Test.testNexusMatrixParsing() ) {
295 System.out.println( "OK." );
299 System.out.println( "failed." );
302 System.out.print( "Basic phyloXML parsing: " );
303 if ( Test.testBasicPhyloXMLparsing() ) {
304 System.out.println( "OK." );
308 System.out.println( "failed." );
311 System.out.print( "Basic phyloXML parsing (validating against schema): " );
312 if ( testBasicPhyloXMLparsingValidating() ) {
313 System.out.println( "OK." );
317 System.out.println( "failed." );
320 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
321 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
322 System.out.println( "OK." );
326 System.out.println( "failed." );
329 System.out.print( "phyloXML Distribution Element: " );
330 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
331 System.out.println( "OK." );
335 System.out.println( "failed." );
338 System.out.print( "Tol XML parsing: " );
339 if ( Test.testBasicTolXMLparsing() ) {
340 System.out.println( "OK." );
344 System.out.println( "failed." );
347 System.out.print( "Copying of node data: " );
348 if ( Test.testCopyOfNodeData() ) {
349 System.out.println( "OK." );
353 System.out.println( "failed." );
356 System.out.print( "Basic tree methods: " );
357 if ( Test.testBasicTreeMethods() ) {
358 System.out.println( "OK." );
362 System.out.println( "failed." );
365 System.out.print( "Postorder Iterator: " );
366 if ( Test.testPostOrderIterator() ) {
367 System.out.println( "OK." );
371 System.out.println( "failed." );
374 System.out.print( "Preorder Iterator: " );
375 if ( Test.testPreOrderIterator() ) {
376 System.out.println( "OK." );
380 System.out.println( "failed." );
383 System.out.print( "Levelorder Iterator: " );
384 if ( Test.testLevelOrderIterator() ) {
385 System.out.println( "OK." );
389 System.out.println( "failed." );
392 System.out.print( "Re-id methods: " );
393 if ( Test.testReIdMethods() ) {
394 System.out.println( "OK." );
398 System.out.println( "failed." );
401 System.out.print( "Methods on last external nodes: " );
402 if ( Test.testLastExternalNodeMethods() ) {
403 System.out.println( "OK." );
407 System.out.println( "failed." );
410 System.out.print( "Methods on external nodes: " );
411 if ( Test.testExternalNodeRelatedMethods() ) {
412 System.out.println( "OK." );
416 System.out.println( "failed." );
419 System.out.print( "Deletion of external nodes: " );
420 if ( Test.testDeletionOfExternalNodes() ) {
421 System.out.println( "OK." );
425 System.out.println( "failed." );
428 System.out.print( "Subtree deletion: " );
429 if ( Test.testSubtreeDeletion() ) {
430 System.out.println( "OK." );
434 System.out.println( "failed." );
437 System.out.print( "Phylogeny branch: " );
438 if ( Test.testPhylogenyBranch() ) {
439 System.out.println( "OK." );
443 System.out.println( "failed." );
446 System.out.print( "Rerooting: " );
447 if ( Test.testRerooting() ) {
448 System.out.println( "OK." );
452 System.out.println( "failed." );
455 System.out.print( "Mipoint rooting: " );
456 if ( Test.testMidpointrooting() ) {
457 System.out.println( "OK." );
461 System.out.println( "failed." );
464 System.out.print( "Support count: " );
465 if ( Test.testSupportCount() ) {
466 System.out.println( "OK." );
470 System.out.println( "failed." );
473 System.out.print( "Support transfer: " );
474 if ( Test.testSupportTransfer() ) {
475 System.out.println( "OK." );
479 System.out.println( "failed." );
482 System.out.print( "Finding of LCA: " );
483 if ( Test.testGetLCA() ) {
484 System.out.println( "OK." );
488 System.out.println( "failed." );
491 System.out.print( "Finding of LCA 2: " );
492 if ( Test.testGetLCA2() ) {
493 System.out.println( "OK." );
497 System.out.println( "failed." );
500 System.out.print( "Calculation of distance between nodes: " );
501 if ( Test.testGetDistance() ) {
502 System.out.println( "OK." );
506 System.out.println( "failed." );
509 System.out.print( "Descriptive statistics: " );
510 if ( Test.testDescriptiveStatistics() ) {
511 System.out.println( "OK." );
515 System.out.println( "failed." );
518 System.out.print( "Data objects and methods: " );
519 if ( Test.testDataObjects() ) {
520 System.out.println( "OK." );
524 System.out.println( "failed." );
527 System.out.print( "Properties map: " );
528 if ( Test.testPropertiesMap() ) {
529 System.out.println( "OK." );
533 System.out.println( "failed." );
536 System.out.print( "SDIse: " );
537 if ( Test.testSDIse() ) {
538 System.out.println( "OK." );
542 System.out.println( "failed." );
545 System.out.print( "SDIunrooted: " );
546 if ( Test.testSDIunrooted() ) {
547 System.out.println( "OK." );
551 System.out.println( "failed." );
554 System.out.print( "GSDI: " );
555 if ( TestGSDI.test() ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "RIO: " );
564 if ( TestRIO.test() ) {
565 System.out.println( "OK." );
569 System.out.println( "failed." );
572 System.out.print( "Phylogeny reconstruction:" );
573 System.out.println();
574 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
575 System.out.println( "OK." );
579 System.out.println( "failed." );
582 System.out.print( "Analysis of domain architectures: " );
583 System.out.println();
584 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
585 System.out.println( "OK." );
589 System.out.println( "failed." );
592 System.out.print( "GO: " );
593 System.out.println();
594 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
595 System.out.println( "OK." );
599 System.out.println( "failed." );
602 System.out.print( "Modeling tools: " );
603 if ( TestPccx.test() ) {
604 System.out.println( "OK." );
608 System.out.println( "failed." );
611 System.out.print( "Split Matrix strict: " );
612 if ( Test.testSplitStrict() ) {
613 System.out.println( "OK." );
617 System.out.println( "failed." );
620 System.out.print( "Split Matrix: " );
621 if ( Test.testSplit() ) {
622 System.out.println( "OK." );
626 System.out.println( "failed." );
629 System.out.print( "Confidence Assessor: " );
630 if ( Test.testConfidenceAssessor() ) {
631 System.out.println( "OK." );
635 System.out.println( "failed." );
638 System.out.print( "Basic table: " );
639 if ( Test.testBasicTable() ) {
640 System.out.println( "OK." );
644 System.out.println( "failed." );
647 System.out.print( "General table: " );
648 if ( Test.testGeneralTable() ) {
649 System.out.println( "OK." );
653 System.out.println( "failed." );
656 System.out.print( "Amino acid sequence: " );
657 if ( Test.testAminoAcidSequence() ) {
658 System.out.println( "OK." );
662 System.out.println( "failed." );
665 System.out.print( "General MSA parser: " );
666 if ( Test.testGeneralMsaParser() ) {
667 System.out.println( "OK." );
671 System.out.println( "failed." );
674 System.out.print( "Fasta parser for msa: " );
675 if ( Test.testFastaParser() ) {
676 System.out.println( "OK." );
680 System.out.println( "failed." );
683 System.out.print( "Creation of balanced phylogeny: " );
684 if ( Test.testCreateBalancedPhylogeny() ) {
685 System.out.println( "OK." );
689 System.out.println( "failed." );
692 System.out.print( "EMBL Entry Retrieval: " );
693 if ( Test.testEmblEntryRetrieval() ) {
694 System.out.println( "OK." );
698 System.out.println( "failed." );
701 System.out.print( "Uniprot Entry Retrieval: " );
702 if ( Test.testUniprotEntryRetrieval() ) {
703 System.out.println( "OK." );
707 System.out.println( "failed." );
710 System.out.print( "Uniprot Taxonomy Search: " );
711 if ( Test.testUniprotTaxonomySearch() ) {
712 System.out.println( "OK." );
716 System.out.println( "failed." );
721 final String os = ForesterUtil.OS_NAME.toLowerCase();
722 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
723 path = "/usr/local/bin/mafft";
725 else if ( os.indexOf( "win" ) >= 0 ) {
726 path = "C:\\Program Files\\mafft-win\\mafft.bat";
729 path = "/home/czmasek/bin/mafft";
731 if ( !MsaInferrer.isInstalled( path ) ) {
734 if ( !MsaInferrer.isInstalled( path ) ) {
735 path = "/usr/local/bin/mafft";
737 if ( MsaInferrer.isInstalled( path ) ) {
738 System.out.print( "MAFFT (external program): " );
739 if ( Test.testMafft( path ) ) {
740 System.out.println( "OK." );
744 System.out.println( "failed [will not count towards failed tests]" );
748 System.out.print( "Next nodes with collapsed: " );
749 if ( Test.testNextNodeWithCollapsing() ) {
750 System.out.println( "OK." );
754 System.out.println( "failed." );
757 System.out.print( "Simple MSA quality: " );
758 if ( Test.testMsaQualityMethod() ) {
759 System.out.println( "OK." );
763 System.out.println( "failed." );
766 System.out.println();
767 final Runtime rt = java.lang.Runtime.getRuntime();
768 final long free_memory = rt.freeMemory() / 1000000;
769 final long total_memory = rt.totalMemory() / 1000000;
770 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
771 + free_memory + "MB, total memory: " + total_memory + "MB)" );
772 System.out.println();
773 System.out.println( "Successful tests: " + succeeded );
774 System.out.println( "Failed tests: " + failed );
775 System.out.println();
777 System.out.println( "OK." );
780 System.out.println( "Not OK." );
784 private static boolean testExtractTaxonomyCodeFromNodeName() {
786 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
789 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
792 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
795 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
796 .equals( "MOUSE" ) ) {
799 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
800 .equals( "MOUSE" ) ) {
803 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
804 .equals( "MOUSE" ) ) {
807 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
810 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
813 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
817 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
821 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
825 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
828 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
831 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
834 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
838 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
839 .equals( "MOUSE" ) ) {
842 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
843 .equals( "MOUSE" ) ) {
847 catch ( final Exception e ) {
848 e.printStackTrace( System.out );
854 private static boolean testBasicNodeMethods() {
856 if ( PhylogenyNode.getNodeCount() != 0 ) {
859 final PhylogenyNode n1 = new PhylogenyNode();
860 final PhylogenyNode n2 = PhylogenyNode
861 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
862 final PhylogenyNode n3 = PhylogenyNode
863 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
864 final PhylogenyNode n4 = PhylogenyNode
865 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
866 if ( n1.isHasAssignedEvent() ) {
869 if ( PhylogenyNode.getNodeCount() != 4 ) {
872 if ( n3.getIndicator() != 0 ) {
875 if ( n3.getNumberOfExternalNodes() != 1 ) {
878 if ( !n3.isExternal() ) {
881 if ( !n3.isRoot() ) {
884 if ( !n4.getName().equals( "n4" ) ) {
888 catch ( final Exception e ) {
889 e.printStackTrace( System.out );
895 private static boolean testBasicPhyloXMLparsing() {
897 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
898 final PhyloXmlParser xml_parser = new PhyloXmlParser();
899 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
901 if ( xml_parser.getErrorCount() > 0 ) {
902 System.out.println( xml_parser.getErrorMessages().toString() );
905 if ( phylogenies_0.length != 4 ) {
908 final Phylogeny t1 = phylogenies_0[ 0 ];
909 final Phylogeny t2 = phylogenies_0[ 1 ];
910 final Phylogeny t3 = phylogenies_0[ 2 ];
911 final Phylogeny t4 = phylogenies_0[ 3 ];
912 if ( t1.getNumberOfExternalNodes() != 1 ) {
915 if ( !t1.isRooted() ) {
918 if ( t1.isRerootable() ) {
921 if ( !t1.getType().equals( "gene_tree" ) ) {
924 if ( t2.getNumberOfExternalNodes() != 2 ) {
927 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
930 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
933 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
936 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
939 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
942 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
945 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
946 .startsWith( "actgtgggggt" ) ) {
949 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
950 .startsWith( "ctgtgatgcat" ) ) {
953 if ( t3.getNumberOfExternalNodes() != 4 ) {
956 if ( !t1.getName().equals( "t1" ) ) {
959 if ( !t2.getName().equals( "t2" ) ) {
962 if ( !t3.getName().equals( "t3" ) ) {
965 if ( !t4.getName().equals( "t4" ) ) {
968 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
971 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
974 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
977 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
978 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
981 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
984 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
987 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
990 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
991 .equals( "apoptosis" ) ) {
994 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
995 .equals( "GO:0006915" ) ) {
998 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
999 .equals( "UniProtKB" ) ) {
1002 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1003 .equals( "experimental" ) ) {
1006 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1007 .equals( "function" ) ) {
1010 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1011 .getValue() != 1 ) {
1014 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1015 .getType().equals( "ml" ) ) {
1018 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1019 .equals( "apoptosis" ) ) {
1022 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1023 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1026 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1027 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1030 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1031 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1034 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1035 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1038 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1039 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1042 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1043 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1046 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1047 .equals( "GO:0005829" ) ) {
1050 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1051 .equals( "intracellular organelle" ) ) {
1054 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1057 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1058 .equals( "UniProt link" ) ) ) {
1061 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1065 catch ( final Exception e ) {
1066 e.printStackTrace( System.out );
1072 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1074 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1075 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1076 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1077 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1080 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1082 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1084 if ( xml_parser.getErrorCount() > 0 ) {
1085 System.out.println( xml_parser.getErrorMessages().toString() );
1088 if ( phylogenies_0.length != 4 ) {
1091 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1092 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1093 if ( phylogenies_t1.length != 1 ) {
1096 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1097 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1100 if ( !t1_rt.isRooted() ) {
1103 if ( t1_rt.isRerootable() ) {
1106 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1109 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1110 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1111 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1112 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1115 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1118 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1121 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1124 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1125 .startsWith( "actgtgggggt" ) ) {
1128 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1129 .startsWith( "ctgtgatgcat" ) ) {
1132 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1133 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1134 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1135 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1136 if ( phylogenies_1.length != 1 ) {
1139 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1140 if ( !t3_rt.getName().equals( "t3" ) ) {
1143 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1146 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1149 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1152 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1155 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1156 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1159 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1162 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1165 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1166 .equals( "UniProtKB" ) ) {
1169 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1170 .equals( "apoptosis" ) ) {
1173 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1174 .equals( "GO:0006915" ) ) {
1177 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1178 .equals( "UniProtKB" ) ) {
1181 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1182 .equals( "experimental" ) ) {
1185 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1186 .equals( "function" ) ) {
1189 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1190 .getValue() != 1 ) {
1193 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1194 .getType().equals( "ml" ) ) {
1197 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1198 .equals( "apoptosis" ) ) {
1201 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1202 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1205 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1206 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1209 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1210 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1213 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1214 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1217 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1218 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1221 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1222 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1225 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1226 .equals( "GO:0005829" ) ) {
1229 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1230 .equals( "intracellular organelle" ) ) {
1233 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1236 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1237 .equals( "UniProt link" ) ) ) {
1240 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1243 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1246 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1247 .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." ) ) ) {
1250 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1253 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1256 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1259 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1262 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1263 .equals( "ncbi" ) ) {
1266 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1269 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1270 .getName().equals( "B" ) ) {
1273 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1274 .getFrom() != 21 ) {
1277 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1280 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1281 .getLength() != 24 ) {
1284 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1285 .getConfidence() != 2144 ) {
1288 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1289 .equals( "pfam" ) ) {
1292 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1295 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1298 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1301 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1304 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1305 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1308 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1311 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1314 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1317 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1320 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1323 if ( taxbb.getSynonyms().size() != 2 ) {
1326 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1329 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1332 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1335 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1338 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1341 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1342 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1346 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1349 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1352 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1355 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1358 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1361 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1364 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1368 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1371 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1372 .equalsIgnoreCase( "435" ) ) {
1375 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1378 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1379 .equalsIgnoreCase( "443.7" ) ) {
1382 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1385 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1388 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1389 .equalsIgnoreCase( "433" ) ) {
1393 catch ( final Exception e ) {
1394 e.printStackTrace( System.out );
1400 private static boolean testBasicPhyloXMLparsingValidating() {
1402 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1403 PhyloXmlParser xml_parser = null;
1405 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1407 catch ( final Exception e ) {
1408 // Do nothing -- means were not running from jar.
1410 if ( xml_parser == null ) {
1411 xml_parser = new PhyloXmlParser();
1412 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1413 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1416 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1419 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1421 if ( xml_parser.getErrorCount() > 0 ) {
1422 System.out.println( xml_parser.getErrorMessages().toString() );
1425 if ( phylogenies_0.length != 4 ) {
1428 final Phylogeny t1 = phylogenies_0[ 0 ];
1429 final Phylogeny t2 = phylogenies_0[ 1 ];
1430 final Phylogeny t3 = phylogenies_0[ 2 ];
1431 final Phylogeny t4 = phylogenies_0[ 3 ];
1432 if ( !t1.getName().equals( "t1" ) ) {
1435 if ( !t2.getName().equals( "t2" ) ) {
1438 if ( !t3.getName().equals( "t3" ) ) {
1441 if ( !t4.getName().equals( "t4" ) ) {
1444 if ( t1.getNumberOfExternalNodes() != 1 ) {
1447 if ( t2.getNumberOfExternalNodes() != 2 ) {
1450 if ( t3.getNumberOfExternalNodes() != 4 ) {
1453 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1454 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1455 if ( xml_parser.getErrorCount() > 0 ) {
1456 System.out.println( "errors:" );
1457 System.out.println( xml_parser.getErrorMessages().toString() );
1460 if ( phylogenies_1.length != 4 ) {
1463 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1465 if ( xml_parser.getErrorCount() > 0 ) {
1466 System.out.println( "errors:" );
1467 System.out.println( xml_parser.getErrorMessages().toString() );
1470 if ( phylogenies_2.length != 1 ) {
1473 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1476 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1478 if ( xml_parser.getErrorCount() > 0 ) {
1479 System.out.println( xml_parser.getErrorMessages().toString() );
1482 if ( phylogenies_3.length != 2 ) {
1485 final Phylogeny a = phylogenies_3[ 0 ];
1486 if ( !a.getName().equals( "tree 4" ) ) {
1489 if ( a.getNumberOfExternalNodes() != 3 ) {
1492 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1495 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1498 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1500 if ( xml_parser.getErrorCount() > 0 ) {
1501 System.out.println( xml_parser.getErrorMessages().toString() );
1504 if ( phylogenies_4.length != 1 ) {
1507 final Phylogeny s = phylogenies_4[ 0 ];
1508 if ( s.getNumberOfExternalNodes() != 6 ) {
1511 s.getNode( "first" );
1513 s.getNode( "\"<a'b&c'd\">\"" );
1514 s.getNode( "'''\"" );
1515 s.getNode( "\"\"\"" );
1516 s.getNode( "dick & doof" );
1518 catch ( final Exception e ) {
1519 e.printStackTrace( System.out );
1525 private static boolean testBasicTable() {
1527 final BasicTable<String> t0 = new BasicTable<String>();
1528 if ( t0.getNumberOfColumns() != 0 ) {
1531 if ( t0.getNumberOfRows() != 0 ) {
1534 t0.setValue( 3, 2, "23" );
1535 t0.setValue( 10, 1, "error" );
1536 t0.setValue( 10, 1, "110" );
1537 t0.setValue( 9, 1, "19" );
1538 t0.setValue( 1, 10, "101" );
1539 t0.setValue( 10, 10, "1010" );
1540 t0.setValue( 100, 10, "10100" );
1541 t0.setValue( 0, 0, "00" );
1542 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1545 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1548 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1551 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1554 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1557 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1560 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1563 if ( t0.getNumberOfColumns() != 101 ) {
1566 if ( t0.getNumberOfRows() != 11 ) {
1569 if ( t0.getValueAsString( 49, 4 ) != null ) {
1572 final String l = ForesterUtil.getLineSeparator();
1573 final StringBuffer source = new StringBuffer();
1574 source.append( "" + l );
1575 source.append( "# 1 1 1 1 1 1 1 1" + l );
1576 source.append( " 00 01 02 03" + l );
1577 source.append( " 10 11 12 13 " + l );
1578 source.append( "20 21 22 23 " + l );
1579 source.append( " 30 31 32 33" + l );
1580 source.append( "40 41 42 43" + l );
1581 source.append( " # 1 1 1 1 1 " + l );
1582 source.append( "50 51 52 53 54" + l );
1583 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1584 if ( t1.getNumberOfColumns() != 5 ) {
1587 if ( t1.getNumberOfRows() != 6 ) {
1590 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1593 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1596 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1599 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1602 final StringBuffer source1 = new StringBuffer();
1603 source1.append( "" + l );
1604 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1605 source1.append( " 00; 01 ;02;03" + l );
1606 source1.append( " 10; 11; 12; 13 " + l );
1607 source1.append( "20; 21; 22; 23 " + l );
1608 source1.append( " 30; 31; 32; 33" + l );
1609 source1.append( "40;41;42;43" + l );
1610 source1.append( " # 1 1 1 1 1 " + l );
1611 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1612 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1613 if ( t2.getNumberOfColumns() != 5 ) {
1616 if ( t2.getNumberOfRows() != 6 ) {
1619 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1622 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1625 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1628 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1631 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1634 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1637 final StringBuffer source2 = new StringBuffer();
1638 source2.append( "" + l );
1639 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1640 source2.append( " 00; 01 ;02;03" + l );
1641 source2.append( " 10; 11; 12; 13 " + l );
1642 source2.append( "20; 21; 22; 23 " + l );
1643 source2.append( " " + l );
1644 source2.append( " 30; 31; 32; 33" + l );
1645 source2.append( "40;41;42;43" + l );
1646 source2.append( " comment: 1 1 1 1 1 " + l );
1647 source2.append( ";;;50 ; 52; 53;;54 " + l );
1648 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1654 if ( tl.size() != 2 ) {
1657 final BasicTable<String> t3 = tl.get( 0 );
1658 final BasicTable<String> t4 = tl.get( 1 );
1659 if ( t3.getNumberOfColumns() != 4 ) {
1662 if ( t3.getNumberOfRows() != 3 ) {
1665 if ( t4.getNumberOfColumns() != 4 ) {
1668 if ( t4.getNumberOfRows() != 3 ) {
1671 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1674 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1678 catch ( final Exception e ) {
1679 e.printStackTrace( System.out );
1685 private static boolean testBasicTolXMLparsing() {
1687 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1688 final TolParser parser = new TolParser();
1689 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1690 if ( parser.getErrorCount() > 0 ) {
1691 System.out.println( parser.getErrorMessages().toString() );
1694 if ( phylogenies_0.length != 1 ) {
1697 final Phylogeny t1 = phylogenies_0[ 0 ];
1698 if ( t1.getNumberOfExternalNodes() != 5 ) {
1701 if ( !t1.isRooted() ) {
1704 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1707 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1710 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1713 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1716 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1717 if ( parser.getErrorCount() > 0 ) {
1718 System.out.println( parser.getErrorMessages().toString() );
1721 if ( phylogenies_1.length != 1 ) {
1724 final Phylogeny t2 = phylogenies_1[ 0 ];
1725 if ( t2.getNumberOfExternalNodes() != 664 ) {
1728 if ( !t2.isRooted() ) {
1731 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1734 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1737 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1740 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1743 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1746 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1747 .equals( "Aquifex" ) ) {
1750 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1751 if ( parser.getErrorCount() > 0 ) {
1752 System.out.println( parser.getErrorMessages().toString() );
1755 if ( phylogenies_2.length != 1 ) {
1758 final Phylogeny t3 = phylogenies_2[ 0 ];
1759 if ( t3.getNumberOfExternalNodes() != 184 ) {
1762 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1765 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1768 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1771 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1772 if ( parser.getErrorCount() > 0 ) {
1773 System.out.println( parser.getErrorMessages().toString() );
1776 if ( phylogenies_3.length != 1 ) {
1779 final Phylogeny t4 = phylogenies_3[ 0 ];
1780 if ( t4.getNumberOfExternalNodes() != 1 ) {
1783 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1786 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1789 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1792 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1793 if ( parser.getErrorCount() > 0 ) {
1794 System.out.println( parser.getErrorMessages().toString() );
1797 if ( phylogenies_4.length != 1 ) {
1800 final Phylogeny t5 = phylogenies_4[ 0 ];
1801 if ( t5.getNumberOfExternalNodes() != 13 ) {
1804 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1807 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1810 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1814 catch ( final Exception e ) {
1815 e.printStackTrace( System.out );
1821 private static boolean testBasicTreeMethods() {
1823 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1824 final Phylogeny t1 = factory.create();
1825 if ( !t1.isEmpty() ) {
1828 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1829 if ( t2.getNumberOfExternalNodes() != 4 ) {
1832 if ( t2.getHeight() != 8.5 ) {
1835 if ( !t2.isCompletelyBinary() ) {
1838 if ( t2.isEmpty() ) {
1841 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1842 if ( t3.getNumberOfExternalNodes() != 5 ) {
1845 if ( t3.getHeight() != 11 ) {
1848 if ( t3.isCompletelyBinary() ) {
1851 final PhylogenyNode n = t3.getNode( "ABC" );
1852 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 ];
1853 if ( t4.getNumberOfExternalNodes() != 9 ) {
1856 if ( t4.getHeight() != 11 ) {
1859 if ( t4.isCompletelyBinary() ) {
1862 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)" );
1863 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1864 if ( t5.getNumberOfExternalNodes() != 8 ) {
1867 if ( t5.getHeight() != 15 ) {
1870 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)" );
1871 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1872 if ( t6.getHeight() != 15 ) {
1875 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)" );
1876 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1877 if ( t7.getHeight() != 15 ) {
1880 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)" );
1881 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1882 if ( t8.getNumberOfExternalNodes() != 10 ) {
1885 if ( t8.getHeight() != 15 ) {
1888 final char[] a9 = new char[] {};
1889 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1890 if ( t9.getHeight() != 0 ) {
1893 final char[] a10 = new char[] { 'a', ':', '6' };
1894 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1895 if ( t10.getHeight() != 6 ) {
1899 catch ( final Exception e ) {
1900 e.printStackTrace( System.out );
1906 private static boolean testConfidenceAssessor() {
1908 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1909 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1910 final Phylogeny[] ev0 = factory
1911 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1913 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1914 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1917 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1920 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1921 final Phylogeny[] ev1 = factory
1922 .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)));",
1924 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1925 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1928 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1931 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1932 final Phylogeny[] ev_b = factory
1933 .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",
1935 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1936 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1939 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1943 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1944 final Phylogeny[] ev1x = factory
1945 .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)));",
1947 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1948 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1951 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1954 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1955 final Phylogeny[] ev_bx = factory
1956 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
1958 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1959 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1962 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1966 final Phylogeny[] t2 = factory
1967 .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);",
1969 final Phylogeny[] ev2 = factory
1970 .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);",
1972 for( final Phylogeny target : t2 ) {
1973 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
1976 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
1977 new NHXParser() )[ 0 ];
1978 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
1979 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
1980 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1983 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
1986 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1990 catch ( final Exception e ) {
1991 e.printStackTrace();
1997 private static boolean testCopyOfNodeData() {
1999 final PhylogenyNode n1 = PhylogenyNode
2000 .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]" );
2001 final PhylogenyNode n2 = n1.copyNodeData();
2002 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2006 catch ( final Exception e ) {
2007 e.printStackTrace();
2013 private static boolean testDataObjects() {
2015 final Confidence s0 = new Confidence();
2016 final Confidence s1 = new Confidence();
2017 if ( !s0.isEqual( s1 ) ) {
2020 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2021 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2022 if ( s2.isEqual( s1 ) ) {
2025 if ( !s2.isEqual( s3 ) ) {
2028 final Confidence s4 = ( Confidence ) s3.copy();
2029 if ( !s4.isEqual( s3 ) ) {
2036 final Taxonomy t1 = new Taxonomy();
2037 final Taxonomy t2 = new Taxonomy();
2038 final Taxonomy t3 = new Taxonomy();
2039 final Taxonomy t4 = new Taxonomy();
2040 final Taxonomy t5 = new Taxonomy();
2041 t1.setIdentifier( new Identifier( "ecoli" ) );
2042 t1.setTaxonomyCode( "ECOLI" );
2043 t1.setScientificName( "E. coli" );
2044 t1.setCommonName( "coli" );
2045 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2046 if ( !t1.isEqual( t0 ) ) {
2049 t2.setIdentifier( new Identifier( "ecoli" ) );
2050 t2.setTaxonomyCode( "OTHER" );
2051 t2.setScientificName( "what" );
2052 t2.setCommonName( "something" );
2053 if ( !t1.isEqual( t2 ) ) {
2056 t2.setIdentifier( new Identifier( "nemve" ) );
2057 if ( t1.isEqual( t2 ) ) {
2060 t1.setIdentifier( null );
2061 t3.setTaxonomyCode( "ECOLI" );
2062 t3.setScientificName( "what" );
2063 t3.setCommonName( "something" );
2064 if ( !t1.isEqual( t3 ) ) {
2067 t1.setIdentifier( null );
2068 t1.setTaxonomyCode( "" );
2069 t4.setScientificName( "E. ColI" );
2070 t4.setCommonName( "something" );
2071 if ( !t1.isEqual( t4 ) ) {
2074 t4.setScientificName( "B. subtilis" );
2075 t4.setCommonName( "something" );
2076 if ( t1.isEqual( t4 ) ) {
2079 t1.setIdentifier( null );
2080 t1.setTaxonomyCode( "" );
2081 t1.setScientificName( "" );
2082 t5.setCommonName( "COLI" );
2083 if ( !t1.isEqual( t5 ) ) {
2086 t5.setCommonName( "vibrio" );
2087 if ( t1.isEqual( t5 ) ) {
2092 final Identifier id0 = new Identifier( "123", "pfam" );
2093 final Identifier id1 = ( Identifier ) id0.copy();
2094 if ( !id1.isEqual( id1 ) ) {
2097 if ( !id1.isEqual( id0 ) ) {
2100 if ( !id0.isEqual( id1 ) ) {
2107 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2108 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2109 if ( !pd1.isEqual( pd1 ) ) {
2112 if ( !pd1.isEqual( pd0 ) ) {
2117 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2118 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2119 if ( !pd3.isEqual( pd3 ) ) {
2122 if ( !pd2.isEqual( pd3 ) ) {
2125 if ( !pd0.isEqual( pd3 ) ) {
2130 // DomainArchitecture
2131 // ------------------
2132 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2133 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2134 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2135 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2136 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2137 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2142 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2143 if ( ds0.getNumberOfDomains() != 4 ) {
2146 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2147 if ( !ds0.isEqual( ds0 ) ) {
2150 if ( !ds0.isEqual( ds1 ) ) {
2153 if ( ds1.getNumberOfDomains() != 4 ) {
2156 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2161 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2162 if ( ds0.isEqual( ds2 ) ) {
2168 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2169 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2170 System.out.println( ds3.toNHX() );
2173 if ( ds3.getNumberOfDomains() != 3 ) {
2178 final Event e1 = new Event( Event.EventType.fusion );
2179 if ( e1.isDuplication() ) {
2182 if ( !e1.isFusion() ) {
2185 if ( !e1.asText().toString().equals( "fusion" ) ) {
2188 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2191 final Event e11 = new Event( Event.EventType.fusion );
2192 if ( !e11.isEqual( e1 ) ) {
2195 if ( !e11.toNHX().toString().equals( "" ) ) {
2198 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2199 if ( e2.isDuplication() ) {
2202 if ( !e2.isSpeciationOrDuplication() ) {
2205 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2208 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2211 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2214 if ( e11.isEqual( e2 ) ) {
2217 final Event e2c = ( Event ) e2.copy();
2218 if ( !e2c.isEqual( e2 ) ) {
2221 Event e3 = new Event( 1, 2, 3 );
2222 if ( e3.isDuplication() ) {
2225 if ( e3.isSpeciation() ) {
2228 if ( e3.isGeneLoss() ) {
2231 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2234 final Event e3c = ( Event ) e3.copy();
2235 final Event e3cc = ( Event ) e3c.copy();
2236 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2240 if ( !e3c.isEqual( e3cc ) ) {
2243 Event e4 = new Event( 1, 2, 3 );
2244 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2247 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2250 final Event e4c = ( Event ) e4.copy();
2252 final Event e4cc = ( Event ) e4c.copy();
2253 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2256 if ( !e4c.isEqual( e4cc ) ) {
2259 final Event e5 = new Event();
2260 if ( !e5.isUnassigned() ) {
2263 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2266 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2269 final Event e6 = new Event( 1, 0, 0 );
2270 if ( !e6.asText().toString().equals( "duplication" ) ) {
2273 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2276 final Event e7 = new Event( 0, 1, 0 );
2277 if ( !e7.asText().toString().equals( "speciation" ) ) {
2280 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2283 final Event e8 = new Event( 0, 0, 1 );
2284 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2287 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2291 catch ( final Exception e ) {
2292 e.printStackTrace( System.out );
2298 private static boolean testDeletionOfExternalNodes() {
2300 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2301 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2302 final PhylogenyWriter w = new PhylogenyWriter();
2303 if ( t0.isEmpty() ) {
2306 if ( t0.getNumberOfExternalNodes() != 1 ) {
2309 t0.deleteSubtree( t0.getNode( "A" ), false );
2310 if ( t0.getNumberOfExternalNodes() != 0 ) {
2313 if ( !t0.isEmpty() ) {
2316 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2317 if ( t1.getNumberOfExternalNodes() != 2 ) {
2320 t1.deleteSubtree( t1.getNode( "A" ), false );
2321 if ( t1.getNumberOfExternalNodes() != 1 ) {
2324 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2327 t1.deleteSubtree( t1.getNode( "B" ), false );
2328 if ( t1.getNumberOfExternalNodes() != 1 ) {
2331 t1.deleteSubtree( t1.getNode( "r" ), false );
2332 if ( !t1.isEmpty() ) {
2335 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2336 if ( t2.getNumberOfExternalNodes() != 3 ) {
2339 t2.deleteSubtree( t2.getNode( "B" ), false );
2340 if ( t2.getNumberOfExternalNodes() != 2 ) {
2343 t2.toNewHampshireX();
2344 PhylogenyNode n = t2.getNode( "A" );
2345 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2348 t2.deleteSubtree( t2.getNode( "A" ), false );
2349 if ( t2.getNumberOfExternalNodes() != 2 ) {
2352 t2.deleteSubtree( t2.getNode( "C" ), true );
2353 if ( t2.getNumberOfExternalNodes() != 1 ) {
2356 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2357 if ( t3.getNumberOfExternalNodes() != 4 ) {
2360 t3.deleteSubtree( t3.getNode( "B" ), true );
2361 if ( t3.getNumberOfExternalNodes() != 3 ) {
2364 n = t3.getNode( "A" );
2365 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2368 n = n.getNextExternalNode();
2369 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2372 t3.deleteSubtree( t3.getNode( "A" ), true );
2373 if ( t3.getNumberOfExternalNodes() != 2 ) {
2376 n = t3.getNode( "C" );
2377 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2380 t3.deleteSubtree( t3.getNode( "C" ), true );
2381 if ( t3.getNumberOfExternalNodes() != 1 ) {
2384 t3.deleteSubtree( t3.getNode( "D" ), true );
2385 if ( t3.getNumberOfExternalNodes() != 0 ) {
2388 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2389 if ( t4.getNumberOfExternalNodes() != 6 ) {
2392 t4.deleteSubtree( t4.getNode( "B2" ), true );
2393 if ( t4.getNumberOfExternalNodes() != 5 ) {
2396 String s = w.toNewHampshire( t4, false, true ).toString();
2397 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2400 t4.deleteSubtree( t4.getNode( "B11" ), true );
2401 if ( t4.getNumberOfExternalNodes() != 4 ) {
2404 t4.deleteSubtree( t4.getNode( "C" ), true );
2405 if ( t4.getNumberOfExternalNodes() != 3 ) {
2408 n = t4.getNode( "A" );
2409 n = n.getNextExternalNode();
2410 if ( !n.getName().equals( "B12" ) ) {
2413 n = n.getNextExternalNode();
2414 if ( !n.getName().equals( "D" ) ) {
2417 s = w.toNewHampshire( t4, false, true ).toString();
2418 if ( !s.equals( "((A,B12),D);" ) ) {
2421 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2422 t5.deleteSubtree( t5.getNode( "A" ), true );
2423 if ( t5.getNumberOfExternalNodes() != 5 ) {
2426 s = w.toNewHampshire( t5, false, true ).toString();
2427 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2430 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2431 t6.deleteSubtree( t6.getNode( "B11" ), true );
2432 if ( t6.getNumberOfExternalNodes() != 5 ) {
2435 s = w.toNewHampshire( t6, false, false ).toString();
2436 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2439 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2440 t7.deleteSubtree( t7.getNode( "B12" ), true );
2441 if ( t7.getNumberOfExternalNodes() != 5 ) {
2444 s = w.toNewHampshire( t7, false, true ).toString();
2445 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2448 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2449 t8.deleteSubtree( t8.getNode( "B2" ), true );
2450 if ( t8.getNumberOfExternalNodes() != 5 ) {
2453 s = w.toNewHampshire( t8, false, false ).toString();
2454 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2457 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2458 t9.deleteSubtree( t9.getNode( "C" ), true );
2459 if ( t9.getNumberOfExternalNodes() != 5 ) {
2462 s = w.toNewHampshire( t9, false, true ).toString();
2463 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2466 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2467 t10.deleteSubtree( t10.getNode( "D" ), true );
2468 if ( t10.getNumberOfExternalNodes() != 5 ) {
2471 s = w.toNewHampshire( t10, false, true ).toString();
2472 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2475 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2476 t11.deleteSubtree( t11.getNode( "A" ), true );
2477 if ( t11.getNumberOfExternalNodes() != 2 ) {
2480 s = w.toNewHampshire( t11, false, true ).toString();
2481 if ( !s.equals( "(B,C);" ) ) {
2484 t11.deleteSubtree( t11.getNode( "C" ), true );
2485 if ( t11.getNumberOfExternalNodes() != 1 ) {
2488 s = w.toNewHampshire( t11, false, false ).toString();
2489 if ( !s.equals( "B;" ) ) {
2492 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2493 t12.deleteSubtree( t12.getNode( "B2" ), true );
2494 if ( t12.getNumberOfExternalNodes() != 8 ) {
2497 s = w.toNewHampshire( t12, false, true ).toString();
2498 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2501 t12.deleteSubtree( t12.getNode( "B3" ), true );
2502 if ( t12.getNumberOfExternalNodes() != 7 ) {
2505 s = w.toNewHampshire( t12, false, true ).toString();
2506 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2509 t12.deleteSubtree( t12.getNode( "C3" ), true );
2510 if ( t12.getNumberOfExternalNodes() != 6 ) {
2513 s = w.toNewHampshire( t12, false, true ).toString();
2514 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2517 t12.deleteSubtree( t12.getNode( "A1" ), true );
2518 if ( t12.getNumberOfExternalNodes() != 5 ) {
2521 s = w.toNewHampshire( t12, false, true ).toString();
2522 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2525 t12.deleteSubtree( t12.getNode( "B1" ), true );
2526 if ( t12.getNumberOfExternalNodes() != 4 ) {
2529 s = w.toNewHampshire( t12, false, true ).toString();
2530 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2533 t12.deleteSubtree( t12.getNode( "A3" ), true );
2534 if ( t12.getNumberOfExternalNodes() != 3 ) {
2537 s = w.toNewHampshire( t12, false, true ).toString();
2538 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2541 t12.deleteSubtree( t12.getNode( "A2" ), true );
2542 if ( t12.getNumberOfExternalNodes() != 2 ) {
2545 s = w.toNewHampshire( t12, false, true ).toString();
2546 if ( !s.equals( "(C1,C2);" ) ) {
2549 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2550 t13.deleteSubtree( t13.getNode( "D" ), true );
2551 if ( t13.getNumberOfExternalNodes() != 4 ) {
2554 s = w.toNewHampshire( t13, false, true ).toString();
2555 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2558 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2559 t14.deleteSubtree( t14.getNode( "E" ), true );
2560 if ( t14.getNumberOfExternalNodes() != 5 ) {
2563 s = w.toNewHampshire( t14, false, true ).toString();
2564 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2567 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2568 t15.deleteSubtree( t15.getNode( "B2" ), true );
2569 if ( t15.getNumberOfExternalNodes() != 11 ) {
2572 t15.deleteSubtree( t15.getNode( "B1" ), true );
2573 if ( t15.getNumberOfExternalNodes() != 10 ) {
2576 t15.deleteSubtree( t15.getNode( "B3" ), true );
2577 if ( t15.getNumberOfExternalNodes() != 9 ) {
2580 t15.deleteSubtree( t15.getNode( "B4" ), true );
2581 if ( t15.getNumberOfExternalNodes() != 8 ) {
2584 t15.deleteSubtree( t15.getNode( "A1" ), true );
2585 if ( t15.getNumberOfExternalNodes() != 7 ) {
2588 t15.deleteSubtree( t15.getNode( "C4" ), true );
2589 if ( t15.getNumberOfExternalNodes() != 6 ) {
2593 catch ( final Exception e ) {
2594 e.printStackTrace( System.out );
2600 private static boolean testDescriptiveStatistics() {
2602 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2603 dss1.addValue( 82 );
2604 dss1.addValue( 78 );
2605 dss1.addValue( 70 );
2606 dss1.addValue( 58 );
2607 dss1.addValue( 42 );
2608 if ( dss1.getN() != 5 ) {
2611 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2614 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2617 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2620 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2623 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2626 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2629 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2632 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2635 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2638 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2641 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2644 dss1.addValue( 123 );
2645 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2648 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2651 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2654 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2655 dss2.addValue( -1.85 );
2656 dss2.addValue( 57.5 );
2657 dss2.addValue( 92.78 );
2658 dss2.addValue( 57.78 );
2659 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2662 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2665 final double[] a = dss2.getDataAsDoubleArray();
2666 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2669 dss2.addValue( -100 );
2670 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2673 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2676 final double[] ds = new double[ 14 ];
2691 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2692 if ( bins.length != 4 ) {
2695 if ( bins[ 0 ] != 2 ) {
2698 if ( bins[ 1 ] != 3 ) {
2701 if ( bins[ 2 ] != 4 ) {
2704 if ( bins[ 3 ] != 5 ) {
2707 final double[] ds1 = new double[ 9 ];
2717 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2718 if ( bins1.length != 4 ) {
2721 if ( bins1[ 0 ] != 2 ) {
2724 if ( bins1[ 1 ] != 3 ) {
2727 if ( bins1[ 2 ] != 0 ) {
2730 if ( bins1[ 3 ] != 4 ) {
2733 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2734 if ( bins1_1.length != 3 ) {
2737 if ( bins1_1[ 0 ] != 3 ) {
2740 if ( bins1_1[ 1 ] != 2 ) {
2743 if ( bins1_1[ 2 ] != 4 ) {
2746 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2747 if ( bins1_2.length != 3 ) {
2750 if ( bins1_2[ 0 ] != 2 ) {
2753 if ( bins1_2[ 1 ] != 2 ) {
2756 if ( bins1_2[ 2 ] != 2 ) {
2759 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2773 dss3.addValue( 10 );
2774 dss3.addValue( 10 );
2775 dss3.addValue( 10 );
2776 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2777 histo.toStringBuffer( 10, '=', 40, 5 );
2778 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2780 catch ( final Exception e ) {
2781 e.printStackTrace( System.out );
2787 private static boolean testDir( final String file ) {
2789 final File f = new File( file );
2790 if ( !f.exists() ) {
2793 if ( !f.isDirectory() ) {
2796 if ( !f.canRead() ) {
2800 catch ( final Exception e ) {
2806 private static boolean testExternalNodeRelatedMethods() {
2808 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2809 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2810 PhylogenyNode n = t1.getNode( "A" );
2811 n = n.getNextExternalNode();
2812 if ( !n.getName().equals( "B" ) ) {
2815 n = n.getNextExternalNode();
2816 if ( !n.getName().equals( "C" ) ) {
2819 n = n.getNextExternalNode();
2820 if ( !n.getName().equals( "D" ) ) {
2823 n = t1.getNode( "B" );
2824 while ( !n.isLastExternalNode() ) {
2825 n = n.getNextExternalNode();
2827 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2828 n = t2.getNode( "A" );
2829 n = n.getNextExternalNode();
2830 if ( !n.getName().equals( "B" ) ) {
2833 n = n.getNextExternalNode();
2834 if ( !n.getName().equals( "C" ) ) {
2837 n = n.getNextExternalNode();
2838 if ( !n.getName().equals( "D" ) ) {
2841 n = t2.getNode( "B" );
2842 while ( !n.isLastExternalNode() ) {
2843 n = n.getNextExternalNode();
2845 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2846 n = t3.getNode( "A" );
2847 n = n.getNextExternalNode();
2848 if ( !n.getName().equals( "B" ) ) {
2851 n = n.getNextExternalNode();
2852 if ( !n.getName().equals( "C" ) ) {
2855 n = n.getNextExternalNode();
2856 if ( !n.getName().equals( "D" ) ) {
2859 n = n.getNextExternalNode();
2860 if ( !n.getName().equals( "E" ) ) {
2863 n = n.getNextExternalNode();
2864 if ( !n.getName().equals( "F" ) ) {
2867 n = n.getNextExternalNode();
2868 if ( !n.getName().equals( "G" ) ) {
2871 n = n.getNextExternalNode();
2872 if ( !n.getName().equals( "H" ) ) {
2875 n = t3.getNode( "B" );
2876 while ( !n.isLastExternalNode() ) {
2877 n = n.getNextExternalNode();
2879 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2880 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2881 final PhylogenyNode node = iter.next();
2883 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2884 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2885 final PhylogenyNode node = iter.next();
2888 catch ( final Exception e ) {
2889 e.printStackTrace( System.out );
2895 private static boolean testGeneralTable() {
2897 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2898 t0.setValue( 3, 2, "23" );
2899 t0.setValue( 10, 1, "error" );
2900 t0.setValue( 10, 1, "110" );
2901 t0.setValue( 9, 1, "19" );
2902 t0.setValue( 1, 10, "101" );
2903 t0.setValue( 10, 10, "1010" );
2904 t0.setValue( 100, 10, "10100" );
2905 t0.setValue( 0, 0, "00" );
2906 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2909 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2912 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2915 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2918 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2921 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2924 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2927 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2930 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2933 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2934 t1.setValue( "3", "2", "23" );
2935 t1.setValue( "10", "1", "error" );
2936 t1.setValue( "10", "1", "110" );
2937 t1.setValue( "9", "1", "19" );
2938 t1.setValue( "1", "10", "101" );
2939 t1.setValue( "10", "10", "1010" );
2940 t1.setValue( "100", "10", "10100" );
2941 t1.setValue( "0", "0", "00" );
2942 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2943 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2946 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2949 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2952 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2955 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2958 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
2961 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
2964 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
2967 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
2970 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
2974 catch ( final Exception e ) {
2975 e.printStackTrace( System.out );
2981 private static boolean testGetDistance() {
2983 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2984 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",
2985 new NHXParser() )[ 0 ];
2986 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
2987 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
2990 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
2993 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
2996 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
2999 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3002 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3005 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3008 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3011 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3014 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3017 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3020 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3023 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3026 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3029 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3032 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3035 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3038 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3041 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3044 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3047 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3050 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3053 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3056 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3059 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3062 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3065 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3068 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3071 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3074 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3077 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3080 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",
3081 new NHXParser() )[ 0 ];
3082 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3085 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3088 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3091 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3094 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3097 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3100 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3103 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3106 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3109 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3112 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3116 catch ( final Exception e ) {
3117 e.printStackTrace( System.out );
3123 private static boolean testGetLCA() {
3125 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3126 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3127 new NHXParser() )[ 0 ];
3128 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3129 if ( !A.getName().equals( "A" ) ) {
3132 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3133 if ( !gh.getName().equals( "gh" ) ) {
3136 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3137 if ( !ab.getName().equals( "ab" ) ) {
3140 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3141 if ( !ab2.getName().equals( "ab" ) ) {
3144 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3145 if ( !gh2.getName().equals( "gh" ) ) {
3148 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3149 if ( !gh3.getName().equals( "gh" ) ) {
3152 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3153 if ( !abc.getName().equals( "abc" ) ) {
3156 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3157 if ( !abc2.getName().equals( "abc" ) ) {
3160 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3161 if ( !abcd.getName().equals( "abcd" ) ) {
3164 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3165 if ( !abcd2.getName().equals( "abcd" ) ) {
3168 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3169 if ( !abcdef.getName().equals( "abcdef" ) ) {
3172 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3173 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3176 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3177 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3180 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3181 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3184 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3185 if ( !abcde.getName().equals( "abcde" ) ) {
3188 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3189 if ( !abcde2.getName().equals( "abcde" ) ) {
3192 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3193 if ( !r.getName().equals( "abcdefgh" ) ) {
3196 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3197 if ( !r2.getName().equals( "abcdefgh" ) ) {
3200 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3201 if ( !r3.getName().equals( "abcdefgh" ) ) {
3204 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3205 if ( !abcde3.getName().equals( "abcde" ) ) {
3208 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3209 if ( !abcde4.getName().equals( "abcde" ) ) {
3212 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3213 if ( !ab3.getName().equals( "ab" ) ) {
3216 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3217 if ( !ab4.getName().equals( "ab" ) ) {
3220 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3221 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3222 if ( !cd.getName().equals( "cd" ) ) {
3225 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3226 if ( !cd2.getName().equals( "cd" ) ) {
3229 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3230 if ( !cde.getName().equals( "cde" ) ) {
3233 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3234 if ( !cde2.getName().equals( "cde" ) ) {
3237 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3238 if ( !cdef.getName().equals( "cdef" ) ) {
3241 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3242 if ( !cdef2.getName().equals( "cdef" ) ) {
3245 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3246 if ( !cdef3.getName().equals( "cdef" ) ) {
3249 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3250 if ( !rt.getName().equals( "r" ) ) {
3253 final Phylogeny p3 = factory
3254 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3255 new NHXParser() )[ 0 ];
3256 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3257 if ( !bc_3.getName().equals( "bc" ) ) {
3260 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3261 if ( !ac_3.getName().equals( "abc" ) ) {
3264 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3265 if ( !ad_3.getName().equals( "abcde" ) ) {
3268 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3269 if ( !af_3.getName().equals( "abcdef" ) ) {
3272 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3273 if ( !ag_3.getName().equals( "" ) ) {
3276 if ( !ag_3.isRoot() ) {
3279 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3280 if ( !al_3.getName().equals( "" ) ) {
3283 if ( !al_3.isRoot() ) {
3286 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3287 if ( !kl_3.getName().equals( "" ) ) {
3290 if ( !kl_3.isRoot() ) {
3293 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3294 if ( !fl_3.getName().equals( "" ) ) {
3297 if ( !fl_3.isRoot() ) {
3300 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3301 if ( !gk_3.getName().equals( "ghijk" ) ) {
3304 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3305 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3306 if ( !r_4.getName().equals( "r" ) ) {
3309 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3310 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3311 if ( !r_5.getName().equals( "root" ) ) {
3314 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3315 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3316 if ( !r_6.getName().equals( "rot" ) ) {
3319 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3320 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3321 if ( !r_7.getName().equals( "rott" ) ) {
3325 catch ( final Exception e ) {
3326 e.printStackTrace( System.out );
3332 private static boolean testGetLCA2() {
3334 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3335 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3336 PhylogenyMethods.preOrderReId( p_a );
3337 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3338 p_a.getNode( "a" ) );
3339 if ( !p_a_1.getName().equals( "a" ) ) {
3342 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3343 PhylogenyMethods.preOrderReId( p_b );
3344 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3345 p_b.getNode( "a" ) );
3346 if ( !p_b_1.getName().equals( "b" ) ) {
3349 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3350 p_b.getNode( "b" ) );
3351 if ( !p_b_2.getName().equals( "b" ) ) {
3354 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3355 PhylogenyMethods.preOrderReId( p_c );
3356 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3357 p_c.getNode( "a" ) );
3358 if ( !p_c_1.getName().equals( "b" ) ) {
3361 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3362 p_c.getNode( "c" ) );
3363 if ( !p_c_2.getName().equals( "c" ) ) {
3364 System.out.println( p_c_2.getName() );
3368 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3369 p_c.getNode( "b" ) );
3370 if ( !p_c_3.getName().equals( "b" ) ) {
3373 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3374 p_c.getNode( "a" ) );
3375 if ( !p_c_4.getName().equals( "c" ) ) {
3378 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3379 new NHXParser() )[ 0 ];
3380 PhylogenyMethods.preOrderReId( p1 );
3381 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3382 p1.getNode( "A" ) );
3383 if ( !A.getName().equals( "A" ) ) {
3386 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3387 p1.getNode( "gh" ) );
3388 if ( !gh.getName().equals( "gh" ) ) {
3391 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3392 p1.getNode( "B" ) );
3393 if ( !ab.getName().equals( "ab" ) ) {
3396 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3397 p1.getNode( "A" ) );
3398 if ( !ab2.getName().equals( "ab" ) ) {
3401 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3402 p1.getNode( "G" ) );
3403 if ( !gh2.getName().equals( "gh" ) ) {
3406 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3407 p1.getNode( "H" ) );
3408 if ( !gh3.getName().equals( "gh" ) ) {
3411 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3412 p1.getNode( "A" ) );
3413 if ( !abc.getName().equals( "abc" ) ) {
3416 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3417 p1.getNode( "C" ) );
3418 if ( !abc2.getName().equals( "abc" ) ) {
3421 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3422 p1.getNode( "D" ) );
3423 if ( !abcd.getName().equals( "abcd" ) ) {
3426 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3427 p1.getNode( "A" ) );
3428 if ( !abcd2.getName().equals( "abcd" ) ) {
3431 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3432 p1.getNode( "F" ) );
3433 if ( !abcdef.getName().equals( "abcdef" ) ) {
3436 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3437 p1.getNode( "A" ) );
3438 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3441 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3442 p1.getNode( "F" ) );
3443 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3446 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3447 p1.getNode( "ab" ) );
3448 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3451 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3452 p1.getNode( "E" ) );
3453 if ( !abcde.getName().equals( "abcde" ) ) {
3456 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3457 p1.getNode( "A" ) );
3458 if ( !abcde2.getName().equals( "abcde" ) ) {
3461 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3462 p1.getNode( "abcdefgh" ) );
3463 if ( !r.getName().equals( "abcdefgh" ) ) {
3466 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3467 p1.getNode( "H" ) );
3468 if ( !r2.getName().equals( "abcdefgh" ) ) {
3471 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3472 p1.getNode( "A" ) );
3473 if ( !r3.getName().equals( "abcdefgh" ) ) {
3476 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3477 p1.getNode( "abcde" ) );
3478 if ( !abcde3.getName().equals( "abcde" ) ) {
3481 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3482 p1.getNode( "E" ) );
3483 if ( !abcde4.getName().equals( "abcde" ) ) {
3486 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3487 p1.getNode( "B" ) );
3488 if ( !ab3.getName().equals( "ab" ) ) {
3491 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3492 p1.getNode( "ab" ) );
3493 if ( !ab4.getName().equals( "ab" ) ) {
3496 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3497 PhylogenyMethods.preOrderReId( p2 );
3498 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3499 p2.getNode( "d" ) );
3500 if ( !cd.getName().equals( "cd" ) ) {
3503 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3504 p2.getNode( "c" ) );
3505 if ( !cd2.getName().equals( "cd" ) ) {
3508 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3509 p2.getNode( "e" ) );
3510 if ( !cde.getName().equals( "cde" ) ) {
3513 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3514 p2.getNode( "c" ) );
3515 if ( !cde2.getName().equals( "cde" ) ) {
3518 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3519 p2.getNode( "f" ) );
3520 if ( !cdef.getName().equals( "cdef" ) ) {
3523 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3524 p2.getNode( "f" ) );
3525 if ( !cdef2.getName().equals( "cdef" ) ) {
3528 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3529 p2.getNode( "d" ) );
3530 if ( !cdef3.getName().equals( "cdef" ) ) {
3533 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3534 p2.getNode( "a" ) );
3535 if ( !rt.getName().equals( "r" ) ) {
3538 final Phylogeny p3 = factory
3539 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3540 new NHXParser() )[ 0 ];
3541 PhylogenyMethods.preOrderReId( p3 );
3542 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3543 p3.getNode( "c" ) );
3544 if ( !bc_3.getName().equals( "bc" ) ) {
3547 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3548 p3.getNode( "c" ) );
3549 if ( !ac_3.getName().equals( "abc" ) ) {
3552 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3553 p3.getNode( "d" ) );
3554 if ( !ad_3.getName().equals( "abcde" ) ) {
3557 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3558 p3.getNode( "f" ) );
3559 if ( !af_3.getName().equals( "abcdef" ) ) {
3562 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3563 p3.getNode( "g" ) );
3564 if ( !ag_3.getName().equals( "" ) ) {
3567 if ( !ag_3.isRoot() ) {
3570 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3571 p3.getNode( "l" ) );
3572 if ( !al_3.getName().equals( "" ) ) {
3575 if ( !al_3.isRoot() ) {
3578 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3579 p3.getNode( "l" ) );
3580 if ( !kl_3.getName().equals( "" ) ) {
3583 if ( !kl_3.isRoot() ) {
3586 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3587 p3.getNode( "l" ) );
3588 if ( !fl_3.getName().equals( "" ) ) {
3591 if ( !fl_3.isRoot() ) {
3594 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3595 p3.getNode( "k" ) );
3596 if ( !gk_3.getName().equals( "ghijk" ) ) {
3599 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3600 PhylogenyMethods.preOrderReId( p4 );
3601 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3602 p4.getNode( "c" ) );
3603 if ( !r_4.getName().equals( "r" ) ) {
3606 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3607 PhylogenyMethods.preOrderReId( p5 );
3608 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3609 p5.getNode( "c" ) );
3610 if ( !r_5.getName().equals( "root" ) ) {
3613 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3614 PhylogenyMethods.preOrderReId( p6 );
3615 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3616 p6.getNode( "a" ) );
3617 if ( !r_6.getName().equals( "rot" ) ) {
3620 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3621 PhylogenyMethods.preOrderReId( p7 );
3622 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3623 p7.getNode( "e" ) );
3624 if ( !r_7.getName().equals( "rott" ) ) {
3627 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3628 p7.getNode( "a" ) );
3629 if ( !r_71.getName().equals( "rott" ) ) {
3632 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3633 p7.getNode( "rott" ) );
3634 if ( !r_72.getName().equals( "rott" ) ) {
3637 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3638 p7.getNode( "a" ) );
3639 if ( !r_73.getName().equals( "rott" ) ) {
3642 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3643 p7.getNode( "rott" ) );
3644 if ( !r_74.getName().equals( "rott" ) ) {
3647 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3648 p7.getNode( "e" ) );
3649 if ( !r_75.getName().equals( "e" ) ) {
3653 catch ( final Exception e ) {
3654 e.printStackTrace( System.out );
3660 private static boolean testHmmscanOutputParser() {
3661 final String test_dir = Test.PATH_TO_TEST_DATA;
3663 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3664 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3666 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3667 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3668 final List<Protein> proteins = parser2.parse();
3669 if ( parser2.getProteinsEncountered() != 4 ) {
3672 if ( proteins.size() != 4 ) {
3675 if ( parser2.getDomainsEncountered() != 69 ) {
3678 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3681 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3684 final Protein p1 = proteins.get( 0 );
3685 if ( p1.getNumberOfProteinDomains() != 15 ) {
3688 if ( p1.getLength() != 850 ) {
3691 final Protein p2 = proteins.get( 1 );
3692 if ( p2.getNumberOfProteinDomains() != 51 ) {
3695 if ( p2.getLength() != 1291 ) {
3698 final Protein p3 = proteins.get( 2 );
3699 if ( p3.getNumberOfProteinDomains() != 2 ) {
3702 final Protein p4 = proteins.get( 3 );
3703 if ( p4.getNumberOfProteinDomains() != 1 ) {
3706 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3709 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3712 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3715 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3718 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3721 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3724 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3727 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3730 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3734 catch ( final Exception e ) {
3735 e.printStackTrace( System.out );
3741 private static boolean testLastExternalNodeMethods() {
3743 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3744 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3745 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3746 final PhylogenyNode n1 = t0.getNode( "A" );
3747 if ( n1.isLastExternalNode() ) {
3750 final PhylogenyNode n2 = t0.getNode( "B" );
3751 if ( n2.isLastExternalNode() ) {
3754 final PhylogenyNode n3 = t0.getNode( "C" );
3755 if ( n3.isLastExternalNode() ) {
3758 final PhylogenyNode n4 = t0.getNode( "D" );
3759 if ( !n4.isLastExternalNode() ) {
3763 catch ( final Exception e ) {
3764 e.printStackTrace( System.out );
3770 private static boolean testLevelOrderIterator() {
3772 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3773 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3774 PhylogenyNodeIterator it0;
3775 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3778 for( it0.reset(); it0.hasNext(); ) {
3781 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3782 if ( !it.next().getName().equals( "r" ) ) {
3785 if ( !it.next().getName().equals( "ab" ) ) {
3788 if ( !it.next().getName().equals( "cd" ) ) {
3791 if ( !it.next().getName().equals( "A" ) ) {
3794 if ( !it.next().getName().equals( "B" ) ) {
3797 if ( !it.next().getName().equals( "C" ) ) {
3800 if ( !it.next().getName().equals( "D" ) ) {
3803 if ( it.hasNext() ) {
3806 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",
3807 new NHXParser() )[ 0 ];
3808 PhylogenyNodeIterator it2;
3809 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3812 for( it2.reset(); it2.hasNext(); ) {
3815 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3816 if ( !it3.next().getName().equals( "r" ) ) {
3819 if ( !it3.next().getName().equals( "abc" ) ) {
3822 if ( !it3.next().getName().equals( "defg" ) ) {
3825 if ( !it3.next().getName().equals( "A" ) ) {
3828 if ( !it3.next().getName().equals( "B" ) ) {
3831 if ( !it3.next().getName().equals( "C" ) ) {
3834 if ( !it3.next().getName().equals( "D" ) ) {
3837 if ( !it3.next().getName().equals( "E" ) ) {
3840 if ( !it3.next().getName().equals( "F" ) ) {
3843 if ( !it3.next().getName().equals( "G" ) ) {
3846 if ( !it3.next().getName().equals( "1" ) ) {
3849 if ( !it3.next().getName().equals( "2" ) ) {
3852 if ( !it3.next().getName().equals( "3" ) ) {
3855 if ( !it3.next().getName().equals( "4" ) ) {
3858 if ( !it3.next().getName().equals( "5" ) ) {
3861 if ( !it3.next().getName().equals( "6" ) ) {
3864 if ( !it3.next().getName().equals( "f1" ) ) {
3867 if ( !it3.next().getName().equals( "f2" ) ) {
3870 if ( !it3.next().getName().equals( "f3" ) ) {
3873 if ( !it3.next().getName().equals( "a" ) ) {
3876 if ( !it3.next().getName().equals( "b" ) ) {
3879 if ( !it3.next().getName().equals( "f21" ) ) {
3882 if ( !it3.next().getName().equals( "X" ) ) {
3885 if ( !it3.next().getName().equals( "Y" ) ) {
3888 if ( !it3.next().getName().equals( "Z" ) ) {
3891 if ( it3.hasNext() ) {
3894 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3895 PhylogenyNodeIterator it4;
3896 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3899 for( it4.reset(); it4.hasNext(); ) {
3902 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3903 if ( !it5.next().getName().equals( "r" ) ) {
3906 if ( !it5.next().getName().equals( "A" ) ) {
3909 if ( !it5.next().getName().equals( "B" ) ) {
3912 if ( !it5.next().getName().equals( "C" ) ) {
3915 if ( !it5.next().getName().equals( "D" ) ) {
3918 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3919 PhylogenyNodeIterator it6;
3920 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3923 for( it6.reset(); it6.hasNext(); ) {
3926 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3927 if ( !it7.next().getName().equals( "A" ) ) {
3930 if ( it.hasNext() ) {
3934 catch ( final Exception e ) {
3935 e.printStackTrace( System.out );
3941 private static boolean testMidpointrooting() {
3943 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3944 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",
3945 new NHXParser() )[ 0 ];
3946 if ( !t1.isRooted() ) {
3949 PhylogenyMethods.midpointRoot( t1 );
3950 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3953 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3956 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3959 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3962 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3965 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3968 t1.reRoot( t1.getNode( "A" ) );
3969 PhylogenyMethods.midpointRoot( t1 );
3970 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3973 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3976 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3979 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3982 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3985 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3989 catch ( final Exception e ) {
3990 e.printStackTrace( System.out );
3996 private static boolean testNexusCharactersParsing() {
3998 final NexusCharactersParser parser = new NexusCharactersParser();
3999 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4001 String[] labels = parser.getCharStateLabels();
4002 if ( labels.length != 7 ) {
4005 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4008 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4011 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4014 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4017 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4020 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4023 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4026 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4028 labels = parser.getCharStateLabels();
4029 if ( labels.length != 7 ) {
4032 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4035 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4038 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4041 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4044 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4047 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4050 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4054 catch ( final Exception e ) {
4055 e.printStackTrace( System.out );
4061 private static boolean testNexusMatrixParsing() {
4063 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4064 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4066 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4067 if ( m.getNumberOfCharacters() != 9 ) {
4070 if ( m.getNumberOfIdentifiers() != 5 ) {
4073 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4076 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4079 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4082 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4085 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4088 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4091 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4094 // if ( labels.length != 7 ) {
4097 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4100 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4103 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4106 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4109 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4112 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4115 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4118 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4120 // labels = parser.getCharStateLabels();
4121 // if ( labels.length != 7 ) {
4124 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4127 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4130 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4133 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4136 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4139 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4142 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4146 catch ( final Exception e ) {
4147 e.printStackTrace( System.out );
4153 private static boolean testNexusTreeParsing() {
4155 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4156 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4157 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4158 if ( phylogenies.length != 1 ) {
4161 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4164 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4168 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4169 if ( phylogenies.length != 1 ) {
4172 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4175 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4179 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4180 if ( phylogenies.length != 1 ) {
4183 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4186 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4189 if ( phylogenies[ 0 ].isRooted() ) {
4193 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4194 if ( phylogenies.length != 18 ) {
4197 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4200 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4203 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4206 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4209 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4212 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4215 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4218 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4221 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4224 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4227 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4230 if ( phylogenies[ 8 ].isRooted() ) {
4233 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4236 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4239 if ( !phylogenies[ 9 ].isRooted() ) {
4242 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4245 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4248 if ( !phylogenies[ 10 ].isRooted() ) {
4251 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4254 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4257 if ( phylogenies[ 11 ].isRooted() ) {
4260 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4263 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4266 if ( !phylogenies[ 12 ].isRooted() ) {
4269 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4272 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4275 if ( !phylogenies[ 13 ].isRooted() ) {
4278 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4281 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4284 if ( !phylogenies[ 14 ].isRooted() ) {
4287 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4290 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4293 if ( phylogenies[ 15 ].isRooted() ) {
4296 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4299 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4302 if ( !phylogenies[ 16 ].isRooted() ) {
4305 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4308 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4311 if ( phylogenies[ 17 ].isRooted() ) {
4314 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4318 catch ( final Exception e ) {
4319 e.printStackTrace( System.out );
4325 private static boolean testNexusTreeParsingTranslating() {
4327 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4328 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4329 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4330 if ( phylogenies.length != 1 ) {
4333 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4336 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4339 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4342 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4345 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4346 .equals( "Aranaeus" ) ) {
4350 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4351 if ( phylogenies.length != 3 ) {
4354 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4357 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4360 if ( phylogenies[ 0 ].isRooted() ) {
4363 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4366 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4369 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4370 .equals( "Aranaeus" ) ) {
4373 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4376 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4379 if ( phylogenies[ 1 ].isRooted() ) {
4382 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4385 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4388 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4389 .equals( "Aranaeus" ) ) {
4392 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4395 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4398 if ( !phylogenies[ 2 ].isRooted() ) {
4401 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4404 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4407 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4408 .equals( "Aranaeus" ) ) {
4412 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4413 if ( phylogenies.length != 3 ) {
4416 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4419 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4422 if ( phylogenies[ 0 ].isRooted() ) {
4425 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4428 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4431 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4432 .equals( "Aranaeus" ) ) {
4435 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4438 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4441 if ( phylogenies[ 1 ].isRooted() ) {
4444 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4447 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4450 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4451 .equals( "Aranaeus" ) ) {
4454 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4457 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4460 if ( !phylogenies[ 2 ].isRooted() ) {
4463 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4466 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4469 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4470 .equals( "Aranaeus" ) ) {
4474 catch ( final Exception e ) {
4475 e.printStackTrace( System.out );
4481 private static boolean testNHParsing() {
4483 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4484 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4485 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4488 final NHXParser nhxp = new NHXParser();
4489 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4490 nhxp.setReplaceUnderscores( true );
4491 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4492 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4495 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4498 final Phylogeny p1b = factory
4499 .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 ",
4500 new NHXParser() )[ 0 ];
4501 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4504 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4507 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4508 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4509 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4510 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4511 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4512 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4513 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4514 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4515 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4516 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4517 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4518 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4519 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4521 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4524 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4527 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4530 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4533 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4534 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4535 final String p16_S = "((A,B),C)";
4536 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4537 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4540 final String p17_S = "(C,(A,B))";
4541 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4542 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4545 final String p18_S = "((A,B),(C,D))";
4546 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4547 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4550 final String p19_S = "(((A,B),C),D)";
4551 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4552 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4555 final String p20_S = "(A,(B,(C,D)))";
4556 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4557 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4560 final String p21_S = "(A,(B,(C,(D,E))))";
4561 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4562 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4565 final String p22_S = "((((A,B),C),D),E)";
4566 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4567 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4570 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4571 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4572 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4575 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4576 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4577 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4580 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4581 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4582 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4583 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4586 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4589 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4590 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4591 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4592 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4593 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4594 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4595 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4596 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4597 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4598 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4601 final String p26_S = "(A,B)ab";
4602 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4603 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4606 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4607 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4609 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4612 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4613 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4614 final String p28_S3 = "(A,B)ab";
4615 final String p28_S4 = "((((A,B),C),D),;E;)";
4616 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4618 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4621 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4624 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4627 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4630 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";
4631 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4632 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4635 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";
4636 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4637 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4640 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4641 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4642 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4645 final String p33_S = "A";
4646 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4647 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4650 final String p34_S = "B;";
4651 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4652 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4655 final String p35_S = "B:0.2";
4656 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4657 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4660 final String p36_S = "(A)";
4661 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4662 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4665 final String p37_S = "((A))";
4666 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4667 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4670 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4671 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4672 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4675 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4676 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4677 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4680 final String p40_S = "(A,B,C)";
4681 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4682 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4685 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4686 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4687 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4690 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4691 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4692 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4695 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)";
4696 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4697 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4700 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)))";
4701 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4702 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4705 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4706 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4707 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4710 final String p46_S = "";
4711 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4712 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4715 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4716 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4719 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4720 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4723 final Phylogeny p49 = factory
4724 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4725 new NHXParser() )[ 0 ];
4726 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4729 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4730 if ( p50.getNode( "A" ) == null ) {
4733 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4734 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4737 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4740 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4741 .equals( "((A,B)88:2.0,C);" ) ) {
4744 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4745 if ( p51.getNode( "A(A" ) == null ) {
4748 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4749 if ( p52.getNode( "A(A" ) == null ) {
4752 final Phylogeny p53 = factory
4753 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4754 new NHXParser() )[ 0 ];
4755 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4759 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4760 if ( p54.getNode( "A" ) == null ) {
4763 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4764 .equals( "((A,B)[88],C);" ) ) {
4768 catch ( final Exception e ) {
4769 e.printStackTrace( System.out );
4775 private static boolean testNHXconversion() {
4777 final PhylogenyNode n1 = new PhylogenyNode();
4778 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4779 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4780 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4781 final PhylogenyNode n5 = PhylogenyNode
4782 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4783 final PhylogenyNode n6 = PhylogenyNode
4784 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4785 if ( !n1.toNewHampshireX().equals( "" ) ) {
4788 if ( !n2.toNewHampshireX().equals( "" ) ) {
4791 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4794 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4797 if ( !n5.toNewHampshireX()
4798 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
4801 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
4805 catch ( final Exception e ) {
4806 e.printStackTrace( System.out );
4812 private static boolean testNHXNodeParsing() {
4814 final PhylogenyNode n1 = new PhylogenyNode();
4815 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4816 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4817 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4818 final PhylogenyNode n5 = PhylogenyNode
4819 .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]" );
4820 if ( !n3.getName().equals( "n3" ) ) {
4823 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4826 if ( n3.isDuplication() ) {
4829 if ( n3.isHasAssignedEvent() ) {
4832 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4835 if ( !n4.getName().equals( "n4" ) ) {
4838 if ( n4.getDistanceToParent() != 0.01 ) {
4841 if ( !n5.getName().equals( "n5" ) ) {
4844 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4847 if ( n5.getDistanceToParent() != 0.1 ) {
4850 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4853 if ( !n5.isDuplication() ) {
4856 if ( !n5.isHasAssignedEvent() ) {
4859 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4862 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4865 final PhylogenyNode n8 = PhylogenyNode
4866 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4867 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4870 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4873 final PhylogenyNode n9 = PhylogenyNode
4874 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4875 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4878 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4881 final PhylogenyNode n10 = PhylogenyNode
4882 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4883 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4886 final PhylogenyNode n20 = PhylogenyNode
4887 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4888 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4891 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4894 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
4895 NHXParser.TAXONOMY_EXTRACTION.YES );
4896 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4899 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4902 final PhylogenyNode n20xx = PhylogenyNode
4903 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4904 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4907 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4910 final PhylogenyNode n20xxx = PhylogenyNode
4911 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4912 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4915 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4918 final PhylogenyNode n20xxxx = PhylogenyNode
4919 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4920 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4923 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4926 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
4927 NHXParser.TAXONOMY_EXTRACTION.YES );
4928 if ( !n21.getName().equals( "n21_PIG" ) ) {
4931 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4934 final PhylogenyNode n21x = PhylogenyNode
4935 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4936 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4939 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4942 final PhylogenyNode n22 = PhylogenyNode
4943 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4944 if ( !n22.getName().equals( "n22/PIG" ) ) {
4947 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4950 final PhylogenyNode n23 = PhylogenyNode
4951 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4952 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4955 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4958 final PhylogenyNode a = PhylogenyNode
4959 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4960 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4963 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4966 final PhylogenyNode b = PhylogenyNode
4967 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4968 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4971 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4974 final PhylogenyNode c = PhylogenyNode
4975 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4976 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4977 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4980 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4983 final PhylogenyNode c1 = PhylogenyNode
4984 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
4985 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4986 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
4989 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
4992 final PhylogenyNode c2 = PhylogenyNode
4993 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
4994 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4995 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
4998 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5001 final PhylogenyNode d = PhylogenyNode
5002 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5003 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5006 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5009 final PhylogenyNode e = PhylogenyNode
5010 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5011 if ( !e.getName().equals( "n10_RAT1" ) ) {
5014 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5017 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5018 NHXParser.TAXONOMY_EXTRACTION.YES );
5019 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5022 if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5025 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5026 NHXParser.TAXONOMY_EXTRACTION.YES );
5027 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5030 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5033 final PhylogenyNode n11 = PhylogenyNode
5034 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5035 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5036 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5039 if ( n11.getDistanceToParent() != 0.4 ) {
5042 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5045 final PhylogenyNode n12 = PhylogenyNode
5046 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5047 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5048 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5051 if ( n12.getDistanceToParent() != 0.4 ) {
5054 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5057 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5058 NHXParser.TAXONOMY_EXTRACTION.YES );
5059 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5062 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5065 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5066 NHXParser.TAXONOMY_EXTRACTION.YES );
5067 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5070 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5073 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
5074 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
5075 if ( !tvu1.getRef().equals( "tag1" ) ) {
5078 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
5081 if ( !tvu1.getUnit().equals( "unit1" ) ) {
5084 if ( !tvu1.getValue().equals( "value1" ) ) {
5087 if ( !tvu3.getRef().equals( "tag3" ) ) {
5090 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
5093 if ( !tvu3.getUnit().equals( "unit3" ) ) {
5096 if ( !tvu3.getValue().equals( "value3" ) ) {
5099 if ( n1.getName().compareTo( "" ) != 0 ) {
5102 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5105 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5108 if ( n2.getName().compareTo( "" ) != 0 ) {
5111 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5114 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5117 final PhylogenyNode n00 = PhylogenyNode
5118 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
5119 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
5122 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5125 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5128 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
5131 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
5134 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
5137 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
5140 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
5143 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5144 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5147 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
5148 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
5151 final PhylogenyNode n13 = PhylogenyNode
5152 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5153 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5156 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5159 final PhylogenyNode n14 = PhylogenyNode
5160 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5161 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5164 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5167 final PhylogenyNode n15 = PhylogenyNode
5168 .createInstanceFromNhxString( "something_wicked[123]",
5169 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5170 if ( !n15.getName().equals( "something_wicked" ) ) {
5173 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5176 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5179 final PhylogenyNode n16 = PhylogenyNode
5180 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5181 if ( !n16.getName().equals( "something_wicked2" ) ) {
5184 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5187 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5190 final PhylogenyNode n17 = PhylogenyNode
5191 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5192 if ( !n17.getName().equals( "something_wicked3" ) ) {
5195 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5198 final PhylogenyNode n18 = PhylogenyNode
5199 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5200 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5203 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5206 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5210 catch ( final Exception e ) {
5211 e.printStackTrace( System.out );
5217 private static boolean testNHXParsing() {
5219 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5220 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5221 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5224 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]";
5225 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5226 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5229 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]";
5230 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5231 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5234 final Phylogeny[] p3 = factory
5235 .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]",
5237 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5240 final Phylogeny[] p4 = factory
5241 .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(]",
5243 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5246 final Phylogeny[] p5 = factory
5247 .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(((]",
5249 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5252 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)";
5253 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)";
5254 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5255 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5258 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)))";
5259 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)))";
5260 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5261 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5264 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]) ))[,,, ])))))))";
5265 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5266 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5267 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5270 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5271 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5274 final Phylogeny p10 = factory
5275 .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]",
5276 new NHXParser() )[ 0 ];
5277 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5281 catch ( final Exception e ) {
5282 e.printStackTrace( System.out );
5288 private static boolean testNHXParsingQuotes() {
5290 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5291 final NHXParser p = new NHXParser();
5292 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5293 if ( phylogenies_0.length != 5 ) {
5296 final Phylogeny phy = phylogenies_0[ 4 ];
5297 if ( phy.getNumberOfExternalNodes() != 7 ) {
5300 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5303 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5306 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5307 .getScientificName().equals( "hsapiens" ) ) {
5310 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5313 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5316 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5319 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5322 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5325 final NHXParser p1p = new NHXParser();
5326 p1p.setIgnoreQuotes( true );
5327 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5328 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5331 final NHXParser p2p = new NHXParser();
5332 p1p.setIgnoreQuotes( false );
5333 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5334 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5337 final NHXParser p3p = new NHXParser();
5338 p3p.setIgnoreQuotes( false );
5339 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5340 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5343 final NHXParser p4p = new NHXParser();
5344 p4p.setIgnoreQuotes( false );
5345 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5346 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5349 final Phylogeny p10 = factory
5350 .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]",
5351 new NHXParser() )[ 0 ];
5352 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]";
5353 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5356 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5357 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5361 final Phylogeny p12 = factory
5362 .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]",
5363 new NHXParser() )[ 0 ];
5364 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]";
5365 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5368 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5369 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5372 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;";
5373 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5376 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5377 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5381 catch ( final Exception e ) {
5382 e.printStackTrace( System.out );
5388 private static boolean testNHXParsingMB() {
5390 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5391 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5392 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5393 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5394 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5395 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5396 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5397 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5398 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5399 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5400 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5403 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5406 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5407 0.1100000000000000e+00 ) ) {
5410 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5413 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5416 final Phylogeny p2 = factory
5417 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5418 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5419 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5420 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5421 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5422 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5423 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5424 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5425 + "7.369400000000000e-02}])",
5426 new NHXParser() )[ 0 ];
5427 if ( p2.getNode( "1" ) == null ) {
5430 if ( p2.getNode( "2" ) == null ) {
5434 catch ( final Exception e ) {
5435 e.printStackTrace( System.out );
5442 private static boolean testPhylogenyBranch() {
5444 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5445 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5446 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5447 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5448 if ( !a1b1.equals( a1b1 ) ) {
5451 if ( !a1b1.equals( b1a1 ) ) {
5454 if ( !b1a1.equals( a1b1 ) ) {
5457 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5458 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5459 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5460 if ( a1_b1.equals( b1_a1 ) ) {
5463 if ( a1_b1.equals( a1_b1_ ) ) {
5466 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5467 if ( !a1_b1.equals( b1_a1_ ) ) {
5470 if ( a1_b1_.equals( b1_a1_ ) ) {
5473 if ( !a1_b1_.equals( b1_a1 ) ) {
5477 catch ( final Exception e ) {
5478 e.printStackTrace( System.out );
5484 private static boolean testPhyloXMLparsingOfDistributionElement() {
5486 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5487 PhyloXmlParser xml_parser = null;
5489 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5491 catch ( final Exception e ) {
5492 // Do nothing -- means were not running from jar.
5494 if ( xml_parser == null ) {
5495 xml_parser = new PhyloXmlParser();
5496 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5497 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5500 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5503 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5505 if ( xml_parser.getErrorCount() > 0 ) {
5506 System.out.println( xml_parser.getErrorMessages().toString() );
5509 if ( phylogenies_0.length != 1 ) {
5512 final Phylogeny t1 = phylogenies_0[ 0 ];
5513 PhylogenyNode n = null;
5514 Distribution d = null;
5515 n = t1.getNode( "root node" );
5516 if ( !n.getNodeData().isHasDistribution() ) {
5519 if ( n.getNodeData().getDistributions().size() != 1 ) {
5522 d = n.getNodeData().getDistribution();
5523 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5526 if ( d.getPoints().size() != 1 ) {
5529 if ( d.getPolygons() != null ) {
5532 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5535 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5538 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5541 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5544 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5547 n = t1.getNode( "node a" );
5548 if ( !n.getNodeData().isHasDistribution() ) {
5551 if ( n.getNodeData().getDistributions().size() != 2 ) {
5554 d = n.getNodeData().getDistribution( 1 );
5555 if ( !d.getDesc().equals( "San Diego" ) ) {
5558 if ( d.getPoints().size() != 1 ) {
5561 if ( d.getPolygons() != null ) {
5564 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5567 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5570 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5573 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5576 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5579 n = t1.getNode( "node bb" );
5580 if ( !n.getNodeData().isHasDistribution() ) {
5583 if ( n.getNodeData().getDistributions().size() != 1 ) {
5586 d = n.getNodeData().getDistribution( 0 );
5587 if ( d.getPoints().size() != 3 ) {
5590 if ( d.getPolygons().size() != 2 ) {
5593 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5596 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5599 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5602 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5605 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5608 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5611 Polygon p = d.getPolygons().get( 0 );
5612 if ( p.getPoints().size() != 3 ) {
5615 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5618 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5621 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5624 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5627 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5630 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5633 p = d.getPolygons().get( 1 );
5634 if ( p.getPoints().size() != 3 ) {
5637 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5640 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5643 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5647 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5648 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5649 if ( rt.length != 1 ) {
5652 final Phylogeny t1_rt = rt[ 0 ];
5653 n = t1_rt.getNode( "root node" );
5654 if ( !n.getNodeData().isHasDistribution() ) {
5657 if ( n.getNodeData().getDistributions().size() != 1 ) {
5660 d = n.getNodeData().getDistribution();
5661 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5664 if ( d.getPoints().size() != 1 ) {
5667 if ( d.getPolygons() != null ) {
5670 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5673 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5676 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5679 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5682 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5685 n = t1_rt.getNode( "node a" );
5686 if ( !n.getNodeData().isHasDistribution() ) {
5689 if ( n.getNodeData().getDistributions().size() != 2 ) {
5692 d = n.getNodeData().getDistribution( 1 );
5693 if ( !d.getDesc().equals( "San Diego" ) ) {
5696 if ( d.getPoints().size() != 1 ) {
5699 if ( d.getPolygons() != null ) {
5702 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5705 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5708 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5711 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5714 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5717 n = t1_rt.getNode( "node bb" );
5718 if ( !n.getNodeData().isHasDistribution() ) {
5721 if ( n.getNodeData().getDistributions().size() != 1 ) {
5724 d = n.getNodeData().getDistribution( 0 );
5725 if ( d.getPoints().size() != 3 ) {
5728 if ( d.getPolygons().size() != 2 ) {
5731 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5734 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5737 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5740 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5743 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5746 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5749 p = d.getPolygons().get( 0 );
5750 if ( p.getPoints().size() != 3 ) {
5753 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5756 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5759 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5762 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5765 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5768 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5771 p = d.getPolygons().get( 1 );
5772 if ( p.getPoints().size() != 3 ) {
5775 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5778 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5781 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5785 catch ( final Exception e ) {
5786 e.printStackTrace( System.out );
5792 private static boolean testPostOrderIterator() {
5794 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5795 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5796 PhylogenyNodeIterator it0;
5797 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5800 for( it0.reset(); it0.hasNext(); ) {
5803 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5804 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5805 if ( !it.next().getName().equals( "A" ) ) {
5808 if ( !it.next().getName().equals( "B" ) ) {
5811 if ( !it.next().getName().equals( "ab" ) ) {
5814 if ( !it.next().getName().equals( "C" ) ) {
5817 if ( !it.next().getName().equals( "D" ) ) {
5820 if ( !it.next().getName().equals( "cd" ) ) {
5823 if ( !it.next().getName().equals( "abcd" ) ) {
5826 if ( !it.next().getName().equals( "E" ) ) {
5829 if ( !it.next().getName().equals( "F" ) ) {
5832 if ( !it.next().getName().equals( "ef" ) ) {
5835 if ( !it.next().getName().equals( "G" ) ) {
5838 if ( !it.next().getName().equals( "H" ) ) {
5841 if ( !it.next().getName().equals( "gh" ) ) {
5844 if ( !it.next().getName().equals( "efgh" ) ) {
5847 if ( !it.next().getName().equals( "r" ) ) {
5850 if ( it.hasNext() ) {
5854 catch ( final Exception e ) {
5855 e.printStackTrace( System.out );
5861 private static boolean testPreOrderIterator() {
5863 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5864 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5865 PhylogenyNodeIterator it0;
5866 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5869 for( it0.reset(); it0.hasNext(); ) {
5872 PhylogenyNodeIterator it = t0.iteratorPreorder();
5873 if ( !it.next().getName().equals( "r" ) ) {
5876 if ( !it.next().getName().equals( "ab" ) ) {
5879 if ( !it.next().getName().equals( "A" ) ) {
5882 if ( !it.next().getName().equals( "B" ) ) {
5885 if ( !it.next().getName().equals( "cd" ) ) {
5888 if ( !it.next().getName().equals( "C" ) ) {
5891 if ( !it.next().getName().equals( "D" ) ) {
5894 if ( it.hasNext() ) {
5897 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5898 it = t1.iteratorPreorder();
5899 if ( !it.next().getName().equals( "r" ) ) {
5902 if ( !it.next().getName().equals( "abcd" ) ) {
5905 if ( !it.next().getName().equals( "ab" ) ) {
5908 if ( !it.next().getName().equals( "A" ) ) {
5911 if ( !it.next().getName().equals( "B" ) ) {
5914 if ( !it.next().getName().equals( "cd" ) ) {
5917 if ( !it.next().getName().equals( "C" ) ) {
5920 if ( !it.next().getName().equals( "D" ) ) {
5923 if ( !it.next().getName().equals( "efgh" ) ) {
5926 if ( !it.next().getName().equals( "ef" ) ) {
5929 if ( !it.next().getName().equals( "E" ) ) {
5932 if ( !it.next().getName().equals( "F" ) ) {
5935 if ( !it.next().getName().equals( "gh" ) ) {
5938 if ( !it.next().getName().equals( "G" ) ) {
5941 if ( !it.next().getName().equals( "H" ) ) {
5944 if ( it.hasNext() ) {
5948 catch ( final Exception e ) {
5949 e.printStackTrace( System.out );
5955 private static boolean testPropertiesMap() {
5957 final PropertiesMap pm = new PropertiesMap();
5958 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5959 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5960 final Property p2 = new Property( "something:else",
5962 "improbable:research",
5965 pm.addProperty( p0 );
5966 pm.addProperty( p1 );
5967 pm.addProperty( p2 );
5968 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5971 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5974 if ( pm.getProperties().size() != 3 ) {
5977 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5980 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5983 if ( pm.getProperties().size() != 3 ) {
5986 pm.removeProperty( "dimensions:diameter" );
5987 if ( pm.getProperties().size() != 2 ) {
5990 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5993 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5997 catch ( final Exception e ) {
5998 e.printStackTrace( System.out );
6004 private static boolean testReIdMethods() {
6006 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6007 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6008 final int count = PhylogenyNode.getNodeCount();
6010 if ( p.getNode( "r" ).getId() != count ) {
6013 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6016 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6019 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6022 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6025 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6028 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6031 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6034 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6037 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6040 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6043 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6046 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6049 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6052 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6056 catch ( final Exception e ) {
6057 e.printStackTrace( System.out );
6063 private static boolean testRerooting() {
6065 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6066 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",
6067 new NHXParser() )[ 0 ];
6068 if ( !t1.isRooted() ) {
6071 t1.reRoot( t1.getNode( "D" ) );
6072 t1.reRoot( t1.getNode( "CD" ) );
6073 t1.reRoot( t1.getNode( "A" ) );
6074 t1.reRoot( t1.getNode( "B" ) );
6075 t1.reRoot( t1.getNode( "AB" ) );
6076 t1.reRoot( t1.getNode( "D" ) );
6077 t1.reRoot( t1.getNode( "C" ) );
6078 t1.reRoot( t1.getNode( "CD" ) );
6079 t1.reRoot( t1.getNode( "A" ) );
6080 t1.reRoot( t1.getNode( "B" ) );
6081 t1.reRoot( t1.getNode( "AB" ) );
6082 t1.reRoot( t1.getNode( "D" ) );
6083 t1.reRoot( t1.getNode( "D" ) );
6084 t1.reRoot( t1.getNode( "C" ) );
6085 t1.reRoot( t1.getNode( "A" ) );
6086 t1.reRoot( t1.getNode( "B" ) );
6087 t1.reRoot( t1.getNode( "AB" ) );
6088 t1.reRoot( t1.getNode( "C" ) );
6089 t1.reRoot( t1.getNode( "D" ) );
6090 t1.reRoot( t1.getNode( "CD" ) );
6091 t1.reRoot( t1.getNode( "D" ) );
6092 t1.reRoot( t1.getNode( "A" ) );
6093 t1.reRoot( t1.getNode( "B" ) );
6094 t1.reRoot( t1.getNode( "AB" ) );
6095 t1.reRoot( t1.getNode( "C" ) );
6096 t1.reRoot( t1.getNode( "D" ) );
6097 t1.reRoot( t1.getNode( "CD" ) );
6098 t1.reRoot( t1.getNode( "D" ) );
6099 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6102 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6105 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6108 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6111 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6114 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6117 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",
6118 new NHXParser() )[ 0 ];
6119 t2.reRoot( t2.getNode( "A" ) );
6120 t2.reRoot( t2.getNode( "D" ) );
6121 t2.reRoot( t2.getNode( "ABC" ) );
6122 t2.reRoot( t2.getNode( "A" ) );
6123 t2.reRoot( t2.getNode( "B" ) );
6124 t2.reRoot( t2.getNode( "D" ) );
6125 t2.reRoot( t2.getNode( "C" ) );
6126 t2.reRoot( t2.getNode( "ABC" ) );
6127 t2.reRoot( t2.getNode( "A" ) );
6128 t2.reRoot( t2.getNode( "B" ) );
6129 t2.reRoot( t2.getNode( "AB" ) );
6130 t2.reRoot( t2.getNode( "AB" ) );
6131 t2.reRoot( t2.getNode( "D" ) );
6132 t2.reRoot( t2.getNode( "C" ) );
6133 t2.reRoot( t2.getNode( "B" ) );
6134 t2.reRoot( t2.getNode( "AB" ) );
6135 t2.reRoot( t2.getNode( "D" ) );
6136 t2.reRoot( t2.getNode( "D" ) );
6137 t2.reRoot( t2.getNode( "ABC" ) );
6138 t2.reRoot( t2.getNode( "A" ) );
6139 t2.reRoot( t2.getNode( "B" ) );
6140 t2.reRoot( t2.getNode( "AB" ) );
6141 t2.reRoot( t2.getNode( "D" ) );
6142 t2.reRoot( t2.getNode( "C" ) );
6143 t2.reRoot( t2.getNode( "ABC" ) );
6144 t2.reRoot( t2.getNode( "A" ) );
6145 t2.reRoot( t2.getNode( "B" ) );
6146 t2.reRoot( t2.getNode( "AB" ) );
6147 t2.reRoot( t2.getNode( "D" ) );
6148 t2.reRoot( t2.getNode( "D" ) );
6149 t2.reRoot( t2.getNode( "C" ) );
6150 t2.reRoot( t2.getNode( "A" ) );
6151 t2.reRoot( t2.getNode( "B" ) );
6152 t2.reRoot( t2.getNode( "AB" ) );
6153 t2.reRoot( t2.getNode( "C" ) );
6154 t2.reRoot( t2.getNode( "D" ) );
6155 t2.reRoot( t2.getNode( "ABC" ) );
6156 t2.reRoot( t2.getNode( "D" ) );
6157 t2.reRoot( t2.getNode( "A" ) );
6158 t2.reRoot( t2.getNode( "B" ) );
6159 t2.reRoot( t2.getNode( "AB" ) );
6160 t2.reRoot( t2.getNode( "C" ) );
6161 t2.reRoot( t2.getNode( "D" ) );
6162 t2.reRoot( t2.getNode( "ABC" ) );
6163 t2.reRoot( t2.getNode( "D" ) );
6164 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6167 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6170 t2.reRoot( t2.getNode( "ABC" ) );
6171 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6174 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6177 t2.reRoot( t2.getNode( "AB" ) );
6178 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6181 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6184 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6187 t2.reRoot( t2.getNode( "AB" ) );
6188 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6191 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6194 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6197 t2.reRoot( t2.getNode( "D" ) );
6198 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6201 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6204 t2.reRoot( t2.getNode( "ABC" ) );
6205 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6208 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6211 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6212 new NHXParser() )[ 0 ];
6213 t3.reRoot( t3.getNode( "B" ) );
6214 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6217 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6220 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6223 t3.reRoot( t3.getNode( "B" ) );
6224 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6227 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6230 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6233 t3.reRoot( t3.getRoot() );
6234 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6237 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6240 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6244 catch ( final Exception e ) {
6245 e.printStackTrace( System.out );
6251 private static boolean testSDIse() {
6253 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6254 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6255 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6256 gene1.setRooted( true );
6257 species1.setRooted( true );
6258 final SDI sdi = new SDIse( gene1, species1 );
6259 if ( !gene1.getRoot().isDuplication() ) {
6262 final Phylogeny species2 = factory
6263 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6264 new NHXParser() )[ 0 ];
6265 final Phylogeny gene2 = factory
6266 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6267 new NHXParser() )[ 0 ];
6268 species2.setRooted( true );
6269 gene2.setRooted( true );
6270 final SDI sdi2 = new SDIse( gene2, species2 );
6271 if ( sdi2.getDuplicationsSum() != 0 ) {
6274 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6277 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6280 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6283 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6286 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6289 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6292 final Phylogeny species3 = factory
6293 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6294 new NHXParser() )[ 0 ];
6295 final Phylogeny gene3 = factory
6296 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6297 new NHXParser() )[ 0 ];
6298 species3.setRooted( true );
6299 gene3.setRooted( true );
6300 final SDI sdi3 = new SDIse( gene3, species3 );
6301 if ( sdi3.getDuplicationsSum() != 1 ) {
6304 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6307 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6310 final Phylogeny species4 = factory
6311 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6312 new NHXParser() )[ 0 ];
6313 final Phylogeny gene4 = factory
6314 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6315 new NHXParser() )[ 0 ];
6316 species4.setRooted( true );
6317 gene4.setRooted( true );
6318 final SDI sdi4 = new SDIse( gene4, species4 );
6319 if ( sdi4.getDuplicationsSum() != 1 ) {
6322 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6325 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6328 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6331 if ( species4.getNumberOfExternalNodes() != 6 ) {
6334 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6337 final Phylogeny species5 = factory
6338 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6339 new NHXParser() )[ 0 ];
6340 final Phylogeny gene5 = factory
6341 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6342 new NHXParser() )[ 0 ];
6343 species5.setRooted( true );
6344 gene5.setRooted( true );
6345 final SDI sdi5 = new SDIse( gene5, species5 );
6346 if ( sdi5.getDuplicationsSum() != 2 ) {
6349 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6352 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6355 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6358 if ( species5.getNumberOfExternalNodes() != 6 ) {
6361 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6364 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6365 // Conjecture for Comparing Molecular Phylogenies"
6366 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6367 final Phylogeny species6 = factory
6368 .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,"
6369 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6370 new NHXParser() )[ 0 ];
6371 final Phylogeny gene6 = factory
6372 .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,"
6373 + "((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,"
6374 + "(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;",
6375 new NHXParser() )[ 0 ];
6376 species6.setRooted( true );
6377 gene6.setRooted( true );
6378 final SDI sdi6 = new SDIse( gene6, species6 );
6379 if ( sdi6.getDuplicationsSum() != 3 ) {
6382 if ( !gene6.getNode( "r" ).isDuplication() ) {
6385 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6388 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6391 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6394 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6397 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6400 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6403 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6406 sdi6.computeMappingCostL();
6407 if ( sdi6.computeMappingCostL() != 17 ) {
6410 if ( species6.getNumberOfExternalNodes() != 9 ) {
6413 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6416 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6417 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6418 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6419 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6420 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6421 species7.setRooted( true );
6422 final Phylogeny gene7_1 = Test
6423 .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])" );
6424 gene7_1.setRooted( true );
6425 final SDI sdi7 = new SDIse( gene7_1, species7 );
6426 if ( sdi7.getDuplicationsSum() != 0 ) {
6429 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6432 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6435 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6438 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6441 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6444 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6447 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6450 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6453 final Phylogeny gene7_2 = Test
6454 .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])" );
6455 gene7_2.setRooted( true );
6456 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6457 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6460 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6463 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6466 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6469 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6472 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6475 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6478 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6481 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6484 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6488 catch ( final Exception e ) {
6494 private static boolean testSDIunrooted() {
6496 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6497 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6498 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6499 final Iterator<PhylogenyBranch> iter = l.iterator();
6500 PhylogenyBranch br = iter.next();
6501 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6504 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6508 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6511 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6515 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6518 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6522 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6525 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6529 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6532 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6536 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6539 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6543 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6546 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6550 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6553 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6557 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6560 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6564 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6567 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6571 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6574 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6578 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6581 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6585 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6588 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6592 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6595 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6599 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6602 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6605 if ( iter.hasNext() ) {
6608 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6609 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6610 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6612 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6615 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6619 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6622 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6626 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6629 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6632 if ( iter1.hasNext() ) {
6635 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6636 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6637 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6639 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6642 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6646 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6649 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6653 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6656 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6659 if ( iter2.hasNext() ) {
6662 final Phylogeny species0 = factory
6663 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6664 new NHXParser() )[ 0 ];
6665 final Phylogeny gene1 = factory
6666 .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])",
6667 new NHXParser() )[ 0 ];
6668 species0.setRooted( true );
6669 gene1.setRooted( true );
6670 final SDIR sdi_unrooted = new SDIR();
6671 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6672 if ( sdi_unrooted.getCount() != 1 ) {
6675 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6678 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6681 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6684 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6687 final Phylogeny gene2 = factory
6688 .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])",
6689 new NHXParser() )[ 0 ];
6690 gene2.setRooted( true );
6691 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6692 if ( sdi_unrooted.getCount() != 1 ) {
6695 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6698 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6701 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6704 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6707 final Phylogeny species6 = factory
6708 .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,"
6709 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6710 new NHXParser() )[ 0 ];
6711 final Phylogeny gene6 = factory
6712 .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],"
6713 + "(((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],"
6714 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6715 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6716 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6717 new NHXParser() )[ 0 ];
6718 species6.setRooted( true );
6719 gene6.setRooted( true );
6720 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6721 if ( sdi_unrooted.getCount() != 1 ) {
6724 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6727 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6730 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6733 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6736 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6739 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6742 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6745 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6748 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6751 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6754 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6757 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6761 final Phylogeny species7 = factory
6762 .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,"
6763 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6764 new NHXParser() )[ 0 ];
6765 final Phylogeny gene7 = factory
6766 .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],"
6767 + "(((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],"
6768 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6769 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6770 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6771 new NHXParser() )[ 0 ];
6772 species7.setRooted( true );
6773 gene7.setRooted( true );
6774 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6775 if ( sdi_unrooted.getCount() != 1 ) {
6778 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6781 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6784 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6787 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6790 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6793 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6796 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6799 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6802 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6805 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6808 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6811 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6815 final Phylogeny species8 = factory
6816 .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,"
6817 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6818 new NHXParser() )[ 0 ];
6819 final Phylogeny gene8 = factory
6820 .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],"
6821 + "(((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],"
6822 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6823 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6824 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6825 new NHXParser() )[ 0 ];
6826 species8.setRooted( true );
6827 gene8.setRooted( true );
6828 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6829 if ( sdi_unrooted.getCount() != 1 ) {
6832 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6835 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6838 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6841 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6844 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6847 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6850 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6853 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6856 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6859 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6862 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6865 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6870 catch ( final Exception e ) {
6871 e.printStackTrace( System.out );
6877 private static boolean testSplit() {
6879 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6880 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6881 //Archaeopteryx.createApplication( p0 );
6882 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6883 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6884 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6885 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6886 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6887 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6888 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6889 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6890 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6891 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6892 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6893 // System.out.println( s0.toString() );
6895 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6898 if ( s0.match( query_nodes ) ) {
6901 query_nodes = new HashSet<PhylogenyNode>();
6902 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6903 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6904 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6907 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6908 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6909 if ( !s0.match( query_nodes ) ) {
6913 query_nodes = new HashSet<PhylogenyNode>();
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6917 if ( !s0.match( query_nodes ) ) {
6921 query_nodes = new HashSet<PhylogenyNode>();
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6926 if ( !s0.match( query_nodes ) ) {
6930 query_nodes = new HashSet<PhylogenyNode>();
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6933 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6934 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6935 if ( !s0.match( query_nodes ) ) {
6939 query_nodes = new HashSet<PhylogenyNode>();
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6943 if ( !s0.match( query_nodes ) ) {
6947 query_nodes = new HashSet<PhylogenyNode>();
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6950 if ( !s0.match( query_nodes ) ) {
6954 query_nodes = new HashSet<PhylogenyNode>();
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6960 if ( !s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6967 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6968 if ( !s0.match( query_nodes ) ) {
6972 query_nodes = new HashSet<PhylogenyNode>();
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6977 if ( !s0.match( query_nodes ) ) {
6981 query_nodes = new HashSet<PhylogenyNode>();
6982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6984 if ( s0.match( query_nodes ) ) {
6988 query_nodes = new HashSet<PhylogenyNode>();
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6993 if ( s0.match( query_nodes ) ) {
6997 query_nodes = new HashSet<PhylogenyNode>();
6998 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7003 if ( s0.match( query_nodes ) ) {
7007 query_nodes = new HashSet<PhylogenyNode>();
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7010 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7011 if ( s0.match( query_nodes ) ) {
7015 query_nodes = new HashSet<PhylogenyNode>();
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7018 if ( s0.match( query_nodes ) ) {
7022 query_nodes = new HashSet<PhylogenyNode>();
7023 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7024 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7025 if ( s0.match( query_nodes ) ) {
7029 query_nodes = new HashSet<PhylogenyNode>();
7030 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7031 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7032 if ( s0.match( query_nodes ) ) {
7036 query_nodes = new HashSet<PhylogenyNode>();
7037 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7038 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7039 if ( s0.match( query_nodes ) ) {
7043 query_nodes = new HashSet<PhylogenyNode>();
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7046 if ( s0.match( query_nodes ) ) {
7050 query_nodes = new HashSet<PhylogenyNode>();
7051 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7053 if ( s0.match( query_nodes ) ) {
7057 query_nodes = new HashSet<PhylogenyNode>();
7058 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7059 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7061 if ( s0.match( query_nodes ) ) {
7065 query_nodes = new HashSet<PhylogenyNode>();
7066 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7067 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7069 if ( s0.match( query_nodes ) ) {
7073 query_nodes = new HashSet<PhylogenyNode>();
7074 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7077 if ( s0.match( query_nodes ) ) {
7081 query_nodes = new HashSet<PhylogenyNode>();
7082 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7086 if ( s0.match( query_nodes ) ) {
7090 // query_nodes = new HashSet<PhylogenyNode>();
7091 // query_nodes.add( new PhylogenyNode( "X" ) );
7092 // query_nodes.add( new PhylogenyNode( "Y" ) );
7093 // query_nodes.add( new PhylogenyNode( "A" ) );
7094 // query_nodes.add( new PhylogenyNode( "B" ) );
7095 // query_nodes.add( new PhylogenyNode( "C" ) );
7096 // query_nodes.add( new PhylogenyNode( "D" ) );
7097 // query_nodes.add( new PhylogenyNode( "E" ) );
7098 // query_nodes.add( new PhylogenyNode( "F" ) );
7099 // query_nodes.add( new PhylogenyNode( "G" ) );
7100 // if ( !s0.match( query_nodes ) ) {
7103 // query_nodes = new HashSet<PhylogenyNode>();
7104 // query_nodes.add( new PhylogenyNode( "X" ) );
7105 // query_nodes.add( new PhylogenyNode( "Y" ) );
7106 // query_nodes.add( new PhylogenyNode( "A" ) );
7107 // query_nodes.add( new PhylogenyNode( "B" ) );
7108 // query_nodes.add( new PhylogenyNode( "C" ) );
7109 // if ( !s0.match( query_nodes ) ) {
7113 // query_nodes = new HashSet<PhylogenyNode>();
7114 // query_nodes.add( new PhylogenyNode( "X" ) );
7115 // query_nodes.add( new PhylogenyNode( "Y" ) );
7116 // query_nodes.add( new PhylogenyNode( "D" ) );
7117 // query_nodes.add( new PhylogenyNode( "E" ) );
7118 // query_nodes.add( new PhylogenyNode( "F" ) );
7119 // query_nodes.add( new PhylogenyNode( "G" ) );
7120 // if ( !s0.match( query_nodes ) ) {
7124 // query_nodes = new HashSet<PhylogenyNode>();
7125 // query_nodes.add( new PhylogenyNode( "X" ) );
7126 // query_nodes.add( new PhylogenyNode( "Y" ) );
7127 // query_nodes.add( new PhylogenyNode( "A" ) );
7128 // query_nodes.add( new PhylogenyNode( "B" ) );
7129 // query_nodes.add( new PhylogenyNode( "C" ) );
7130 // query_nodes.add( new PhylogenyNode( "D" ) );
7131 // if ( !s0.match( query_nodes ) ) {
7135 // query_nodes = new HashSet<PhylogenyNode>();
7136 // query_nodes.add( new PhylogenyNode( "X" ) );
7137 // query_nodes.add( new PhylogenyNode( "Y" ) );
7138 // query_nodes.add( new PhylogenyNode( "E" ) );
7139 // query_nodes.add( new PhylogenyNode( "F" ) );
7140 // query_nodes.add( new PhylogenyNode( "G" ) );
7141 // if ( !s0.match( query_nodes ) ) {
7145 // query_nodes = new HashSet<PhylogenyNode>();
7146 // query_nodes.add( new PhylogenyNode( "X" ) );
7147 // query_nodes.add( new PhylogenyNode( "Y" ) );
7148 // query_nodes.add( new PhylogenyNode( "F" ) );
7149 // query_nodes.add( new PhylogenyNode( "G" ) );
7150 // if ( !s0.match( query_nodes ) ) {
7154 query_nodes = new HashSet<PhylogenyNode>();
7155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7158 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7159 if ( s0.match( query_nodes ) ) {
7163 query_nodes = new HashSet<PhylogenyNode>();
7164 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7165 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7166 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7167 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7168 if ( s0.match( query_nodes ) ) {
7171 ///////////////////////////
7173 query_nodes = new HashSet<PhylogenyNode>();
7174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7177 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7178 if ( s0.match( query_nodes ) ) {
7182 query_nodes = new HashSet<PhylogenyNode>();
7183 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7184 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7185 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7186 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7187 if ( s0.match( query_nodes ) ) {
7191 query_nodes = new HashSet<PhylogenyNode>();
7192 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7196 if ( s0.match( query_nodes ) ) {
7200 query_nodes = new HashSet<PhylogenyNode>();
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7203 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7205 if ( s0.match( query_nodes ) ) {
7209 query_nodes = new HashSet<PhylogenyNode>();
7210 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7211 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7212 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7213 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7214 if ( s0.match( query_nodes ) ) {
7218 query_nodes = new HashSet<PhylogenyNode>();
7219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7222 if ( s0.match( query_nodes ) ) {
7226 query_nodes = new HashSet<PhylogenyNode>();
7227 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7230 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7232 if ( s0.match( query_nodes ) ) {
7236 query_nodes = new HashSet<PhylogenyNode>();
7237 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7238 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7239 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7240 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7241 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7242 if ( s0.match( query_nodes ) ) {
7246 query_nodes = new HashSet<PhylogenyNode>();
7247 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7248 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7249 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7250 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7251 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7252 if ( s0.match( query_nodes ) ) {
7256 query_nodes = new HashSet<PhylogenyNode>();
7257 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7258 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7259 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7260 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7261 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7263 if ( s0.match( query_nodes ) ) {
7267 catch ( final Exception e ) {
7268 e.printStackTrace();
7274 private static boolean testSplitStrict() {
7276 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7277 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7278 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7279 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7280 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7281 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7282 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7283 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7284 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7285 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7286 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7287 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7288 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7289 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7290 if ( s0.match( query_nodes ) ) {
7293 query_nodes = new HashSet<PhylogenyNode>();
7294 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7295 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7297 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7298 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7299 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7300 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7301 if ( !s0.match( query_nodes ) ) {
7305 query_nodes = new HashSet<PhylogenyNode>();
7306 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7307 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7308 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7309 if ( !s0.match( query_nodes ) ) {
7313 query_nodes = new HashSet<PhylogenyNode>();
7314 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7315 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7316 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7317 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7318 if ( !s0.match( query_nodes ) ) {
7322 query_nodes = new HashSet<PhylogenyNode>();
7323 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7324 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7325 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7326 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7327 if ( !s0.match( query_nodes ) ) {
7331 query_nodes = new HashSet<PhylogenyNode>();
7332 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7333 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7334 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7335 if ( !s0.match( query_nodes ) ) {
7339 query_nodes = new HashSet<PhylogenyNode>();
7340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7342 if ( !s0.match( query_nodes ) ) {
7346 query_nodes = new HashSet<PhylogenyNode>();
7347 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7350 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7351 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7352 if ( !s0.match( query_nodes ) ) {
7356 query_nodes = new HashSet<PhylogenyNode>();
7357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7359 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7360 if ( !s0.match( query_nodes ) ) {
7364 query_nodes = new HashSet<PhylogenyNode>();
7365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7366 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7367 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7368 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7369 if ( !s0.match( query_nodes ) ) {
7373 query_nodes = new HashSet<PhylogenyNode>();
7374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7375 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7376 if ( s0.match( query_nodes ) ) {
7380 query_nodes = new HashSet<PhylogenyNode>();
7381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7383 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7384 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7385 if ( s0.match( query_nodes ) ) {
7389 query_nodes = new HashSet<PhylogenyNode>();
7390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7391 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7393 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7394 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7395 if ( s0.match( query_nodes ) ) {
7399 query_nodes = new HashSet<PhylogenyNode>();
7400 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7401 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7402 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7403 if ( s0.match( query_nodes ) ) {
7407 query_nodes = new HashSet<PhylogenyNode>();
7408 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7409 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7410 if ( s0.match( query_nodes ) ) {
7414 query_nodes = new HashSet<PhylogenyNode>();
7415 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7416 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7417 if ( s0.match( query_nodes ) ) {
7421 query_nodes = new HashSet<PhylogenyNode>();
7422 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7423 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7424 if ( s0.match( query_nodes ) ) {
7428 query_nodes = new HashSet<PhylogenyNode>();
7429 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7430 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7431 if ( s0.match( query_nodes ) ) {
7435 query_nodes = new HashSet<PhylogenyNode>();
7436 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7437 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7438 if ( s0.match( query_nodes ) ) {
7442 query_nodes = new HashSet<PhylogenyNode>();
7443 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7444 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7445 if ( s0.match( query_nodes ) ) {
7449 query_nodes = new HashSet<PhylogenyNode>();
7450 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7451 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7452 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7453 if ( s0.match( query_nodes ) ) {
7457 query_nodes = new HashSet<PhylogenyNode>();
7458 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7459 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7460 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7461 if ( s0.match( query_nodes ) ) {
7465 query_nodes = new HashSet<PhylogenyNode>();
7466 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7467 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7468 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7469 if ( s0.match( query_nodes ) ) {
7473 query_nodes = new HashSet<PhylogenyNode>();
7474 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7475 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7476 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7477 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7478 if ( s0.match( query_nodes ) ) {
7482 catch ( final Exception e ) {
7483 e.printStackTrace();
7489 private static boolean testSubtreeDeletion() {
7491 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7492 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7493 t1.deleteSubtree( t1.getNode( "A" ), false );
7494 if ( t1.getNumberOfExternalNodes() != 5 ) {
7497 t1.toNewHampshireX();
7498 t1.deleteSubtree( t1.getNode( "E" ), false );
7499 if ( t1.getNumberOfExternalNodes() != 4 ) {
7502 t1.toNewHampshireX();
7503 t1.deleteSubtree( t1.getNode( "F" ), false );
7504 if ( t1.getNumberOfExternalNodes() != 3 ) {
7507 t1.toNewHampshireX();
7508 t1.deleteSubtree( t1.getNode( "D" ), false );
7509 t1.toNewHampshireX();
7510 if ( t1.getNumberOfExternalNodes() != 3 ) {
7513 t1.deleteSubtree( t1.getNode( "def" ), false );
7514 t1.toNewHampshireX();
7515 if ( t1.getNumberOfExternalNodes() != 2 ) {
7518 t1.deleteSubtree( t1.getNode( "B" ), false );
7519 t1.toNewHampshireX();
7520 if ( t1.getNumberOfExternalNodes() != 1 ) {
7523 t1.deleteSubtree( t1.getNode( "C" ), false );
7524 t1.toNewHampshireX();
7525 if ( t1.getNumberOfExternalNodes() != 1 ) {
7528 t1.deleteSubtree( t1.getNode( "abc" ), false );
7529 t1.toNewHampshireX();
7530 if ( t1.getNumberOfExternalNodes() != 1 ) {
7533 t1.deleteSubtree( t1.getNode( "r" ), false );
7534 if ( t1.getNumberOfExternalNodes() != 0 ) {
7537 if ( !t1.isEmpty() ) {
7540 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7541 t2.deleteSubtree( t2.getNode( "A" ), false );
7542 t2.toNewHampshireX();
7543 if ( t2.getNumberOfExternalNodes() != 5 ) {
7546 t2.deleteSubtree( t2.getNode( "abc" ), false );
7547 t2.toNewHampshireX();
7548 if ( t2.getNumberOfExternalNodes() != 3 ) {
7551 t2.deleteSubtree( t2.getNode( "def" ), false );
7552 t2.toNewHampshireX();
7553 if ( t2.getNumberOfExternalNodes() != 1 ) {
7557 catch ( final Exception e ) {
7558 e.printStackTrace( System.out );
7564 private static boolean testSupportCount() {
7566 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7567 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7568 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7569 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7570 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7571 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7572 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7574 SupportCount.count( t0_1, phylogenies_1, true, false );
7575 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7576 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7577 + "(((((A,B),C),D),E),((F,G),X))"
7578 + "(((((A,Y),B),C),D),((F,G),E))"
7579 + "(((((A,B),C),D),E),(F,G))"
7580 + "(((((A,B),C),D),E),(F,G))"
7581 + "(((((A,B),C),D),E),(F,G))"
7582 + "(((((A,B),C),D),E),(F,G),Z)"
7583 + "(((((A,B),C),D),E),(F,G))"
7584 + "((((((A,B),C),D),E),F),G)"
7585 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7587 SupportCount.count( t0_2, phylogenies_2, true, false );
7588 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7589 while ( it.hasNext() ) {
7590 final PhylogenyNode n = it.next();
7591 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7595 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7596 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7597 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7598 SupportCount.count( t0_3, phylogenies_3, true, false );
7599 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7600 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7603 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7606 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7609 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7612 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7615 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7618 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7621 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7624 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7627 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7630 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7631 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7632 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7633 SupportCount.count( t0_4, phylogenies_4, true, false );
7634 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7635 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7638 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7641 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7644 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7647 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7650 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7653 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7656 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7659 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7662 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7665 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7666 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7667 double d = SupportCount.compare( b1, a, true, true, true );
7668 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7671 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7672 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7673 d = SupportCount.compare( b2, a, true, true, true );
7674 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7677 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7678 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7679 d = SupportCount.compare( b3, a, true, true, true );
7680 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7683 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7684 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7685 d = SupportCount.compare( b4, a, true, true, false );
7686 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7690 catch ( final Exception e ) {
7691 e.printStackTrace( System.out );
7697 private static boolean testSupportTransfer() {
7699 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7700 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)",
7701 new NHXParser() )[ 0 ];
7702 final Phylogeny p2 = factory
7703 .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 ];
7704 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7707 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7710 support_transfer.moveBranchLengthsToBootstrap( p1 );
7711 support_transfer.transferSupportValues( p1, p2 );
7712 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7715 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7718 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7721 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7724 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7727 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7730 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7733 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7737 catch ( final Exception e ) {
7738 e.printStackTrace( System.out );
7744 private static boolean testUniprotTaxonomySearch() {
7746 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
7748 if ( results.size() != 1 ) {
7751 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7754 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7757 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7760 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7763 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7767 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7768 if ( results.size() != 1 ) {
7771 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7774 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7777 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7780 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7783 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7787 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
7788 if ( results.size() != 1 ) {
7791 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7794 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7797 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7800 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7803 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7807 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7808 if ( results.size() != 1 ) {
7811 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7814 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7817 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7820 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7823 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7826 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7829 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7832 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7833 .equals( "Nematostella vectensis" ) ) {
7834 System.out.println( results.get( 0 ).getLineage() );
7838 catch ( final IOException e ) {
7839 System.out.println();
7840 System.out.println( "the following might be due to absence internet connection:" );
7841 e.printStackTrace( System.out );
7844 catch ( final Exception e ) {
7850 private static boolean testEmblEntryRetrieval() {
7851 //The format for GenBank Accession numbers are:
7852 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7853 //Protein: 3 letters + 5 numerals
7854 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7855 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7858 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7861 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
7864 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
7867 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
7870 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
7873 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7876 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7879 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
7882 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
7885 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7888 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7891 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
7897 private static boolean testUniprotEntryRetrieval() {
7898 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7901 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7904 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7907 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7910 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7913 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7916 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7919 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7922 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7925 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7928 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7931 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7934 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7938 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
7939 if ( !entry.getAccession().equals( "P12345" ) ) {
7942 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7945 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7948 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7951 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7955 catch ( final IOException e ) {
7956 System.out.println();
7957 System.out.println( "the following might be due to absence internet connection:" );
7958 e.printStackTrace( System.out );
7961 catch ( final Exception e ) {
7967 private static boolean testWabiTxSearch() {
7970 result = TxSearch.searchSimple( "nematostella" );
7971 result = TxSearch.getTxId( "nematostella" );
7972 if ( !result.equals( "45350" ) ) {
7975 result = TxSearch.getTxName( "45350" );
7976 if ( !result.equals( "Nematostella" ) ) {
7979 result = TxSearch.getTxId( "nematostella vectensis" );
7980 if ( !result.equals( "45351" ) ) {
7983 result = TxSearch.getTxName( "45351" );
7984 if ( !result.equals( "Nematostella vectensis" ) ) {
7987 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7988 if ( !result.equals( "536089" ) ) {
7991 result = TxSearch.getTxName( "536089" );
7992 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7995 final List<String> queries = new ArrayList<String>();
7996 queries.add( "Campylobacter coli" );
7997 queries.add( "Escherichia coli" );
7998 queries.add( "Arabidopsis" );
7999 queries.add( "Trichoplax" );
8000 queries.add( "Samanea saman" );
8001 queries.add( "Kluyveromyces marxianus" );
8002 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8003 queries.add( "Bornavirus parrot/PDD/2008" );
8004 final List<RANKS> ranks = new ArrayList<RANKS>();
8005 ranks.add( RANKS.SUPERKINGDOM );
8006 ranks.add( RANKS.KINGDOM );
8007 ranks.add( RANKS.FAMILY );
8008 ranks.add( RANKS.GENUS );
8009 ranks.add( RANKS.TRIBE );
8010 result = TxSearch.searchLineage( queries, ranks );
8011 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8012 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8014 catch ( final Exception e ) {
8015 System.out.println();
8016 System.out.println( "the following might be due to absence internet connection:" );
8017 e.printStackTrace( System.out );
8023 private static boolean testAminoAcidSequence() {
8025 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8026 if ( aa1.getLength() != 13 ) {
8029 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8032 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8035 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8038 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8039 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8042 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8043 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8046 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8047 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8051 catch ( final Exception e ) {
8052 e.printStackTrace();
8058 private static boolean testCreateBalancedPhylogeny() {
8060 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8061 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8064 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8067 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8068 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8071 if ( p1.getNumberOfExternalNodes() != 100 ) {
8075 catch ( final Exception e ) {
8076 e.printStackTrace();
8082 private static boolean testFastaParser() {
8084 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8087 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8090 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8091 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8094 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8097 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8100 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8103 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8106 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8110 catch ( final Exception e ) {
8111 e.printStackTrace();
8117 private static boolean testGeneralMsaParser() {
8119 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8120 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8121 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8122 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8123 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8124 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8125 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8126 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8127 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8130 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8133 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8136 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8139 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8142 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8145 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8148 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8151 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8154 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8157 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8160 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8163 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8164 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8167 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8170 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8173 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8174 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8177 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8180 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8183 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8184 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8187 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8190 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8194 catch ( final Exception e ) {
8195 e.printStackTrace();
8201 private static boolean testMafft( final String path ) {
8203 final List<String> opts = new ArrayList<String>();
8204 opts.add( "--maxiterate" );
8206 opts.add( "--localpair" );
8207 opts.add( "--quiet" );
8209 final MsaInferrer mafft = Mafft.createInstance( path );
8210 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8211 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8214 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8218 catch ( final Exception e ) {
8219 e.printStackTrace( System.out );
8225 private static boolean testNextNodeWithCollapsing() {
8227 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8229 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8230 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8231 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8232 t0.getNode( "cd" ).setCollapse( true );
8233 t0.getNode( "cde" ).setCollapse( true );
8234 n = t0.getFirstExternalNode();
8235 while ( n != null ) {
8237 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8239 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8242 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8245 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8248 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8251 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8254 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8258 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8259 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8260 t1.getNode( "ab" ).setCollapse( true );
8261 t1.getNode( "cd" ).setCollapse( true );
8262 t1.getNode( "cde" ).setCollapse( true );
8263 n = t1.getNode( "ab" );
8264 ext = new ArrayList<PhylogenyNode>();
8265 while ( n != null ) {
8267 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8269 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8272 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8275 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8278 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8281 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8287 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8288 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8289 t2.getNode( "ab" ).setCollapse( true );
8290 t2.getNode( "cd" ).setCollapse( true );
8291 t2.getNode( "cde" ).setCollapse( true );
8292 t2.getNode( "c" ).setCollapse( true );
8293 t2.getNode( "d" ).setCollapse( true );
8294 t2.getNode( "e" ).setCollapse( true );
8295 t2.getNode( "gh" ).setCollapse( true );
8296 n = t2.getNode( "ab" );
8297 ext = new ArrayList<PhylogenyNode>();
8298 while ( n != null ) {
8300 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8302 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8305 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8308 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8311 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8317 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8318 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8319 t3.getNode( "ab" ).setCollapse( true );
8320 t3.getNode( "cd" ).setCollapse( true );
8321 t3.getNode( "cde" ).setCollapse( true );
8322 t3.getNode( "c" ).setCollapse( true );
8323 t3.getNode( "d" ).setCollapse( true );
8324 t3.getNode( "e" ).setCollapse( true );
8325 t3.getNode( "gh" ).setCollapse( true );
8326 t3.getNode( "fgh" ).setCollapse( true );
8327 n = t3.getNode( "ab" );
8328 ext = new ArrayList<PhylogenyNode>();
8329 while ( n != null ) {
8331 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8333 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8336 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8339 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8345 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8346 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8347 t4.getNode( "ab" ).setCollapse( true );
8348 t4.getNode( "cd" ).setCollapse( true );
8349 t4.getNode( "cde" ).setCollapse( true );
8350 t4.getNode( "c" ).setCollapse( true );
8351 t4.getNode( "d" ).setCollapse( true );
8352 t4.getNode( "e" ).setCollapse( true );
8353 t4.getNode( "gh" ).setCollapse( true );
8354 t4.getNode( "fgh" ).setCollapse( true );
8355 t4.getNode( "abcdefgh" ).setCollapse( true );
8356 n = t4.getNode( "abcdefgh" );
8357 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8362 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8363 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8365 n = t5.getFirstExternalNode();
8366 while ( n != null ) {
8368 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8370 if ( ext.size() != 8 ) {
8373 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8376 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8379 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8382 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8385 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8388 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8391 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8394 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8399 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8400 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8402 t6.getNode( "ab" ).setCollapse( true );
8403 n = t6.getNode( "ab" );
8404 while ( n != null ) {
8406 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8408 if ( ext.size() != 7 ) {
8411 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8414 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8417 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8420 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8423 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8426 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8429 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8434 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8435 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8437 t7.getNode( "cd" ).setCollapse( true );
8438 n = t7.getNode( "a" );
8439 while ( n != null ) {
8441 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8443 if ( ext.size() != 7 ) {
8446 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8449 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8452 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8455 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8458 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8461 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8464 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8469 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8470 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8472 t8.getNode( "cd" ).setCollapse( true );
8473 t8.getNode( "c" ).setCollapse( true );
8474 t8.getNode( "d" ).setCollapse( true );
8475 n = t8.getNode( "a" );
8476 while ( n != null ) {
8478 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8480 if ( ext.size() != 7 ) {
8483 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8486 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8489 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8490 System.out.println( "2 fail" );
8493 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8496 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8499 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8502 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8507 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8508 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8510 t9.getNode( "gh" ).setCollapse( true );
8511 n = t9.getNode( "a" );
8512 while ( n != null ) {
8514 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8516 if ( ext.size() != 7 ) {
8519 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8522 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8525 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8528 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8531 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8534 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8537 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8542 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8543 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8545 t10.getNode( "gh" ).setCollapse( true );
8546 t10.getNode( "g" ).setCollapse( true );
8547 t10.getNode( "h" ).setCollapse( true );
8548 n = t10.getNode( "a" );
8549 while ( n != null ) {
8551 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8553 if ( ext.size() != 7 ) {
8556 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8559 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8562 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8565 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8568 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8571 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8574 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8579 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8580 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8582 t11.getNode( "gh" ).setCollapse( true );
8583 t11.getNode( "fgh" ).setCollapse( true );
8584 n = t11.getNode( "a" );
8585 while ( n != null ) {
8587 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8589 if ( ext.size() != 6 ) {
8592 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8595 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8598 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8601 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8604 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8607 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8612 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8613 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8615 t12.getNode( "gh" ).setCollapse( true );
8616 t12.getNode( "fgh" ).setCollapse( true );
8617 t12.getNode( "g" ).setCollapse( true );
8618 t12.getNode( "h" ).setCollapse( true );
8619 t12.getNode( "f" ).setCollapse( true );
8620 n = t12.getNode( "a" );
8621 while ( n != null ) {
8623 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8625 if ( ext.size() != 6 ) {
8628 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8631 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8634 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8637 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8640 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8643 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8648 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8649 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8651 t13.getNode( "ab" ).setCollapse( true );
8652 t13.getNode( "b" ).setCollapse( true );
8653 t13.getNode( "fgh" ).setCollapse( true );
8654 t13.getNode( "gh" ).setCollapse( true );
8655 n = t13.getNode( "ab" );
8656 while ( n != null ) {
8658 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8660 if ( ext.size() != 5 ) {
8663 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8666 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8669 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8672 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8675 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8680 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8681 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8683 t14.getNode( "ab" ).setCollapse( true );
8684 t14.getNode( "a" ).setCollapse( true );
8685 t14.getNode( "fgh" ).setCollapse( true );
8686 t14.getNode( "gh" ).setCollapse( true );
8687 n = t14.getNode( "ab" );
8688 while ( n != null ) {
8690 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8692 if ( ext.size() != 5 ) {
8695 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8698 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8701 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8704 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8707 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8712 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" );
8713 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8715 t15.getNode( "ab" ).setCollapse( true );
8716 t15.getNode( "a" ).setCollapse( true );
8717 t15.getNode( "fgh" ).setCollapse( true );
8718 t15.getNode( "gh" ).setCollapse( true );
8719 n = t15.getNode( "ab" );
8720 while ( n != null ) {
8722 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8724 if ( ext.size() != 6 ) {
8727 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8730 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8733 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8736 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8739 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8742 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8747 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" );
8748 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8750 t16.getNode( "ab" ).setCollapse( true );
8751 t16.getNode( "a" ).setCollapse( true );
8752 t16.getNode( "fgh" ).setCollapse( true );
8753 t16.getNode( "gh" ).setCollapse( true );
8754 t16.getNode( "cd" ).setCollapse( true );
8755 t16.getNode( "cde" ).setCollapse( true );
8756 t16.getNode( "d" ).setCollapse( true );
8757 t16.getNode( "x" ).setCollapse( true );
8758 n = t16.getNode( "ab" );
8759 while ( n != null ) {
8761 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8763 if ( ext.size() != 4 ) {
8766 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8769 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8772 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8775 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8779 catch ( final Exception e ) {
8780 e.printStackTrace( System.out );
8786 private static boolean testMsaQualityMethod() {
8788 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
8789 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
8790 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
8791 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
8792 final List<Sequence> l = new ArrayList<Sequence>();
8797 final Msa msa = BasicMsa.createInstance( l );
8798 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
8801 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
8804 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
8807 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
8811 catch ( final Exception e ) {
8812 e.printStackTrace( System.out );
8818 private static boolean testSequenceIdParsing() {
8820 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
8821 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8822 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8824 System.out.println( "value =" + id.getValue() );
8825 System.out.println( "provider=" + id.getProvider() );
8830 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
8831 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8832 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8834 System.out.println( "value =" + id.getValue() );
8835 System.out.println( "provider=" + id.getProvider() );
8840 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
8841 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8842 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
8844 System.out.println( "value =" + id.getValue() );
8845 System.out.println( "provider=" + id.getProvider() );
8850 id = SequenceIdParser.parse( "gb_AAA96518_1" );
8851 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8852 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
8854 System.out.println( "value =" + id.getValue() );
8855 System.out.println( "provider=" + id.getProvider() );
8860 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
8861 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8862 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
8864 System.out.println( "value =" + id.getValue() );
8865 System.out.println( "provider=" + id.getProvider() );
8870 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
8871 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8872 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
8874 System.out.println( "value =" + id.getValue() );
8875 System.out.println( "provider=" + id.getProvider() );
8880 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
8881 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8882 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
8884 System.out.println( "value =" + id.getValue() );
8885 System.out.println( "provider=" + id.getProvider() );
8890 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
8891 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8892 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8894 System.out.println( "value =" + id.getValue() );
8895 System.out.println( "provider=" + id.getProvider() );
8900 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
8901 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8902 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
8904 System.out.println( "value =" + id.getValue() );
8905 System.out.println( "provider=" + id.getProvider() );
8910 id = SequenceIdParser.parse( "P4A123" );
8911 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8912 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8914 System.out.println( "value =" + id.getValue() );
8915 System.out.println( "provider=" + id.getProvider() );
8920 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
8921 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
8922 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
8924 System.out.println( "value =" + id.getValue() );
8925 System.out.println( "provider=" + id.getProvider() );
8930 id = SequenceIdParser.parse( "XP_12345" );
8932 System.out.println( "value =" + id.getValue() );
8933 System.out.println( "provider=" + id.getProvider() );
8936 // lcl_91970_unknown_
8938 catch ( final Exception e ) {
8939 e.printStackTrace( System.out );