2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.nhx.NHXParser2;
56 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
57 import org.forester.io.parsers.tol.TolParser;
58 import org.forester.io.parsers.util.ParserUtils;
59 import org.forester.io.writers.PhylogenyWriter;
60 import org.forester.msa.BasicMsa;
61 import org.forester.msa.Mafft;
62 import org.forester.msa.Msa;
63 import org.forester.msa.MsaInferrer;
64 import org.forester.msa.MsaMethods;
65 import org.forester.pccx.TestPccx;
66 import org.forester.phylogeny.Phylogeny;
67 import org.forester.phylogeny.PhylogenyBranch;
68 import org.forester.phylogeny.PhylogenyMethods;
69 import org.forester.phylogeny.PhylogenyNode;
70 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
71 import org.forester.phylogeny.data.BinaryCharacters;
72 import org.forester.phylogeny.data.BranchWidth;
73 import org.forester.phylogeny.data.Confidence;
74 import org.forester.phylogeny.data.Distribution;
75 import org.forester.phylogeny.data.DomainArchitecture;
76 import org.forester.phylogeny.data.Event;
77 import org.forester.phylogeny.data.Identifier;
78 import org.forester.phylogeny.data.PhylogenyData;
79 import org.forester.phylogeny.data.PhylogenyDataUtil;
80 import org.forester.phylogeny.data.Polygon;
81 import org.forester.phylogeny.data.PropertiesMap;
82 import org.forester.phylogeny.data.Property;
83 import org.forester.phylogeny.data.Property.AppliesTo;
84 import org.forester.phylogeny.data.ProteinDomain;
85 import org.forester.phylogeny.data.Taxonomy;
86 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
87 import org.forester.phylogeny.factories.PhylogenyFactory;
88 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
89 import org.forester.protein.Protein;
90 import org.forester.rio.TestRIO;
91 import org.forester.sdi.SDI;
92 import org.forester.sdi.SDIR;
93 import org.forester.sdi.TestGSDI;
94 import org.forester.sequence.BasicSequence;
95 import org.forester.sequence.Sequence;
96 import org.forester.surfacing.TestSurfacing;
97 import org.forester.tools.ConfidenceAssessor;
98 import org.forester.tools.SupportCount;
99 import org.forester.tools.TreeSplitMatrix;
100 import org.forester.util.AsciiHistogram;
101 import org.forester.util.BasicDescriptiveStatistics;
102 import org.forester.util.BasicTable;
103 import org.forester.util.BasicTableParser;
104 import org.forester.util.DescriptiveStatistics;
105 import org.forester.util.ForesterConstants;
106 import org.forester.util.ForesterUtil;
107 import org.forester.util.GeneralTable;
108 import org.forester.util.SequenceIdParser;
109 import org.forester.ws.seqdb.SequenceDatabaseEntry;
110 import org.forester.ws.seqdb.SequenceDbWsTools;
111 import org.forester.ws.seqdb.UniProtTaxonomy;
112 import org.forester.ws.wabi.TxSearch;
113 import org.forester.ws.wabi.TxSearch.RANKS;
114 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
115 import org.forester.ws.wabi.TxSearch.TAX_RANK;
117 @SuppressWarnings( "unused")
118 public final class Test {
120 private final static double ZERO_DIFF = 1.0E-9;
121 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
122 + ForesterUtil.getFileSeparator() + "test_data"
123 + ForesterUtil.getFileSeparator();
124 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
125 + ForesterUtil.getFileSeparator() + "resources"
126 + ForesterUtil.getFileSeparator();
127 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
128 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
129 + ForesterConstants.PHYLO_XML_VERSION + "/"
130 + ForesterConstants.PHYLO_XML_XSD;
131 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
132 + ForesterConstants.PHYLO_XML_VERSION + "/"
133 + ForesterConstants.PHYLO_XML_XSD;
135 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
136 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
140 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
141 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
144 public static boolean isEqual( final double a, final double b ) {
145 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
148 public static void main( final String[] args ) {
149 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
150 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
152 Locale.setDefault( Locale.US );
153 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
156 System.out.print( "[Test if directory with files for testing exists/is readable: " );
157 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
158 System.out.println( "OK.]" );
161 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
162 System.out.println( "Testing aborted." );
165 System.out.print( "[Test if resources directory exists/is readable: " );
166 if ( testDir( PATH_TO_RESOURCES ) ) {
167 System.out.println( "OK.]" );
170 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
171 System.out.println( "Testing aborted." );
174 final long start_time = new Date().getTime();
175 System.out.print( "Sequence id parsing: " );
176 if ( testSequenceIdParsing() ) {
177 System.out.println( "OK." );
181 System.out.println( "failed." );
184 System.out.print( "Hmmscan output parser: " );
185 if ( testHmmscanOutputParser() ) {
186 System.out.println( "OK." );
190 System.out.println( "failed." );
193 System.out.print( "Basic node methods: " );
194 if ( Test.testBasicNodeMethods() ) {
195 System.out.println( "OK." );
199 System.out.println( "failed." );
202 System.out.print( "Taxonomy code extraction: " );
203 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
204 System.out.println( "OK." );
208 System.out.println( "failed." );
211 System.out.print( "Taxonomy extraction (general): " );
212 if ( Test.testTaxonomyExtraction() ) {
213 System.out.println( "OK." );
217 System.out.println( "failed." );
220 System.out.print( "Basic node construction and parsing of NHX (node level): " );
221 if ( Test.testNHXNodeParsing() ) {
222 System.out.println( "OK." );
226 System.out.println( "failed." );
229 System.out.print( "NH parsing: " );
230 if ( Test.testNHParsing() ) {
231 System.out.println( "OK." );
235 System.out.println( "failed." );
238 System.out.print( "Conversion to NHX (node level): " );
239 if ( Test.testNHXconversion() ) {
240 System.out.println( "OK." );
244 System.out.println( "failed." );
247 System.out.print( "NHX parsing: " );
248 if ( Test.testNHXParsing() ) {
249 System.out.println( "OK." );
253 System.out.println( "failed." );
256 System.out.print( "NHX parsing with quotes: " );
257 if ( Test.testNHXParsingQuotes() ) {
258 System.out.println( "OK." );
262 System.out.println( "failed." );
265 System.out.print( "NHX parsing (MrBayes): " );
266 if ( Test.testNHXParsingMB() ) {
267 System.out.println( "OK." );
271 System.out.println( "failed." );
274 System.out.print( "NHX parsing iterating: " );
275 if ( Test.testNHParsingIter() ) {
276 System.out.println( "OK." );
280 System.out.println( "failed." );
284 System.out.print( "Nexus characters parsing: " );
285 if ( Test.testNexusCharactersParsing() ) {
286 System.out.println( "OK." );
290 System.out.println( "failed." );
293 System.out.print( "Nexus tree parsing: " );
294 if ( Test.testNexusTreeParsing() ) {
295 System.out.println( "OK." );
299 System.out.println( "failed." );
302 System.out.print( "Nexus tree parsing (translating): " );
303 if ( Test.testNexusTreeParsingTranslating() ) {
304 System.out.println( "OK." );
308 System.out.println( "failed." );
311 System.out.print( "Nexus matrix parsing: " );
312 if ( Test.testNexusMatrixParsing() ) {
313 System.out.println( "OK." );
317 System.out.println( "failed." );
320 System.out.print( "Basic phyloXML parsing: " );
321 if ( Test.testBasicPhyloXMLparsing() ) {
322 System.out.println( "OK." );
326 System.out.println( "failed." );
329 System.out.print( "Basic phyloXML parsing (validating against schema): " );
330 if ( testBasicPhyloXMLparsingValidating() ) {
331 System.out.println( "OK." );
335 System.out.println( "failed." );
338 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
339 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
340 System.out.println( "OK." );
344 System.out.println( "failed." );
347 System.out.print( "phyloXML Distribution Element: " );
348 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
349 System.out.println( "OK." );
353 System.out.println( "failed." );
356 System.out.print( "Tol XML parsing: " );
357 if ( Test.testBasicTolXMLparsing() ) {
358 System.out.println( "OK." );
362 System.out.println( "failed." );
365 System.out.print( "Copying of node data: " );
366 if ( Test.testCopyOfNodeData() ) {
367 System.out.println( "OK." );
371 System.out.println( "failed." );
374 System.out.print( "Basic tree methods: " );
375 if ( Test.testBasicTreeMethods() ) {
376 System.out.println( "OK." );
380 System.out.println( "failed." );
383 System.out.print( "Postorder Iterator: " );
384 if ( Test.testPostOrderIterator() ) {
385 System.out.println( "OK." );
389 System.out.println( "failed." );
392 System.out.print( "Preorder Iterator: " );
393 if ( Test.testPreOrderIterator() ) {
394 System.out.println( "OK." );
398 System.out.println( "failed." );
401 System.out.print( "Levelorder Iterator: " );
402 if ( Test.testLevelOrderIterator() ) {
403 System.out.println( "OK." );
407 System.out.println( "failed." );
410 System.out.print( "Re-id methods: " );
411 if ( Test.testReIdMethods() ) {
412 System.out.println( "OK." );
416 System.out.println( "failed." );
419 System.out.print( "Methods on last external nodes: " );
420 if ( Test.testLastExternalNodeMethods() ) {
421 System.out.println( "OK." );
425 System.out.println( "failed." );
428 System.out.print( "Methods on external nodes: " );
429 if ( Test.testExternalNodeRelatedMethods() ) {
430 System.out.println( "OK." );
434 System.out.println( "failed." );
437 System.out.print( "Deletion of external nodes: " );
438 if ( Test.testDeletionOfExternalNodes() ) {
439 System.out.println( "OK." );
443 System.out.println( "failed." );
446 System.out.print( "Subtree deletion: " );
447 if ( Test.testSubtreeDeletion() ) {
448 System.out.println( "OK." );
452 System.out.println( "failed." );
455 System.out.print( "Phylogeny branch: " );
456 if ( Test.testPhylogenyBranch() ) {
457 System.out.println( "OK." );
461 System.out.println( "failed." );
464 System.out.print( "Rerooting: " );
465 if ( Test.testRerooting() ) {
466 System.out.println( "OK." );
470 System.out.println( "failed." );
473 System.out.print( "Mipoint rooting: " );
474 if ( Test.testMidpointrooting() ) {
475 System.out.println( "OK." );
479 System.out.println( "failed." );
482 System.out.print( "Node removal: " );
483 if ( Test.testNodeRemoval() ) {
484 System.out.println( "OK." );
488 System.out.println( "failed." );
491 System.out.print( "Support count: " );
492 if ( Test.testSupportCount() ) {
493 System.out.println( "OK." );
497 System.out.println( "failed." );
500 System.out.print( "Support transfer: " );
501 if ( Test.testSupportTransfer() ) {
502 System.out.println( "OK." );
506 System.out.println( "failed." );
509 System.out.print( "Finding of LCA: " );
510 if ( Test.testGetLCA() ) {
511 System.out.println( "OK." );
515 System.out.println( "failed." );
518 System.out.print( "Finding of LCA 2: " );
519 if ( Test.testGetLCA2() ) {
520 System.out.println( "OK." );
524 System.out.println( "failed." );
527 System.out.print( "Calculation of distance between nodes: " );
528 if ( Test.testGetDistance() ) {
529 System.out.println( "OK." );
533 System.out.println( "failed." );
536 System.out.print( "Descriptive statistics: " );
537 if ( Test.testDescriptiveStatistics() ) {
538 System.out.println( "OK." );
542 System.out.println( "failed." );
545 System.out.print( "Data objects and methods: " );
546 if ( Test.testDataObjects() ) {
547 System.out.println( "OK." );
551 System.out.println( "failed." );
554 System.out.print( "Properties map: " );
555 if ( Test.testPropertiesMap() ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "SDIse: " );
564 if ( Test.testSDIse() ) {
565 System.out.println( "OK." );
569 System.out.println( "failed." );
572 System.out.print( "SDIunrooted: " );
573 if ( Test.testSDIunrooted() ) {
574 System.out.println( "OK." );
578 System.out.println( "failed." );
581 System.out.print( "GSDI: " );
582 if ( TestGSDI.test() ) {
583 System.out.println( "OK." );
587 System.out.println( "failed." );
590 System.out.print( "RIO: " );
591 if ( TestRIO.test() ) {
592 System.out.println( "OK." );
596 System.out.println( "failed." );
599 System.out.print( "Phylogeny reconstruction:" );
600 System.out.println();
601 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
602 System.out.println( "OK." );
606 System.out.println( "failed." );
609 System.out.print( "Analysis of domain architectures: " );
610 System.out.println();
611 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
612 System.out.println( "OK." );
616 System.out.println( "failed." );
619 System.out.print( "GO: " );
620 System.out.println();
621 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
622 System.out.println( "OK." );
626 System.out.println( "failed." );
629 System.out.print( "Modeling tools: " );
630 if ( TestPccx.test() ) {
631 System.out.println( "OK." );
635 System.out.println( "failed." );
638 System.out.print( "Split Matrix strict: " );
639 if ( Test.testSplitStrict() ) {
640 System.out.println( "OK." );
644 System.out.println( "failed." );
647 System.out.print( "Split Matrix: " );
648 if ( Test.testSplit() ) {
649 System.out.println( "OK." );
653 System.out.println( "failed." );
656 System.out.print( "Confidence Assessor: " );
657 if ( Test.testConfidenceAssessor() ) {
658 System.out.println( "OK." );
662 System.out.println( "failed." );
665 System.out.print( "Basic table: " );
666 if ( Test.testBasicTable() ) {
667 System.out.println( "OK." );
671 System.out.println( "failed." );
674 System.out.print( "General table: " );
675 if ( Test.testGeneralTable() ) {
676 System.out.println( "OK." );
680 System.out.println( "failed." );
683 System.out.print( "Amino acid sequence: " );
684 if ( Test.testAminoAcidSequence() ) {
685 System.out.println( "OK." );
689 System.out.println( "failed." );
692 System.out.print( "General MSA parser: " );
693 if ( Test.testGeneralMsaParser() ) {
694 System.out.println( "OK." );
698 System.out.println( "failed." );
701 System.out.print( "Fasta parser for msa: " );
702 if ( Test.testFastaParser() ) {
703 System.out.println( "OK." );
707 System.out.println( "failed." );
710 System.out.print( "Creation of balanced phylogeny: " );
711 if ( Test.testCreateBalancedPhylogeny() ) {
712 System.out.println( "OK." );
716 System.out.println( "failed." );
719 System.out.print( "EMBL Entry Retrieval: " );
720 if ( Test.testEmblEntryRetrieval() ) {
721 System.out.println( "OK." );
725 System.out.println( "failed." );
728 System.out.print( "Uniprot Entry Retrieval: " );
729 if ( Test.testUniprotEntryRetrieval() ) {
730 System.out.println( "OK." );
734 System.out.println( "failed." );
737 System.out.print( "Uniprot Taxonomy Search: " );
738 if ( Test.testUniprotTaxonomySearch() ) {
739 System.out.println( "OK." );
743 System.out.println( "failed." );
748 final String os = ForesterUtil.OS_NAME.toLowerCase();
749 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
750 path = "/usr/local/bin/mafft";
752 else if ( os.indexOf( "win" ) >= 0 ) {
753 path = "C:\\Program Files\\mafft-win\\mafft.bat";
756 path = "/home/czmasek/bin/mafft";
758 if ( !MsaInferrer.isInstalled( path ) ) {
761 if ( !MsaInferrer.isInstalled( path ) ) {
762 path = "/usr/local/bin/mafft";
764 if ( MsaInferrer.isInstalled( path ) ) {
765 System.out.print( "MAFFT (external program): " );
766 if ( Test.testMafft( path ) ) {
767 System.out.println( "OK." );
771 System.out.println( "failed [will not count towards failed tests]" );
775 System.out.print( "Next nodes with collapsed: " );
776 if ( Test.testNextNodeWithCollapsing() ) {
777 System.out.println( "OK." );
781 System.out.println( "failed." );
784 System.out.print( "Simple MSA quality: " );
785 if ( Test.testMsaQualityMethod() ) {
786 System.out.println( "OK." );
790 System.out.println( "failed." );
793 System.out.println();
794 final Runtime rt = java.lang.Runtime.getRuntime();
795 final long free_memory = rt.freeMemory() / 1000000;
796 final long total_memory = rt.totalMemory() / 1000000;
797 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
798 + free_memory + "MB, total memory: " + total_memory + "MB)" );
799 System.out.println();
800 System.out.println( "Successful tests: " + succeeded );
801 System.out.println( "Failed tests: " + failed );
802 System.out.println();
804 System.out.println( "OK." );
807 System.out.println( "Not OK." );
811 private static boolean testExtractTaxonomyCodeFromNodeName() {
813 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
816 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
819 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
822 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
823 .equals( "MOUSE" ) ) {
826 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
827 .equals( "MOUSE" ) ) {
830 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
831 .equals( "MOUSE" ) ) {
834 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
837 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
840 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
844 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
848 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
852 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
855 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
858 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
861 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
865 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
866 .equals( "MOUSE" ) ) {
869 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
870 .equals( "MOUSE" ) ) {
874 catch ( final Exception e ) {
875 e.printStackTrace( System.out );
881 private static boolean testBasicNodeMethods() {
883 if ( PhylogenyNode.getNodeCount() != 0 ) {
886 final PhylogenyNode n1 = new PhylogenyNode();
887 final PhylogenyNode n2 = PhylogenyNode
888 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
889 final PhylogenyNode n3 = PhylogenyNode
890 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
891 final PhylogenyNode n4 = PhylogenyNode
892 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
893 if ( n1.isHasAssignedEvent() ) {
896 if ( PhylogenyNode.getNodeCount() != 4 ) {
899 if ( n3.getIndicator() != 0 ) {
902 if ( n3.getNumberOfExternalNodes() != 1 ) {
905 if ( !n3.isExternal() ) {
908 if ( !n3.isRoot() ) {
911 if ( !n4.getName().equals( "n4" ) ) {
915 catch ( final Exception e ) {
916 e.printStackTrace( System.out );
922 private static boolean testBasicPhyloXMLparsing() {
924 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
925 final PhyloXmlParser xml_parser = new PhyloXmlParser();
926 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
928 if ( xml_parser.getErrorCount() > 0 ) {
929 System.out.println( xml_parser.getErrorMessages().toString() );
932 if ( phylogenies_0.length != 4 ) {
935 final Phylogeny t1 = phylogenies_0[ 0 ];
936 final Phylogeny t2 = phylogenies_0[ 1 ];
937 final Phylogeny t3 = phylogenies_0[ 2 ];
938 final Phylogeny t4 = phylogenies_0[ 3 ];
939 if ( t1.getNumberOfExternalNodes() != 1 ) {
942 if ( !t1.isRooted() ) {
945 if ( t1.isRerootable() ) {
948 if ( !t1.getType().equals( "gene_tree" ) ) {
951 if ( t2.getNumberOfExternalNodes() != 2 ) {
954 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
957 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
960 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
963 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
966 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
969 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
972 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
973 .startsWith( "actgtgggggt" ) ) {
976 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
977 .startsWith( "ctgtgatgcat" ) ) {
980 if ( t3.getNumberOfExternalNodes() != 4 ) {
983 if ( !t1.getName().equals( "t1" ) ) {
986 if ( !t2.getName().equals( "t2" ) ) {
989 if ( !t3.getName().equals( "t3" ) ) {
992 if ( !t4.getName().equals( "t4" ) ) {
995 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
998 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1001 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1004 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1005 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1008 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1011 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1014 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1017 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1018 .equals( "apoptosis" ) ) {
1021 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1022 .equals( "GO:0006915" ) ) {
1025 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1026 .equals( "UniProtKB" ) ) {
1029 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1030 .equals( "experimental" ) ) {
1033 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1034 .equals( "function" ) ) {
1037 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1038 .getValue() != 1 ) {
1041 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1042 .getType().equals( "ml" ) ) {
1045 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1046 .equals( "apoptosis" ) ) {
1049 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1050 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1053 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1054 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1057 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1058 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1061 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1062 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1065 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1066 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1069 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1070 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1073 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1074 .equals( "GO:0005829" ) ) {
1077 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1078 .equals( "intracellular organelle" ) ) {
1081 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1084 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1085 .equals( "UniProt link" ) ) ) {
1088 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1092 catch ( final Exception e ) {
1093 e.printStackTrace( System.out );
1099 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1101 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1102 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1103 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1104 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1107 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1109 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1111 if ( xml_parser.getErrorCount() > 0 ) {
1112 System.out.println( xml_parser.getErrorMessages().toString() );
1115 if ( phylogenies_0.length != 4 ) {
1118 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1119 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1120 if ( phylogenies_t1.length != 1 ) {
1123 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1124 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1127 if ( !t1_rt.isRooted() ) {
1130 if ( t1_rt.isRerootable() ) {
1133 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1136 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1137 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1138 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1139 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1142 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1145 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1148 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1151 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1152 .startsWith( "actgtgggggt" ) ) {
1155 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1156 .startsWith( "ctgtgatgcat" ) ) {
1159 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1160 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1161 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1162 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1163 if ( phylogenies_1.length != 1 ) {
1166 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1167 if ( !t3_rt.getName().equals( "t3" ) ) {
1170 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1173 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1176 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1179 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1182 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1183 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1186 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1189 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1192 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1193 .equals( "UniProtKB" ) ) {
1196 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1197 .equals( "apoptosis" ) ) {
1200 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1201 .equals( "GO:0006915" ) ) {
1204 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1205 .equals( "UniProtKB" ) ) {
1208 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1209 .equals( "experimental" ) ) {
1212 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1213 .equals( "function" ) ) {
1216 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1217 .getValue() != 1 ) {
1220 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1221 .getType().equals( "ml" ) ) {
1224 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1225 .equals( "apoptosis" ) ) {
1228 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1229 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1232 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1233 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1236 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1237 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1240 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1241 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1244 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1245 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1249 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1253 .equals( "GO:0005829" ) ) {
1256 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1257 .equals( "intracellular organelle" ) ) {
1260 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1264 .equals( "UniProt link" ) ) ) {
1267 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1270 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1273 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1274 .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
1277 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1280 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1283 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1286 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1289 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1290 .equals( "ncbi" ) ) {
1293 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1296 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1297 .getName().equals( "B" ) ) {
1300 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1301 .getFrom() != 21 ) {
1304 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1307 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1308 .getLength() != 24 ) {
1311 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1312 .getConfidence() != 2144 ) {
1315 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1316 .equals( "pfam" ) ) {
1319 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1322 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1325 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1328 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1331 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1332 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1335 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1338 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1341 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1344 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1347 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1350 if ( taxbb.getSynonyms().size() != 2 ) {
1353 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1356 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1359 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1362 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1365 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1368 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1369 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1373 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1376 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1379 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1382 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1385 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1388 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1391 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1395 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1398 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1399 .equalsIgnoreCase( "435" ) ) {
1402 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1405 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1406 .equalsIgnoreCase( "443.7" ) ) {
1409 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1412 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1415 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1416 .equalsIgnoreCase( "433" ) ) {
1420 catch ( final Exception e ) {
1421 e.printStackTrace( System.out );
1427 private static boolean testBasicPhyloXMLparsingValidating() {
1429 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1430 PhyloXmlParser xml_parser = null;
1432 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1434 catch ( final Exception e ) {
1435 // Do nothing -- means were not running from jar.
1437 if ( xml_parser == null ) {
1438 xml_parser = new PhyloXmlParser();
1439 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1440 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1443 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1446 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1448 if ( xml_parser.getErrorCount() > 0 ) {
1449 System.out.println( xml_parser.getErrorMessages().toString() );
1452 if ( phylogenies_0.length != 4 ) {
1455 final Phylogeny t1 = phylogenies_0[ 0 ];
1456 final Phylogeny t2 = phylogenies_0[ 1 ];
1457 final Phylogeny t3 = phylogenies_0[ 2 ];
1458 final Phylogeny t4 = phylogenies_0[ 3 ];
1459 if ( !t1.getName().equals( "t1" ) ) {
1462 if ( !t2.getName().equals( "t2" ) ) {
1465 if ( !t3.getName().equals( "t3" ) ) {
1468 if ( !t4.getName().equals( "t4" ) ) {
1471 if ( t1.getNumberOfExternalNodes() != 1 ) {
1474 if ( t2.getNumberOfExternalNodes() != 2 ) {
1477 if ( t3.getNumberOfExternalNodes() != 4 ) {
1480 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1481 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1482 if ( xml_parser.getErrorCount() > 0 ) {
1483 System.out.println( "errors:" );
1484 System.out.println( xml_parser.getErrorMessages().toString() );
1487 if ( phylogenies_1.length != 4 ) {
1490 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1492 if ( xml_parser.getErrorCount() > 0 ) {
1493 System.out.println( "errors:" );
1494 System.out.println( xml_parser.getErrorMessages().toString() );
1497 if ( phylogenies_2.length != 1 ) {
1500 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1503 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1505 if ( xml_parser.getErrorCount() > 0 ) {
1506 System.out.println( xml_parser.getErrorMessages().toString() );
1509 if ( phylogenies_3.length != 2 ) {
1512 final Phylogeny a = phylogenies_3[ 0 ];
1513 if ( !a.getName().equals( "tree 4" ) ) {
1516 if ( a.getNumberOfExternalNodes() != 3 ) {
1519 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1522 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1525 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1527 if ( xml_parser.getErrorCount() > 0 ) {
1528 System.out.println( xml_parser.getErrorMessages().toString() );
1531 if ( phylogenies_4.length != 1 ) {
1534 final Phylogeny s = phylogenies_4[ 0 ];
1535 if ( s.getNumberOfExternalNodes() != 6 ) {
1538 s.getNode( "first" );
1540 s.getNode( "\"<a'b&c'd\">\"" );
1541 s.getNode( "'''\"" );
1542 s.getNode( "\"\"\"" );
1543 s.getNode( "dick & doof" );
1545 catch ( final Exception e ) {
1546 e.printStackTrace( System.out );
1552 private static boolean testBasicTable() {
1554 final BasicTable<String> t0 = new BasicTable<String>();
1555 if ( t0.getNumberOfColumns() != 0 ) {
1558 if ( t0.getNumberOfRows() != 0 ) {
1561 t0.setValue( 3, 2, "23" );
1562 t0.setValue( 10, 1, "error" );
1563 t0.setValue( 10, 1, "110" );
1564 t0.setValue( 9, 1, "19" );
1565 t0.setValue( 1, 10, "101" );
1566 t0.setValue( 10, 10, "1010" );
1567 t0.setValue( 100, 10, "10100" );
1568 t0.setValue( 0, 0, "00" );
1569 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1572 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1575 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1578 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1581 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1584 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1587 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1590 if ( t0.getNumberOfColumns() != 101 ) {
1593 if ( t0.getNumberOfRows() != 11 ) {
1596 if ( t0.getValueAsString( 49, 4 ) != null ) {
1599 final String l = ForesterUtil.getLineSeparator();
1600 final StringBuffer source = new StringBuffer();
1601 source.append( "" + l );
1602 source.append( "# 1 1 1 1 1 1 1 1" + l );
1603 source.append( " 00 01 02 03" + l );
1604 source.append( " 10 11 12 13 " + l );
1605 source.append( "20 21 22 23 " + l );
1606 source.append( " 30 31 32 33" + l );
1607 source.append( "40 41 42 43" + l );
1608 source.append( " # 1 1 1 1 1 " + l );
1609 source.append( "50 51 52 53 54" + l );
1610 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1611 if ( t1.getNumberOfColumns() != 5 ) {
1614 if ( t1.getNumberOfRows() != 6 ) {
1617 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1620 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1623 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1626 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1629 final StringBuffer source1 = new StringBuffer();
1630 source1.append( "" + l );
1631 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1632 source1.append( " 00; 01 ;02;03" + l );
1633 source1.append( " 10; 11; 12; 13 " + l );
1634 source1.append( "20; 21; 22; 23 " + l );
1635 source1.append( " 30; 31; 32; 33" + l );
1636 source1.append( "40;41;42;43" + l );
1637 source1.append( " # 1 1 1 1 1 " + l );
1638 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1639 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1640 if ( t2.getNumberOfColumns() != 5 ) {
1643 if ( t2.getNumberOfRows() != 6 ) {
1646 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1649 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1652 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1655 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1658 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1661 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1664 final StringBuffer source2 = new StringBuffer();
1665 source2.append( "" + l );
1666 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1667 source2.append( " 00; 01 ;02;03" + l );
1668 source2.append( " 10; 11; 12; 13 " + l );
1669 source2.append( "20; 21; 22; 23 " + l );
1670 source2.append( " " + l );
1671 source2.append( " 30; 31; 32; 33" + l );
1672 source2.append( "40;41;42;43" + l );
1673 source2.append( " comment: 1 1 1 1 1 " + l );
1674 source2.append( ";;;50 ; 52; 53;;54 " + l );
1675 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1681 if ( tl.size() != 2 ) {
1684 final BasicTable<String> t3 = tl.get( 0 );
1685 final BasicTable<String> t4 = tl.get( 1 );
1686 if ( t3.getNumberOfColumns() != 4 ) {
1689 if ( t3.getNumberOfRows() != 3 ) {
1692 if ( t4.getNumberOfColumns() != 4 ) {
1695 if ( t4.getNumberOfRows() != 3 ) {
1698 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1701 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1705 catch ( final Exception e ) {
1706 e.printStackTrace( System.out );
1712 private static boolean testBasicTolXMLparsing() {
1714 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1715 final TolParser parser = new TolParser();
1716 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1717 if ( parser.getErrorCount() > 0 ) {
1718 System.out.println( parser.getErrorMessages().toString() );
1721 if ( phylogenies_0.length != 1 ) {
1724 final Phylogeny t1 = phylogenies_0[ 0 ];
1725 if ( t1.getNumberOfExternalNodes() != 5 ) {
1728 if ( !t1.isRooted() ) {
1731 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1734 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1737 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1740 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1743 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1744 if ( parser.getErrorCount() > 0 ) {
1745 System.out.println( parser.getErrorMessages().toString() );
1748 if ( phylogenies_1.length != 1 ) {
1751 final Phylogeny t2 = phylogenies_1[ 0 ];
1752 if ( t2.getNumberOfExternalNodes() != 664 ) {
1755 if ( !t2.isRooted() ) {
1758 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1761 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1764 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1767 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1770 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1773 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1774 .equals( "Aquifex" ) ) {
1777 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1778 if ( parser.getErrorCount() > 0 ) {
1779 System.out.println( parser.getErrorMessages().toString() );
1782 if ( phylogenies_2.length != 1 ) {
1785 final Phylogeny t3 = phylogenies_2[ 0 ];
1786 if ( t3.getNumberOfExternalNodes() != 184 ) {
1789 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1792 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1795 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1798 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1799 if ( parser.getErrorCount() > 0 ) {
1800 System.out.println( parser.getErrorMessages().toString() );
1803 if ( phylogenies_3.length != 1 ) {
1806 final Phylogeny t4 = phylogenies_3[ 0 ];
1807 if ( t4.getNumberOfExternalNodes() != 1 ) {
1810 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1813 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1816 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1819 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1820 if ( parser.getErrorCount() > 0 ) {
1821 System.out.println( parser.getErrorMessages().toString() );
1824 if ( phylogenies_4.length != 1 ) {
1827 final Phylogeny t5 = phylogenies_4[ 0 ];
1828 if ( t5.getNumberOfExternalNodes() != 13 ) {
1831 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1834 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1837 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1841 catch ( final Exception e ) {
1842 e.printStackTrace( System.out );
1848 private static boolean testBasicTreeMethods() {
1850 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1851 final Phylogeny t1 = factory.create();
1852 if ( !t1.isEmpty() ) {
1855 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1856 if ( t2.getNumberOfExternalNodes() != 4 ) {
1859 if ( t2.getHeight() != 8.5 ) {
1862 if ( !t2.isCompletelyBinary() ) {
1865 if ( t2.isEmpty() ) {
1868 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1869 if ( t3.getNumberOfExternalNodes() != 5 ) {
1872 if ( t3.getHeight() != 11 ) {
1875 if ( t3.isCompletelyBinary() ) {
1878 final PhylogenyNode n = t3.getNode( "ABC" );
1879 final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
1880 if ( t4.getNumberOfExternalNodes() != 9 ) {
1883 if ( t4.getHeight() != 11 ) {
1886 if ( t4.isCompletelyBinary() ) {
1889 final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1890 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1891 if ( t5.getNumberOfExternalNodes() != 8 ) {
1894 if ( t5.getHeight() != 15 ) {
1897 final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
1898 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1899 if ( t6.getHeight() != 15 ) {
1902 final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
1903 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1904 if ( t7.getHeight() != 15 ) {
1907 final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
1908 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1909 if ( t8.getNumberOfExternalNodes() != 10 ) {
1912 if ( t8.getHeight() != 15 ) {
1915 final char[] a9 = new char[] {};
1916 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1917 if ( t9.getHeight() != 0 ) {
1920 final char[] a10 = new char[] { 'a', ':', '6' };
1921 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1922 if ( t10.getHeight() != 6 ) {
1926 catch ( final Exception e ) {
1927 e.printStackTrace( System.out );
1933 private static boolean testConfidenceAssessor() {
1935 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1936 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1937 final Phylogeny[] ev0 = factory
1938 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1940 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1941 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1944 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1947 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1948 final Phylogeny[] ev1 = factory
1949 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1951 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1952 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1955 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1958 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1959 final Phylogeny[] ev_b = factory
1960 .create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
1962 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1963 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1966 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1970 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1971 final Phylogeny[] ev1x = factory
1972 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));",
1974 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1975 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1978 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1981 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1982 final Phylogeny[] ev_bx = factory
1983 .create( "((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
1985 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1986 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1989 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1993 final Phylogeny[] t2 = factory
1994 .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
1996 final Phylogeny[] ev2 = factory
1997 .create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);",
1999 for( final Phylogeny target : t2 ) {
2000 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2003 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2004 new NHXParser() )[ 0 ];
2005 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2006 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2007 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2010 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2013 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2017 catch ( final Exception e ) {
2018 e.printStackTrace();
2024 private static boolean testCopyOfNodeData() {
2026 final PhylogenyNode n1 = PhylogenyNode
2027 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2028 final PhylogenyNode n2 = n1.copyNodeData();
2029 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2033 catch ( final Exception e ) {
2034 e.printStackTrace();
2040 private static boolean testDataObjects() {
2042 final Confidence s0 = new Confidence();
2043 final Confidence s1 = new Confidence();
2044 if ( !s0.isEqual( s1 ) ) {
2047 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2048 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2049 if ( s2.isEqual( s1 ) ) {
2052 if ( !s2.isEqual( s3 ) ) {
2055 final Confidence s4 = ( Confidence ) s3.copy();
2056 if ( !s4.isEqual( s3 ) ) {
2063 final Taxonomy t1 = new Taxonomy();
2064 final Taxonomy t2 = new Taxonomy();
2065 final Taxonomy t3 = new Taxonomy();
2066 final Taxonomy t4 = new Taxonomy();
2067 final Taxonomy t5 = new Taxonomy();
2068 t1.setIdentifier( new Identifier( "ecoli" ) );
2069 t1.setTaxonomyCode( "ECOLI" );
2070 t1.setScientificName( "E. coli" );
2071 t1.setCommonName( "coli" );
2072 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2073 if ( !t1.isEqual( t0 ) ) {
2076 t2.setIdentifier( new Identifier( "ecoli" ) );
2077 t2.setTaxonomyCode( "OTHER" );
2078 t2.setScientificName( "what" );
2079 t2.setCommonName( "something" );
2080 if ( !t1.isEqual( t2 ) ) {
2083 t2.setIdentifier( new Identifier( "nemve" ) );
2084 if ( t1.isEqual( t2 ) ) {
2087 t1.setIdentifier( null );
2088 t3.setTaxonomyCode( "ECOLI" );
2089 t3.setScientificName( "what" );
2090 t3.setCommonName( "something" );
2091 if ( !t1.isEqual( t3 ) ) {
2094 t1.setIdentifier( null );
2095 t1.setTaxonomyCode( "" );
2096 t4.setScientificName( "E. ColI" );
2097 t4.setCommonName( "something" );
2098 if ( !t1.isEqual( t4 ) ) {
2101 t4.setScientificName( "B. subtilis" );
2102 t4.setCommonName( "something" );
2103 if ( t1.isEqual( t4 ) ) {
2106 t1.setIdentifier( null );
2107 t1.setTaxonomyCode( "" );
2108 t1.setScientificName( "" );
2109 t5.setCommonName( "COLI" );
2110 if ( !t1.isEqual( t5 ) ) {
2113 t5.setCommonName( "vibrio" );
2114 if ( t1.isEqual( t5 ) ) {
2119 final Identifier id0 = new Identifier( "123", "pfam" );
2120 final Identifier id1 = ( Identifier ) id0.copy();
2121 if ( !id1.isEqual( id1 ) ) {
2124 if ( !id1.isEqual( id0 ) ) {
2127 if ( !id0.isEqual( id1 ) ) {
2134 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2135 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2136 if ( !pd1.isEqual( pd1 ) ) {
2139 if ( !pd1.isEqual( pd0 ) ) {
2144 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2145 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2146 if ( !pd3.isEqual( pd3 ) ) {
2149 if ( !pd2.isEqual( pd3 ) ) {
2152 if ( !pd0.isEqual( pd3 ) ) {
2157 // DomainArchitecture
2158 // ------------------
2159 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2160 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2161 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2162 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2163 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2164 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2169 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2170 if ( ds0.getNumberOfDomains() != 4 ) {
2173 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2174 if ( !ds0.isEqual( ds0 ) ) {
2177 if ( !ds0.isEqual( ds1 ) ) {
2180 if ( ds1.getNumberOfDomains() != 4 ) {
2183 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2188 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2189 if ( ds0.isEqual( ds2 ) ) {
2195 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2196 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2197 System.out.println( ds3.toNHX() );
2200 if ( ds3.getNumberOfDomains() != 3 ) {
2205 final Event e1 = new Event( Event.EventType.fusion );
2206 if ( e1.isDuplication() ) {
2209 if ( !e1.isFusion() ) {
2212 if ( !e1.asText().toString().equals( "fusion" ) ) {
2215 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2218 final Event e11 = new Event( Event.EventType.fusion );
2219 if ( !e11.isEqual( e1 ) ) {
2222 if ( !e11.toNHX().toString().equals( "" ) ) {
2225 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2226 if ( e2.isDuplication() ) {
2229 if ( !e2.isSpeciationOrDuplication() ) {
2232 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2235 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2238 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2241 if ( e11.isEqual( e2 ) ) {
2244 final Event e2c = ( Event ) e2.copy();
2245 if ( !e2c.isEqual( e2 ) ) {
2248 Event e3 = new Event( 1, 2, 3 );
2249 if ( e3.isDuplication() ) {
2252 if ( e3.isSpeciation() ) {
2255 if ( e3.isGeneLoss() ) {
2258 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2261 final Event e3c = ( Event ) e3.copy();
2262 final Event e3cc = ( Event ) e3c.copy();
2263 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2267 if ( !e3c.isEqual( e3cc ) ) {
2270 Event e4 = new Event( 1, 2, 3 );
2271 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2274 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2277 final Event e4c = ( Event ) e4.copy();
2279 final Event e4cc = ( Event ) e4c.copy();
2280 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2283 if ( !e4c.isEqual( e4cc ) ) {
2286 final Event e5 = new Event();
2287 if ( !e5.isUnassigned() ) {
2290 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2293 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2296 final Event e6 = new Event( 1, 0, 0 );
2297 if ( !e6.asText().toString().equals( "duplication" ) ) {
2300 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2303 final Event e7 = new Event( 0, 1, 0 );
2304 if ( !e7.asText().toString().equals( "speciation" ) ) {
2307 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2310 final Event e8 = new Event( 0, 0, 1 );
2311 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2314 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2318 catch ( final Exception e ) {
2319 e.printStackTrace( System.out );
2325 private static boolean testDeletionOfExternalNodes() {
2327 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2328 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2329 final PhylogenyWriter w = new PhylogenyWriter();
2330 if ( t0.isEmpty() ) {
2333 if ( t0.getNumberOfExternalNodes() != 1 ) {
2336 t0.deleteSubtree( t0.getNode( "A" ), false );
2337 if ( t0.getNumberOfExternalNodes() != 0 ) {
2340 if ( !t0.isEmpty() ) {
2343 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2344 if ( t1.getNumberOfExternalNodes() != 2 ) {
2347 t1.deleteSubtree( t1.getNode( "A" ), false );
2348 if ( t1.getNumberOfExternalNodes() != 1 ) {
2351 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2354 t1.deleteSubtree( t1.getNode( "B" ), false );
2355 if ( t1.getNumberOfExternalNodes() != 1 ) {
2358 t1.deleteSubtree( t1.getNode( "r" ), false );
2359 if ( !t1.isEmpty() ) {
2362 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2363 if ( t2.getNumberOfExternalNodes() != 3 ) {
2366 t2.deleteSubtree( t2.getNode( "B" ), false );
2367 if ( t2.getNumberOfExternalNodes() != 2 ) {
2370 t2.toNewHampshireX();
2371 PhylogenyNode n = t2.getNode( "A" );
2372 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2375 t2.deleteSubtree( t2.getNode( "A" ), false );
2376 if ( t2.getNumberOfExternalNodes() != 2 ) {
2379 t2.deleteSubtree( t2.getNode( "C" ), true );
2380 if ( t2.getNumberOfExternalNodes() != 1 ) {
2383 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2384 if ( t3.getNumberOfExternalNodes() != 4 ) {
2387 t3.deleteSubtree( t3.getNode( "B" ), true );
2388 if ( t3.getNumberOfExternalNodes() != 3 ) {
2391 n = t3.getNode( "A" );
2392 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2395 n = n.getNextExternalNode();
2396 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2399 t3.deleteSubtree( t3.getNode( "A" ), true );
2400 if ( t3.getNumberOfExternalNodes() != 2 ) {
2403 n = t3.getNode( "C" );
2404 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2407 t3.deleteSubtree( t3.getNode( "C" ), true );
2408 if ( t3.getNumberOfExternalNodes() != 1 ) {
2411 t3.deleteSubtree( t3.getNode( "D" ), true );
2412 if ( t3.getNumberOfExternalNodes() != 0 ) {
2415 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2416 if ( t4.getNumberOfExternalNodes() != 6 ) {
2419 t4.deleteSubtree( t4.getNode( "B2" ), true );
2420 if ( t4.getNumberOfExternalNodes() != 5 ) {
2423 String s = w.toNewHampshire( t4, false, true ).toString();
2424 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2427 t4.deleteSubtree( t4.getNode( "B11" ), true );
2428 if ( t4.getNumberOfExternalNodes() != 4 ) {
2431 t4.deleteSubtree( t4.getNode( "C" ), true );
2432 if ( t4.getNumberOfExternalNodes() != 3 ) {
2435 n = t4.getNode( "A" );
2436 n = n.getNextExternalNode();
2437 if ( !n.getName().equals( "B12" ) ) {
2440 n = n.getNextExternalNode();
2441 if ( !n.getName().equals( "D" ) ) {
2444 s = w.toNewHampshire( t4, false, true ).toString();
2445 if ( !s.equals( "((A,B12),D);" ) ) {
2448 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2449 t5.deleteSubtree( t5.getNode( "A" ), true );
2450 if ( t5.getNumberOfExternalNodes() != 5 ) {
2453 s = w.toNewHampshire( t5, false, true ).toString();
2454 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2457 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2458 t6.deleteSubtree( t6.getNode( "B11" ), true );
2459 if ( t6.getNumberOfExternalNodes() != 5 ) {
2462 s = w.toNewHampshire( t6, false, false ).toString();
2463 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2466 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2467 t7.deleteSubtree( t7.getNode( "B12" ), true );
2468 if ( t7.getNumberOfExternalNodes() != 5 ) {
2471 s = w.toNewHampshire( t7, false, true ).toString();
2472 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2475 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2476 t8.deleteSubtree( t8.getNode( "B2" ), true );
2477 if ( t8.getNumberOfExternalNodes() != 5 ) {
2480 s = w.toNewHampshire( t8, false, false ).toString();
2481 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2484 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2485 t9.deleteSubtree( t9.getNode( "C" ), true );
2486 if ( t9.getNumberOfExternalNodes() != 5 ) {
2489 s = w.toNewHampshire( t9, false, true ).toString();
2490 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2493 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2494 t10.deleteSubtree( t10.getNode( "D" ), true );
2495 if ( t10.getNumberOfExternalNodes() != 5 ) {
2498 s = w.toNewHampshire( t10, false, true ).toString();
2499 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2502 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2503 t11.deleteSubtree( t11.getNode( "A" ), true );
2504 if ( t11.getNumberOfExternalNodes() != 2 ) {
2507 s = w.toNewHampshire( t11, false, true ).toString();
2508 if ( !s.equals( "(B,C);" ) ) {
2511 t11.deleteSubtree( t11.getNode( "C" ), true );
2512 if ( t11.getNumberOfExternalNodes() != 1 ) {
2515 s = w.toNewHampshire( t11, false, false ).toString();
2516 if ( !s.equals( "B;" ) ) {
2519 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2520 t12.deleteSubtree( t12.getNode( "B2" ), true );
2521 if ( t12.getNumberOfExternalNodes() != 8 ) {
2524 s = w.toNewHampshire( t12, false, true ).toString();
2525 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2528 t12.deleteSubtree( t12.getNode( "B3" ), true );
2529 if ( t12.getNumberOfExternalNodes() != 7 ) {
2532 s = w.toNewHampshire( t12, false, true ).toString();
2533 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2536 t12.deleteSubtree( t12.getNode( "C3" ), true );
2537 if ( t12.getNumberOfExternalNodes() != 6 ) {
2540 s = w.toNewHampshire( t12, false, true ).toString();
2541 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2544 t12.deleteSubtree( t12.getNode( "A1" ), true );
2545 if ( t12.getNumberOfExternalNodes() != 5 ) {
2548 s = w.toNewHampshire( t12, false, true ).toString();
2549 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2552 t12.deleteSubtree( t12.getNode( "B1" ), true );
2553 if ( t12.getNumberOfExternalNodes() != 4 ) {
2556 s = w.toNewHampshire( t12, false, true ).toString();
2557 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2560 t12.deleteSubtree( t12.getNode( "A3" ), true );
2561 if ( t12.getNumberOfExternalNodes() != 3 ) {
2564 s = w.toNewHampshire( t12, false, true ).toString();
2565 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2568 t12.deleteSubtree( t12.getNode( "A2" ), true );
2569 if ( t12.getNumberOfExternalNodes() != 2 ) {
2572 s = w.toNewHampshire( t12, false, true ).toString();
2573 if ( !s.equals( "(C1,C2);" ) ) {
2576 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2577 t13.deleteSubtree( t13.getNode( "D" ), true );
2578 if ( t13.getNumberOfExternalNodes() != 4 ) {
2581 s = w.toNewHampshire( t13, false, true ).toString();
2582 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2585 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2586 t14.deleteSubtree( t14.getNode( "E" ), true );
2587 if ( t14.getNumberOfExternalNodes() != 5 ) {
2590 s = w.toNewHampshire( t14, false, true ).toString();
2591 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2594 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2595 t15.deleteSubtree( t15.getNode( "B2" ), true );
2596 if ( t15.getNumberOfExternalNodes() != 11 ) {
2599 t15.deleteSubtree( t15.getNode( "B1" ), true );
2600 if ( t15.getNumberOfExternalNodes() != 10 ) {
2603 t15.deleteSubtree( t15.getNode( "B3" ), true );
2604 if ( t15.getNumberOfExternalNodes() != 9 ) {
2607 t15.deleteSubtree( t15.getNode( "B4" ), true );
2608 if ( t15.getNumberOfExternalNodes() != 8 ) {
2611 t15.deleteSubtree( t15.getNode( "A1" ), true );
2612 if ( t15.getNumberOfExternalNodes() != 7 ) {
2615 t15.deleteSubtree( t15.getNode( "C4" ), true );
2616 if ( t15.getNumberOfExternalNodes() != 6 ) {
2620 catch ( final Exception e ) {
2621 e.printStackTrace( System.out );
2627 private static boolean testDescriptiveStatistics() {
2629 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2630 dss1.addValue( 82 );
2631 dss1.addValue( 78 );
2632 dss1.addValue( 70 );
2633 dss1.addValue( 58 );
2634 dss1.addValue( 42 );
2635 if ( dss1.getN() != 5 ) {
2638 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2641 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2644 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2647 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2650 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2653 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2656 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2659 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2662 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2665 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2668 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2671 dss1.addValue( 123 );
2672 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2675 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2678 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2681 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2682 dss2.addValue( -1.85 );
2683 dss2.addValue( 57.5 );
2684 dss2.addValue( 92.78 );
2685 dss2.addValue( 57.78 );
2686 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2689 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2692 final double[] a = dss2.getDataAsDoubleArray();
2693 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2696 dss2.addValue( -100 );
2697 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2700 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2703 final double[] ds = new double[ 14 ];
2718 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2719 if ( bins.length != 4 ) {
2722 if ( bins[ 0 ] != 2 ) {
2725 if ( bins[ 1 ] != 3 ) {
2728 if ( bins[ 2 ] != 4 ) {
2731 if ( bins[ 3 ] != 5 ) {
2734 final double[] ds1 = new double[ 9 ];
2744 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2745 if ( bins1.length != 4 ) {
2748 if ( bins1[ 0 ] != 2 ) {
2751 if ( bins1[ 1 ] != 3 ) {
2754 if ( bins1[ 2 ] != 0 ) {
2757 if ( bins1[ 3 ] != 4 ) {
2760 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2761 if ( bins1_1.length != 3 ) {
2764 if ( bins1_1[ 0 ] != 3 ) {
2767 if ( bins1_1[ 1 ] != 2 ) {
2770 if ( bins1_1[ 2 ] != 4 ) {
2773 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2774 if ( bins1_2.length != 3 ) {
2777 if ( bins1_2[ 0 ] != 2 ) {
2780 if ( bins1_2[ 1 ] != 2 ) {
2783 if ( bins1_2[ 2 ] != 2 ) {
2786 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2800 dss3.addValue( 10 );
2801 dss3.addValue( 10 );
2802 dss3.addValue( 10 );
2803 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2804 histo.toStringBuffer( 10, '=', 40, 5 );
2805 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2807 catch ( final Exception e ) {
2808 e.printStackTrace( System.out );
2814 private static boolean testDir( final String file ) {
2816 final File f = new File( file );
2817 if ( !f.exists() ) {
2820 if ( !f.isDirectory() ) {
2823 if ( !f.canRead() ) {
2827 catch ( final Exception e ) {
2833 private static boolean testExternalNodeRelatedMethods() {
2835 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2836 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2837 PhylogenyNode n = t1.getNode( "A" );
2838 n = n.getNextExternalNode();
2839 if ( !n.getName().equals( "B" ) ) {
2842 n = n.getNextExternalNode();
2843 if ( !n.getName().equals( "C" ) ) {
2846 n = n.getNextExternalNode();
2847 if ( !n.getName().equals( "D" ) ) {
2850 n = t1.getNode( "B" );
2851 while ( !n.isLastExternalNode() ) {
2852 n = n.getNextExternalNode();
2854 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2855 n = t2.getNode( "A" );
2856 n = n.getNextExternalNode();
2857 if ( !n.getName().equals( "B" ) ) {
2860 n = n.getNextExternalNode();
2861 if ( !n.getName().equals( "C" ) ) {
2864 n = n.getNextExternalNode();
2865 if ( !n.getName().equals( "D" ) ) {
2868 n = t2.getNode( "B" );
2869 while ( !n.isLastExternalNode() ) {
2870 n = n.getNextExternalNode();
2872 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2873 n = t3.getNode( "A" );
2874 n = n.getNextExternalNode();
2875 if ( !n.getName().equals( "B" ) ) {
2878 n = n.getNextExternalNode();
2879 if ( !n.getName().equals( "C" ) ) {
2882 n = n.getNextExternalNode();
2883 if ( !n.getName().equals( "D" ) ) {
2886 n = n.getNextExternalNode();
2887 if ( !n.getName().equals( "E" ) ) {
2890 n = n.getNextExternalNode();
2891 if ( !n.getName().equals( "F" ) ) {
2894 n = n.getNextExternalNode();
2895 if ( !n.getName().equals( "G" ) ) {
2898 n = n.getNextExternalNode();
2899 if ( !n.getName().equals( "H" ) ) {
2902 n = t3.getNode( "B" );
2903 while ( !n.isLastExternalNode() ) {
2904 n = n.getNextExternalNode();
2906 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2907 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2908 final PhylogenyNode node = iter.next();
2910 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2911 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2912 final PhylogenyNode node = iter.next();
2914 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2915 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2916 if ( !iter.next().getName().equals( "A" ) ) {
2919 if ( !iter.next().getName().equals( "B" ) ) {
2922 if ( !iter.next().getName().equals( "C" ) ) {
2925 if ( !iter.next().getName().equals( "D" ) ) {
2928 if ( !iter.next().getName().equals( "E" ) ) {
2931 if ( !iter.next().getName().equals( "F" ) ) {
2934 if ( iter.hasNext() ) {
2938 catch ( final Exception e ) {
2939 e.printStackTrace( System.out );
2945 private static boolean testGeneralTable() {
2947 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2948 t0.setValue( 3, 2, "23" );
2949 t0.setValue( 10, 1, "error" );
2950 t0.setValue( 10, 1, "110" );
2951 t0.setValue( 9, 1, "19" );
2952 t0.setValue( 1, 10, "101" );
2953 t0.setValue( 10, 10, "1010" );
2954 t0.setValue( 100, 10, "10100" );
2955 t0.setValue( 0, 0, "00" );
2956 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2959 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2962 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2965 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2968 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2971 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2974 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2977 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2980 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2983 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2984 t1.setValue( "3", "2", "23" );
2985 t1.setValue( "10", "1", "error" );
2986 t1.setValue( "10", "1", "110" );
2987 t1.setValue( "9", "1", "19" );
2988 t1.setValue( "1", "10", "101" );
2989 t1.setValue( "10", "10", "1010" );
2990 t1.setValue( "100", "10", "10100" );
2991 t1.setValue( "0", "0", "00" );
2992 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2993 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2996 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2999 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3002 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3005 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3008 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3011 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3014 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3017 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3020 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3024 catch ( final Exception e ) {
3025 e.printStackTrace( System.out );
3031 private static boolean testGetDistance() {
3033 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3034 final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
3035 new NHXParser() )[ 0 ];
3036 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3039 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3042 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3045 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3048 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3051 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3054 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3057 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3060 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3063 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3066 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3069 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3072 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3075 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3078 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3081 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3084 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3087 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3090 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3093 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3096 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3099 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3102 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3105 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3108 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3111 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3114 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3117 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3120 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3123 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3126 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3129 final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
3130 new NHXParser() )[ 0 ];
3131 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3134 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3137 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3140 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3143 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3146 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3149 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3152 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3155 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3158 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3161 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3165 catch ( final Exception e ) {
3166 e.printStackTrace( System.out );
3172 private static boolean testGetLCA() {
3174 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3175 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3176 new NHXParser() )[ 0 ];
3177 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3178 if ( !A.getName().equals( "A" ) ) {
3181 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3182 if ( !gh.getName().equals( "gh" ) ) {
3185 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3186 if ( !ab.getName().equals( "ab" ) ) {
3189 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3190 if ( !ab2.getName().equals( "ab" ) ) {
3193 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3194 if ( !gh2.getName().equals( "gh" ) ) {
3197 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3198 if ( !gh3.getName().equals( "gh" ) ) {
3201 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3202 if ( !abc.getName().equals( "abc" ) ) {
3205 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3206 if ( !abc2.getName().equals( "abc" ) ) {
3209 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3210 if ( !abcd.getName().equals( "abcd" ) ) {
3213 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3214 if ( !abcd2.getName().equals( "abcd" ) ) {
3217 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3218 if ( !abcdef.getName().equals( "abcdef" ) ) {
3221 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3222 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3225 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3226 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3229 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3230 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3233 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3234 if ( !abcde.getName().equals( "abcde" ) ) {
3237 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3238 if ( !abcde2.getName().equals( "abcde" ) ) {
3241 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3242 if ( !r.getName().equals( "abcdefgh" ) ) {
3245 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3246 if ( !r2.getName().equals( "abcdefgh" ) ) {
3249 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3250 if ( !r3.getName().equals( "abcdefgh" ) ) {
3253 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3254 if ( !abcde3.getName().equals( "abcde" ) ) {
3257 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3258 if ( !abcde4.getName().equals( "abcde" ) ) {
3261 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3262 if ( !ab3.getName().equals( "ab" ) ) {
3265 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3266 if ( !ab4.getName().equals( "ab" ) ) {
3269 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3270 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3271 if ( !cd.getName().equals( "cd" ) ) {
3274 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3275 if ( !cd2.getName().equals( "cd" ) ) {
3278 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3279 if ( !cde.getName().equals( "cde" ) ) {
3282 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3283 if ( !cde2.getName().equals( "cde" ) ) {
3286 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3287 if ( !cdef.getName().equals( "cdef" ) ) {
3290 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3291 if ( !cdef2.getName().equals( "cdef" ) ) {
3294 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3295 if ( !cdef3.getName().equals( "cdef" ) ) {
3298 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3299 if ( !rt.getName().equals( "r" ) ) {
3302 final Phylogeny p3 = factory
3303 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3304 new NHXParser() )[ 0 ];
3305 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3306 if ( !bc_3.getName().equals( "bc" ) ) {
3309 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3310 if ( !ac_3.getName().equals( "abc" ) ) {
3313 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3314 if ( !ad_3.getName().equals( "abcde" ) ) {
3317 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3318 if ( !af_3.getName().equals( "abcdef" ) ) {
3321 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3322 if ( !ag_3.getName().equals( "" ) ) {
3325 if ( !ag_3.isRoot() ) {
3328 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3329 if ( !al_3.getName().equals( "" ) ) {
3332 if ( !al_3.isRoot() ) {
3335 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3336 if ( !kl_3.getName().equals( "" ) ) {
3339 if ( !kl_3.isRoot() ) {
3342 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3343 if ( !fl_3.getName().equals( "" ) ) {
3346 if ( !fl_3.isRoot() ) {
3349 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3350 if ( !gk_3.getName().equals( "ghijk" ) ) {
3353 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3354 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3355 if ( !r_4.getName().equals( "r" ) ) {
3358 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3359 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3360 if ( !r_5.getName().equals( "root" ) ) {
3363 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3364 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3365 if ( !r_6.getName().equals( "rot" ) ) {
3368 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3369 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3370 if ( !r_7.getName().equals( "rott" ) ) {
3374 catch ( final Exception e ) {
3375 e.printStackTrace( System.out );
3381 private static boolean testGetLCA2() {
3383 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3384 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3385 PhylogenyMethods.preOrderReId( p_a );
3386 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3387 p_a.getNode( "a" ) );
3388 if ( !p_a_1.getName().equals( "a" ) ) {
3391 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3392 PhylogenyMethods.preOrderReId( p_b );
3393 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3394 p_b.getNode( "a" ) );
3395 if ( !p_b_1.getName().equals( "b" ) ) {
3398 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3399 p_b.getNode( "b" ) );
3400 if ( !p_b_2.getName().equals( "b" ) ) {
3403 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3404 PhylogenyMethods.preOrderReId( p_c );
3405 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3406 p_c.getNode( "a" ) );
3407 if ( !p_c_1.getName().equals( "b" ) ) {
3410 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3411 p_c.getNode( "c" ) );
3412 if ( !p_c_2.getName().equals( "c" ) ) {
3413 System.out.println( p_c_2.getName() );
3417 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3418 p_c.getNode( "b" ) );
3419 if ( !p_c_3.getName().equals( "b" ) ) {
3422 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3423 p_c.getNode( "a" ) );
3424 if ( !p_c_4.getName().equals( "c" ) ) {
3427 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3428 new NHXParser() )[ 0 ];
3429 PhylogenyMethods.preOrderReId( p1 );
3430 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3431 p1.getNode( "A" ) );
3432 if ( !A.getName().equals( "A" ) ) {
3435 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3436 p1.getNode( "gh" ) );
3437 if ( !gh.getName().equals( "gh" ) ) {
3440 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3441 p1.getNode( "B" ) );
3442 if ( !ab.getName().equals( "ab" ) ) {
3445 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3446 p1.getNode( "A" ) );
3447 if ( !ab2.getName().equals( "ab" ) ) {
3450 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3451 p1.getNode( "G" ) );
3452 if ( !gh2.getName().equals( "gh" ) ) {
3455 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3456 p1.getNode( "H" ) );
3457 if ( !gh3.getName().equals( "gh" ) ) {
3460 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3461 p1.getNode( "A" ) );
3462 if ( !abc.getName().equals( "abc" ) ) {
3465 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3466 p1.getNode( "C" ) );
3467 if ( !abc2.getName().equals( "abc" ) ) {
3470 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3471 p1.getNode( "D" ) );
3472 if ( !abcd.getName().equals( "abcd" ) ) {
3475 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3476 p1.getNode( "A" ) );
3477 if ( !abcd2.getName().equals( "abcd" ) ) {
3480 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3481 p1.getNode( "F" ) );
3482 if ( !abcdef.getName().equals( "abcdef" ) ) {
3485 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3486 p1.getNode( "A" ) );
3487 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3490 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3491 p1.getNode( "F" ) );
3492 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3495 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3496 p1.getNode( "ab" ) );
3497 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3500 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3501 p1.getNode( "E" ) );
3502 if ( !abcde.getName().equals( "abcde" ) ) {
3505 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3506 p1.getNode( "A" ) );
3507 if ( !abcde2.getName().equals( "abcde" ) ) {
3510 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3511 p1.getNode( "abcdefgh" ) );
3512 if ( !r.getName().equals( "abcdefgh" ) ) {
3515 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3516 p1.getNode( "H" ) );
3517 if ( !r2.getName().equals( "abcdefgh" ) ) {
3520 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3521 p1.getNode( "A" ) );
3522 if ( !r3.getName().equals( "abcdefgh" ) ) {
3525 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3526 p1.getNode( "abcde" ) );
3527 if ( !abcde3.getName().equals( "abcde" ) ) {
3530 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3531 p1.getNode( "E" ) );
3532 if ( !abcde4.getName().equals( "abcde" ) ) {
3535 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3536 p1.getNode( "B" ) );
3537 if ( !ab3.getName().equals( "ab" ) ) {
3540 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3541 p1.getNode( "ab" ) );
3542 if ( !ab4.getName().equals( "ab" ) ) {
3545 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3546 PhylogenyMethods.preOrderReId( p2 );
3547 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3548 p2.getNode( "d" ) );
3549 if ( !cd.getName().equals( "cd" ) ) {
3552 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3553 p2.getNode( "c" ) );
3554 if ( !cd2.getName().equals( "cd" ) ) {
3557 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3558 p2.getNode( "e" ) );
3559 if ( !cde.getName().equals( "cde" ) ) {
3562 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3563 p2.getNode( "c" ) );
3564 if ( !cde2.getName().equals( "cde" ) ) {
3567 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3568 p2.getNode( "f" ) );
3569 if ( !cdef.getName().equals( "cdef" ) ) {
3572 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3573 p2.getNode( "f" ) );
3574 if ( !cdef2.getName().equals( "cdef" ) ) {
3577 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3578 p2.getNode( "d" ) );
3579 if ( !cdef3.getName().equals( "cdef" ) ) {
3582 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3583 p2.getNode( "a" ) );
3584 if ( !rt.getName().equals( "r" ) ) {
3587 final Phylogeny p3 = factory
3588 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3589 new NHXParser() )[ 0 ];
3590 PhylogenyMethods.preOrderReId( p3 );
3591 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3592 p3.getNode( "c" ) );
3593 if ( !bc_3.getName().equals( "bc" ) ) {
3596 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3597 p3.getNode( "c" ) );
3598 if ( !ac_3.getName().equals( "abc" ) ) {
3601 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3602 p3.getNode( "d" ) );
3603 if ( !ad_3.getName().equals( "abcde" ) ) {
3606 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3607 p3.getNode( "f" ) );
3608 if ( !af_3.getName().equals( "abcdef" ) ) {
3611 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3612 p3.getNode( "g" ) );
3613 if ( !ag_3.getName().equals( "" ) ) {
3616 if ( !ag_3.isRoot() ) {
3619 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3620 p3.getNode( "l" ) );
3621 if ( !al_3.getName().equals( "" ) ) {
3624 if ( !al_3.isRoot() ) {
3627 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3628 p3.getNode( "l" ) );
3629 if ( !kl_3.getName().equals( "" ) ) {
3632 if ( !kl_3.isRoot() ) {
3635 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3636 p3.getNode( "l" ) );
3637 if ( !fl_3.getName().equals( "" ) ) {
3640 if ( !fl_3.isRoot() ) {
3643 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3644 p3.getNode( "k" ) );
3645 if ( !gk_3.getName().equals( "ghijk" ) ) {
3648 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3649 PhylogenyMethods.preOrderReId( p4 );
3650 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3651 p4.getNode( "c" ) );
3652 if ( !r_4.getName().equals( "r" ) ) {
3655 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3656 PhylogenyMethods.preOrderReId( p5 );
3657 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3658 p5.getNode( "c" ) );
3659 if ( !r_5.getName().equals( "root" ) ) {
3662 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3663 PhylogenyMethods.preOrderReId( p6 );
3664 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3665 p6.getNode( "a" ) );
3666 if ( !r_6.getName().equals( "rot" ) ) {
3669 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3670 PhylogenyMethods.preOrderReId( p7 );
3671 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3672 p7.getNode( "e" ) );
3673 if ( !r_7.getName().equals( "rott" ) ) {
3676 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3677 p7.getNode( "a" ) );
3678 if ( !r_71.getName().equals( "rott" ) ) {
3681 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3682 p7.getNode( "rott" ) );
3683 if ( !r_72.getName().equals( "rott" ) ) {
3686 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3687 p7.getNode( "a" ) );
3688 if ( !r_73.getName().equals( "rott" ) ) {
3691 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3692 p7.getNode( "rott" ) );
3693 if ( !r_74.getName().equals( "rott" ) ) {
3696 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3697 p7.getNode( "e" ) );
3698 if ( !r_75.getName().equals( "e" ) ) {
3702 catch ( final Exception e ) {
3703 e.printStackTrace( System.out );
3709 private static boolean testHmmscanOutputParser() {
3710 final String test_dir = Test.PATH_TO_TEST_DATA;
3712 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3713 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3715 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3716 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3717 final List<Protein> proteins = parser2.parse();
3718 if ( parser2.getProteinsEncountered() != 4 ) {
3721 if ( proteins.size() != 4 ) {
3724 if ( parser2.getDomainsEncountered() != 69 ) {
3727 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3730 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3733 final Protein p1 = proteins.get( 0 );
3734 if ( p1.getNumberOfProteinDomains() != 15 ) {
3737 if ( p1.getLength() != 850 ) {
3740 final Protein p2 = proteins.get( 1 );
3741 if ( p2.getNumberOfProteinDomains() != 51 ) {
3744 if ( p2.getLength() != 1291 ) {
3747 final Protein p3 = proteins.get( 2 );
3748 if ( p3.getNumberOfProteinDomains() != 2 ) {
3751 final Protein p4 = proteins.get( 3 );
3752 if ( p4.getNumberOfProteinDomains() != 1 ) {
3755 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3758 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3761 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3764 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3767 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3770 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3773 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3776 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3779 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3783 catch ( final Exception e ) {
3784 e.printStackTrace( System.out );
3790 private static boolean testLastExternalNodeMethods() {
3792 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3793 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3794 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3795 final PhylogenyNode n1 = t0.getNode( "A" );
3796 if ( n1.isLastExternalNode() ) {
3799 final PhylogenyNode n2 = t0.getNode( "B" );
3800 if ( n2.isLastExternalNode() ) {
3803 final PhylogenyNode n3 = t0.getNode( "C" );
3804 if ( n3.isLastExternalNode() ) {
3807 final PhylogenyNode n4 = t0.getNode( "D" );
3808 if ( !n4.isLastExternalNode() ) {
3812 catch ( final Exception e ) {
3813 e.printStackTrace( System.out );
3819 private static boolean testLevelOrderIterator() {
3821 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3822 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3823 PhylogenyNodeIterator it0;
3824 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3827 for( it0.reset(); it0.hasNext(); ) {
3830 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3831 if ( !it.next().getName().equals( "r" ) ) {
3834 if ( !it.next().getName().equals( "ab" ) ) {
3837 if ( !it.next().getName().equals( "cd" ) ) {
3840 if ( !it.next().getName().equals( "A" ) ) {
3843 if ( !it.next().getName().equals( "B" ) ) {
3846 if ( !it.next().getName().equals( "C" ) ) {
3849 if ( !it.next().getName().equals( "D" ) ) {
3852 if ( it.hasNext() ) {
3855 final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r",
3856 new NHXParser() )[ 0 ];
3857 PhylogenyNodeIterator it2;
3858 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3861 for( it2.reset(); it2.hasNext(); ) {
3864 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3865 if ( !it3.next().getName().equals( "r" ) ) {
3868 if ( !it3.next().getName().equals( "abc" ) ) {
3871 if ( !it3.next().getName().equals( "defg" ) ) {
3874 if ( !it3.next().getName().equals( "A" ) ) {
3877 if ( !it3.next().getName().equals( "B" ) ) {
3880 if ( !it3.next().getName().equals( "C" ) ) {
3883 if ( !it3.next().getName().equals( "D" ) ) {
3886 if ( !it3.next().getName().equals( "E" ) ) {
3889 if ( !it3.next().getName().equals( "F" ) ) {
3892 if ( !it3.next().getName().equals( "G" ) ) {
3895 if ( !it3.next().getName().equals( "1" ) ) {
3898 if ( !it3.next().getName().equals( "2" ) ) {
3901 if ( !it3.next().getName().equals( "3" ) ) {
3904 if ( !it3.next().getName().equals( "4" ) ) {
3907 if ( !it3.next().getName().equals( "5" ) ) {
3910 if ( !it3.next().getName().equals( "6" ) ) {
3913 if ( !it3.next().getName().equals( "f1" ) ) {
3916 if ( !it3.next().getName().equals( "f2" ) ) {
3919 if ( !it3.next().getName().equals( "f3" ) ) {
3922 if ( !it3.next().getName().equals( "a" ) ) {
3925 if ( !it3.next().getName().equals( "b" ) ) {
3928 if ( !it3.next().getName().equals( "f21" ) ) {
3931 if ( !it3.next().getName().equals( "X" ) ) {
3934 if ( !it3.next().getName().equals( "Y" ) ) {
3937 if ( !it3.next().getName().equals( "Z" ) ) {
3940 if ( it3.hasNext() ) {
3943 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3944 PhylogenyNodeIterator it4;
3945 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3948 for( it4.reset(); it4.hasNext(); ) {
3951 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3952 if ( !it5.next().getName().equals( "r" ) ) {
3955 if ( !it5.next().getName().equals( "A" ) ) {
3958 if ( !it5.next().getName().equals( "B" ) ) {
3961 if ( !it5.next().getName().equals( "C" ) ) {
3964 if ( !it5.next().getName().equals( "D" ) ) {
3967 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3968 PhylogenyNodeIterator it6;
3969 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3972 for( it6.reset(); it6.hasNext(); ) {
3975 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3976 if ( !it7.next().getName().equals( "A" ) ) {
3979 if ( it.hasNext() ) {
3983 catch ( final Exception e ) {
3984 e.printStackTrace( System.out );
3990 private static boolean testNodeRemoval() {
3992 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3993 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3994 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
3995 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
3998 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
3999 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
4000 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4003 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4004 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4005 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4009 catch ( final Exception e ) {
4010 e.printStackTrace( System.out );
4016 private static boolean testMidpointrooting() {
4018 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4019 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4020 PhylogenyMethods.midpointRoot( t0 );
4021 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4024 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4027 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4031 final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5",
4032 new NHXParser() )[ 0 ];
4033 if ( !t1.isRooted() ) {
4036 PhylogenyMethods.midpointRoot( t1 );
4037 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4040 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4043 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4046 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4049 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4052 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4055 t1.reRoot( t1.getNode( "A" ) );
4056 PhylogenyMethods.midpointRoot( t1 );
4057 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4060 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4063 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4066 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4069 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4073 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4077 catch ( final Exception e ) {
4078 e.printStackTrace( System.out );
4084 private static boolean testNexusCharactersParsing() {
4086 final NexusCharactersParser parser = new NexusCharactersParser();
4087 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4089 String[] labels = parser.getCharStateLabels();
4090 if ( labels.length != 7 ) {
4093 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4096 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4099 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4102 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4105 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4108 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4111 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4114 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4116 labels = parser.getCharStateLabels();
4117 if ( labels.length != 7 ) {
4120 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4123 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4126 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4129 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4132 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4135 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4138 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4142 catch ( final Exception e ) {
4143 e.printStackTrace( System.out );
4149 private static boolean testNexusMatrixParsing() {
4151 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4152 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4154 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4155 if ( m.getNumberOfCharacters() != 9 ) {
4158 if ( m.getNumberOfIdentifiers() != 5 ) {
4161 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4164 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4167 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4170 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4173 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4176 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4179 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4182 // if ( labels.length != 7 ) {
4185 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4188 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4191 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4194 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4197 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4200 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4203 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4206 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4208 // labels = parser.getCharStateLabels();
4209 // if ( labels.length != 7 ) {
4212 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4215 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4218 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4221 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4224 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4227 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4230 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4234 catch ( final Exception e ) {
4235 e.printStackTrace( System.out );
4241 private static boolean testNexusTreeParsing() {
4243 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4244 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4245 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4246 if ( phylogenies.length != 1 ) {
4249 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4252 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4256 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4257 if ( phylogenies.length != 1 ) {
4260 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4263 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4267 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4268 if ( phylogenies.length != 1 ) {
4271 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4274 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4277 if ( phylogenies[ 0 ].isRooted() ) {
4281 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4282 if ( phylogenies.length != 18 ) {
4285 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4288 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4291 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4294 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4297 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4300 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4303 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4306 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4309 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4312 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4315 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4318 if ( phylogenies[ 8 ].isRooted() ) {
4321 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4324 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4327 if ( !phylogenies[ 9 ].isRooted() ) {
4330 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4333 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4336 if ( !phylogenies[ 10 ].isRooted() ) {
4339 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4342 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4345 if ( phylogenies[ 11 ].isRooted() ) {
4348 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4351 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4354 if ( !phylogenies[ 12 ].isRooted() ) {
4357 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4360 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4363 if ( !phylogenies[ 13 ].isRooted() ) {
4366 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4369 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4372 if ( !phylogenies[ 14 ].isRooted() ) {
4375 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4378 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4381 if ( phylogenies[ 15 ].isRooted() ) {
4384 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4387 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4390 if ( !phylogenies[ 16 ].isRooted() ) {
4393 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4396 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4399 if ( phylogenies[ 17 ].isRooted() ) {
4402 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4406 catch ( final Exception e ) {
4407 e.printStackTrace( System.out );
4413 private static boolean testNexusTreeParsingTranslating() {
4415 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4416 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4417 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4418 if ( phylogenies.length != 1 ) {
4421 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4424 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4427 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4430 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4433 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4434 .equals( "Aranaeus" ) ) {
4438 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4439 if ( phylogenies.length != 3 ) {
4442 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4445 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4448 if ( phylogenies[ 0 ].isRooted() ) {
4451 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4454 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4457 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4458 .equals( "Aranaeus" ) ) {
4461 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4464 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4467 if ( phylogenies[ 1 ].isRooted() ) {
4470 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4473 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4476 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4477 .equals( "Aranaeus" ) ) {
4480 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4483 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4486 if ( !phylogenies[ 2 ].isRooted() ) {
4489 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4492 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4495 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4496 .equals( "Aranaeus" ) ) {
4500 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4501 if ( phylogenies.length != 3 ) {
4504 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4507 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4510 if ( phylogenies[ 0 ].isRooted() ) {
4513 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4516 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4519 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4520 .equals( "Aranaeus" ) ) {
4523 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4526 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4529 if ( phylogenies[ 1 ].isRooted() ) {
4532 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4535 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4538 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4539 .equals( "Aranaeus" ) ) {
4542 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4545 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4548 if ( !phylogenies[ 2 ].isRooted() ) {
4551 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4554 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4557 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4558 .equals( "Aranaeus" ) ) {
4562 catch ( final Exception e ) {
4563 e.printStackTrace( System.out );
4569 private static boolean testNHParsing() {
4571 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4572 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4573 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4576 final NHXParser nhxp = new NHXParser();
4577 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
4578 nhxp.setReplaceUnderscores( true );
4579 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4580 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4583 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4586 final Phylogeny p1b = factory
4587 .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
4588 new NHXParser() )[ 0 ];
4589 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4592 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4595 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4596 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4597 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4598 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4599 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4600 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4601 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4602 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4603 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4604 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4605 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4606 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4607 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4609 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4612 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4615 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4618 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4621 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4622 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4623 final String p16_S = "((A,B),C)";
4624 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4625 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4628 final String p17_S = "(C,(A,B))";
4629 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4630 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4633 final String p18_S = "((A,B),(C,D))";
4634 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4635 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4638 final String p19_S = "(((A,B),C),D)";
4639 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4640 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4643 final String p20_S = "(A,(B,(C,D)))";
4644 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4645 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4648 final String p21_S = "(A,(B,(C,(D,E))))";
4649 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4650 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4653 final String p22_S = "((((A,B),C),D),E)";
4654 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4655 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4658 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4659 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4660 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4663 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4664 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4665 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4668 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4669 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4670 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4671 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4674 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4677 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4678 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4679 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4680 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4681 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4682 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4683 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4684 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4685 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4686 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4689 final String p26_S = "(A,B)ab";
4690 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4691 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4694 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4695 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4697 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4700 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4701 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4702 final String p28_S3 = "(A,B)ab";
4703 final String p28_S4 = "((((A,B),C),D),;E;)";
4704 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4706 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4709 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4712 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4715 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4718 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";
4719 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4720 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4723 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";
4724 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4725 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4728 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4729 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4730 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4733 final String p33_S = "A";
4734 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4735 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4738 final String p34_S = "B;";
4739 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4740 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4743 final String p35_S = "B:0.2";
4744 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4745 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4748 final String p36_S = "(A)";
4749 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4750 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4753 final String p37_S = "((A))";
4754 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4755 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4758 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4759 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4760 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4763 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4764 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4765 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4768 final String p40_S = "(A,B,C)";
4769 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4770 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4773 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4774 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4775 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4778 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4779 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4780 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4783 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)";
4784 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4785 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4788 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)))";
4789 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4790 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4793 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4794 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4795 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4798 final String p46_S = "";
4799 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4800 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4803 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4804 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4807 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4808 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4811 final Phylogeny p49 = factory
4812 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4813 new NHXParser() )[ 0 ];
4814 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4817 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4818 if ( p50.getNode( "A" ) == null ) {
4821 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4822 .equals( "((A,B)ab:2.0[88],C);" ) ) {
4825 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4828 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4829 .equals( "((A,B)88:2.0,C);" ) ) {
4832 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4833 if ( p51.getNode( "A(A" ) == null ) {
4836 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4837 if ( p52.getNode( "A(A" ) == null ) {
4840 final Phylogeny p53 = factory
4841 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4842 new NHXParser() )[ 0 ];
4843 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4847 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
4848 if ( p54.getNode( "A" ) == null ) {
4851 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4852 .equals( "((A,B)[88],C);" ) ) {
4856 catch ( final Exception e ) {
4857 e.printStackTrace( System.out );
4863 private static boolean testNHParsingIter() {
4865 String p0_str = "(A,B);";
4866 NHXParser2 p = new NHXParser2();
4867 p.setSource( p0_str );
4868 Phylogeny p0 = p.getNext();
4869 if ( !p0.toNewHampshire().equals( p0_str ) ) {
4870 System.out.println( p0.toNewHampshire() );
4873 //if ( p.getNext() != null ) {
4877 String p00_str = "(A,B)root;";
4878 //p = new NHXParser2();
4879 p.setSource( p00_str );
4880 Phylogeny p00 = p.getNext();
4881 if ( !p00.toNewHampshire().equals( p00_str ) ) {
4882 System.out.println( p00.toNewHampshire() );
4886 String p000_str = "A;";
4887 p.setSource( p000_str );
4888 Phylogeny p000 = p.getNext();
4889 if ( !p000.toNewHampshire().equals( p000_str ) ) {
4890 System.out.println( p000.toNewHampshire() );
4894 String p0000_str = "A";
4895 p.setSource( p0000_str );
4896 Phylogeny p0000 = p.getNext();
4897 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
4898 System.out.println( p0000.toNewHampshire() );
4902 p.setSource( "(A)" );
4903 Phylogeny p00000 = p.getNext();
4904 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
4905 System.out.println( p00000.toNewHampshire() );
4909 // p.setSource( " " );
4910 // Phylogeny p000000 = p.getNext();
4911 // if ( !p000000.toNewHampshire().equals( "(A);" ) ) {
4912 // System.out.println( p000000.toNewHampshire() );
4916 String p1_str = "(A,B)(C,D)(E,F)(G,H)";
4917 p.setSource( p1_str );
4918 Phylogeny p1_0 = p.getNext();
4919 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
4920 System.out.println( p1_0.toNewHampshire() );
4923 Phylogeny p1_1 = p.getNext();
4924 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
4925 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
4928 Phylogeny p1_2 = p.getNext();
4929 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
4930 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
4933 Phylogeny p1_3 = p.getNext();
4934 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
4935 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
4939 String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
4940 p.setSource( p2_str );
4941 Phylogeny p2_0 = p.getNext();
4942 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
4943 System.out.println( p2_0.toNewHampshire() );
4946 Phylogeny p2_1 = p.getNext();
4947 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
4948 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
4951 Phylogeny p2_2 = p.getNext();
4952 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
4953 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
4956 Phylogeny p2_3 = p.getNext();
4957 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
4958 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
4961 Phylogeny p2_4 = p.getNext();
4962 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
4963 System.out.println( "(X) != " + p2_4.toNewHampshire() );
4967 catch ( final Exception e ) {
4968 e.printStackTrace( System.out );
4974 private static boolean testNHXconversion() {
4976 final PhylogenyNode n1 = new PhylogenyNode();
4977 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4978 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4979 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4980 final PhylogenyNode n5 = PhylogenyNode
4981 .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]" );
4982 final PhylogenyNode n6 = PhylogenyNode
4983 .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]" );
4984 if ( !n1.toNewHampshireX().equals( "" ) ) {
4987 if ( !n2.toNewHampshireX().equals( "" ) ) {
4990 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4993 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4996 if ( !n5.toNewHampshireX()
4997 .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]" ) ) {
5000 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]" ) ) {
5004 catch ( final Exception e ) {
5005 e.printStackTrace( System.out );
5011 private static boolean testTaxonomyExtraction() {
5013 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5014 NHXParser.TAXONOMY_EXTRACTION.YES );
5015 if ( n0.getNodeData().isHasTaxonomy() ) {
5018 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
5019 NHXParser.TAXONOMY_EXTRACTION.YES );
5020 if ( n1.getNodeData().isHasTaxonomy() ) {
5021 System.out.println( n1.toString() );
5024 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
5025 NHXParser.TAXONOMY_EXTRACTION.YES );
5026 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5027 System.out.println( n2.toString() );
5030 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
5031 NHXParser.TAXONOMY_EXTRACTION.YES );
5032 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5033 System.out.println( n3.toString() );
5036 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
5037 NHXParser.TAXONOMY_EXTRACTION.YES );
5038 if ( n4.getNodeData().isHasTaxonomy() ) {
5039 System.out.println( n4.toString() );
5042 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
5043 NHXParser.TAXONOMY_EXTRACTION.YES );
5044 if ( n5.getNodeData().isHasTaxonomy() ) {
5045 System.out.println( n5.toString() );
5048 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
5049 NHXParser.TAXONOMY_EXTRACTION.YES );
5050 if ( n6.getNodeData().isHasTaxonomy() ) {
5051 System.out.println( n6.toString() );
5054 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
5055 NHXParser.TAXONOMY_EXTRACTION.YES );
5056 if ( n7.getNodeData().isHasTaxonomy() ) {
5057 System.out.println( n7.toString() );
5060 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
5061 NHXParser.TAXONOMY_EXTRACTION.YES );
5062 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5063 System.out.println( n8.toString() );
5066 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
5067 NHXParser.TAXONOMY_EXTRACTION.YES );
5068 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5069 System.out.println( n9.toString() );
5072 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
5073 NHXParser.TAXONOMY_EXTRACTION.YES );
5074 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
5075 System.out.println( n10.toString() );
5078 final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
5079 NHXParser.TAXONOMY_EXTRACTION.YES );
5080 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
5081 System.out.println( n11.toString() );
5084 final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
5085 NHXParser.TAXONOMY_EXTRACTION.YES );
5086 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
5087 System.out.println( n12.toString() );
5090 final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
5091 NHXParser.TAXONOMY_EXTRACTION.YES );
5092 if ( n13.getNodeData().isHasTaxonomy() ) {
5093 System.out.println( n13.toString() );
5096 final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
5097 NHXParser.TAXONOMY_EXTRACTION.YES );
5098 if ( n14.getNodeData().isHasTaxonomy() ) {
5099 System.out.println( n14.toString() );
5102 final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
5103 NHXParser.TAXONOMY_EXTRACTION.YES );
5104 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
5105 System.out.println( n15.toString() );
5108 final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
5109 NHXParser.TAXONOMY_EXTRACTION.YES );
5110 if ( n16.getNodeData().isHasTaxonomy() ) {
5111 System.out.println( n16.toString() );
5114 final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
5115 NHXParser.TAXONOMY_EXTRACTION.YES );
5116 if ( n17.getNodeData().isHasTaxonomy() ) {
5117 System.out.println( n17.toString() );
5121 catch ( final Exception e ) {
5122 e.printStackTrace( System.out );
5128 private static boolean testNHXNodeParsing() {
5130 final PhylogenyNode n1 = new PhylogenyNode();
5131 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5132 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5133 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5134 final PhylogenyNode n5 = PhylogenyNode
5135 .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]" );
5136 if ( !n3.getName().equals( "n3" ) ) {
5139 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5142 if ( n3.isDuplication() ) {
5145 if ( n3.isHasAssignedEvent() ) {
5148 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
5151 if ( !n4.getName().equals( "n4" ) ) {
5154 if ( n4.getDistanceToParent() != 0.01 ) {
5157 if ( !n5.getName().equals( "n5" ) ) {
5160 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
5163 if ( n5.getDistanceToParent() != 0.1 ) {
5166 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
5169 if ( !n5.isDuplication() ) {
5172 if ( !n5.isHasAssignedEvent() ) {
5175 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
5178 final PhylogenyNode n8 = PhylogenyNode
5179 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5180 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
5183 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
5186 final PhylogenyNode n9 = PhylogenyNode
5187 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5188 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
5191 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
5194 final PhylogenyNode n10 = PhylogenyNode
5195 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5196 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
5199 final PhylogenyNode n20 = PhylogenyNode
5200 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5201 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
5204 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
5207 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
5208 NHXParser.TAXONOMY_EXTRACTION.YES );
5209 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
5212 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
5215 final PhylogenyNode n20xx = PhylogenyNode
5216 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5217 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
5220 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
5223 final PhylogenyNode n20xxx = PhylogenyNode
5224 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5225 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
5228 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
5231 final PhylogenyNode n20xxxx = PhylogenyNode
5232 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5233 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
5236 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
5239 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
5240 NHXParser.TAXONOMY_EXTRACTION.YES );
5241 if ( !n21.getName().equals( "n21_PIG" ) ) {
5244 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
5247 final PhylogenyNode n21x = PhylogenyNode
5248 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5249 if ( !n21x.getName().equals( "n21_PIG" ) ) {
5252 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
5255 final PhylogenyNode n22 = PhylogenyNode
5256 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5257 if ( !n22.getName().equals( "n22/PIG" ) ) {
5260 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
5263 final PhylogenyNode n23 = PhylogenyNode
5264 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5265 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
5268 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
5271 final PhylogenyNode a = PhylogenyNode
5272 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5273 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
5276 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
5279 final PhylogenyNode b = PhylogenyNode
5280 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5281 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
5284 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
5287 final PhylogenyNode c = PhylogenyNode
5288 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
5289 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5290 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
5293 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
5296 final PhylogenyNode c1 = PhylogenyNode
5297 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
5298 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5299 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
5302 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
5305 final PhylogenyNode c2 = PhylogenyNode
5306 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
5307 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5308 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
5311 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
5314 final PhylogenyNode d = PhylogenyNode
5315 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5316 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
5319 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
5322 final PhylogenyNode e = PhylogenyNode
5323 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5324 if ( !e.getName().equals( "n10_RAT1" ) ) {
5327 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
5330 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
5331 NHXParser.TAXONOMY_EXTRACTION.YES );
5332 if ( !e2.getName().equals( "n10_RAT1" ) ) {
5335 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
5338 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
5339 NHXParser.TAXONOMY_EXTRACTION.YES );
5340 if ( !e3.getName().equals( "n10_RAT~" ) ) {
5343 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
5346 final PhylogenyNode n11 = PhylogenyNode
5347 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
5348 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5349 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
5352 if ( n11.getDistanceToParent() != 0.4 ) {
5355 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
5358 final PhylogenyNode n12 = PhylogenyNode
5359 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
5360 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5361 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
5364 if ( n12.getDistanceToParent() != 0.4 ) {
5367 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
5370 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
5371 NHXParser.TAXONOMY_EXTRACTION.YES );
5372 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
5375 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
5378 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
5379 NHXParser.TAXONOMY_EXTRACTION.YES );
5380 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
5383 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
5386 if ( n1.getName().compareTo( "" ) != 0 ) {
5389 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5392 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5395 if ( n2.getName().compareTo( "" ) != 0 ) {
5398 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5401 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
5404 final PhylogenyNode n00 = PhylogenyNode
5405 .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]" );
5406 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
5409 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
5412 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
5413 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
5416 final PhylogenyNode n13 = PhylogenyNode
5417 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5418 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
5421 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
5424 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5427 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5430 final PhylogenyNode n14 = PhylogenyNode
5431 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5432 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
5435 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
5438 final PhylogenyNode n15 = PhylogenyNode
5439 .createInstanceFromNhxString( "something_wicked[123]",
5440 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5441 if ( !n15.getName().equals( "something_wicked" ) ) {
5444 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
5447 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
5450 final PhylogenyNode n16 = PhylogenyNode
5451 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5452 if ( !n16.getName().equals( "something_wicked2" ) ) {
5455 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
5458 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
5461 final PhylogenyNode n17 = PhylogenyNode
5462 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5463 if ( !n17.getName().equals( "something_wicked3" ) ) {
5466 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
5469 final PhylogenyNode n18 = PhylogenyNode
5470 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
5471 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
5474 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
5477 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
5480 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
5481 NHXParser.TAXONOMY_EXTRACTION.YES );
5482 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
5485 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5488 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
5489 NHXParser.TAXONOMY_EXTRACTION.YES );
5490 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
5493 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
5496 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
5497 NHXParser.TAXONOMY_EXTRACTION.YES );
5498 if ( n31.getNodeData().isHasTaxonomy() ) {
5501 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5502 NHXParser.TAXONOMY_EXTRACTION.YES );
5503 if ( n32.getNodeData().isHasTaxonomy() ) {
5507 catch ( final Exception e ) {
5508 e.printStackTrace( System.out );
5514 private static boolean testNHXParsing() {
5516 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5517 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
5518 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5521 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]";
5522 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
5523 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5526 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]";
5527 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
5528 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
5531 final Phylogeny[] p3 = factory
5532 .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]",
5534 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5537 final Phylogeny[] p4 = factory
5538 .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(]",
5540 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5543 final Phylogeny[] p5 = factory
5544 .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(((]",
5546 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
5549 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)";
5550 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)";
5551 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
5552 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
5555 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)))";
5556 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)))";
5557 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
5558 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
5561 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]) ))[,,, ])))))))";
5562 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
5563 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
5564 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
5567 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
5568 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5571 final Phylogeny p10 = factory
5572 .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]",
5573 new NHXParser() )[ 0 ];
5574 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
5578 catch ( final Exception e ) {
5579 e.printStackTrace( System.out );
5585 private static boolean testNHXParsingQuotes() {
5587 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5588 final NHXParser p = new NHXParser();
5589 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
5590 if ( phylogenies_0.length != 5 ) {
5593 final Phylogeny phy = phylogenies_0[ 4 ];
5594 if ( phy.getNumberOfExternalNodes() != 7 ) {
5597 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
5600 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5603 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5604 .getScientificName().equals( "hsapiens" ) ) {
5607 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5610 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5613 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5616 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5619 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5622 final NHXParser p1p = new NHXParser();
5623 p1p.setIgnoreQuotes( true );
5624 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5625 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5628 final NHXParser p2p = new NHXParser();
5629 p1p.setIgnoreQuotes( false );
5630 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5631 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5634 final NHXParser p3p = new NHXParser();
5635 p3p.setIgnoreQuotes( false );
5636 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5637 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5640 final NHXParser p4p = new NHXParser();
5641 p4p.setIgnoreQuotes( false );
5642 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5643 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5646 final Phylogeny p10 = factory
5647 .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]",
5648 new NHXParser() )[ 0 ];
5649 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]";
5650 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5653 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5654 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5658 final Phylogeny p12 = factory
5659 .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]",
5660 new NHXParser() )[ 0 ];
5661 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]";
5662 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5665 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5666 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5669 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;";
5670 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5673 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5674 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5678 catch ( final Exception e ) {
5679 e.printStackTrace( System.out );
5685 private static boolean testNHXParsingMB() {
5687 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5688 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5689 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5690 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5691 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5692 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5693 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5694 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5695 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5696 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5697 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5700 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5703 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5704 0.1100000000000000e+00 ) ) {
5707 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5710 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5713 final Phylogeny p2 = factory
5714 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5715 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5716 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5717 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5718 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5719 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5720 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5721 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5722 + "7.369400000000000e-02}])",
5723 new NHXParser() )[ 0 ];
5724 if ( p2.getNode( "1" ) == null ) {
5727 if ( p2.getNode( "2" ) == null ) {
5731 catch ( final Exception e ) {
5732 e.printStackTrace( System.out );
5739 private static boolean testPhylogenyBranch() {
5741 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5742 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5743 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5744 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5745 if ( !a1b1.equals( a1b1 ) ) {
5748 if ( !a1b1.equals( b1a1 ) ) {
5751 if ( !b1a1.equals( a1b1 ) ) {
5754 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5755 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5756 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5757 if ( a1_b1.equals( b1_a1 ) ) {
5760 if ( a1_b1.equals( a1_b1_ ) ) {
5763 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5764 if ( !a1_b1.equals( b1_a1_ ) ) {
5767 if ( a1_b1_.equals( b1_a1_ ) ) {
5770 if ( !a1_b1_.equals( b1_a1 ) ) {
5774 catch ( final Exception e ) {
5775 e.printStackTrace( System.out );
5781 private static boolean testPhyloXMLparsingOfDistributionElement() {
5783 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5784 PhyloXmlParser xml_parser = null;
5786 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5788 catch ( final Exception e ) {
5789 // Do nothing -- means were not running from jar.
5791 if ( xml_parser == null ) {
5792 xml_parser = new PhyloXmlParser();
5793 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5794 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5797 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5800 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5802 if ( xml_parser.getErrorCount() > 0 ) {
5803 System.out.println( xml_parser.getErrorMessages().toString() );
5806 if ( phylogenies_0.length != 1 ) {
5809 final Phylogeny t1 = phylogenies_0[ 0 ];
5810 PhylogenyNode n = null;
5811 Distribution d = null;
5812 n = t1.getNode( "root node" );
5813 if ( !n.getNodeData().isHasDistribution() ) {
5816 if ( n.getNodeData().getDistributions().size() != 1 ) {
5819 d = n.getNodeData().getDistribution();
5820 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5823 if ( d.getPoints().size() != 1 ) {
5826 if ( d.getPolygons() != null ) {
5829 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5832 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5835 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5838 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5841 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5844 n = t1.getNode( "node a" );
5845 if ( !n.getNodeData().isHasDistribution() ) {
5848 if ( n.getNodeData().getDistributions().size() != 2 ) {
5851 d = n.getNodeData().getDistribution( 1 );
5852 if ( !d.getDesc().equals( "San Diego" ) ) {
5855 if ( d.getPoints().size() != 1 ) {
5858 if ( d.getPolygons() != null ) {
5861 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5864 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5867 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5870 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5873 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5876 n = t1.getNode( "node bb" );
5877 if ( !n.getNodeData().isHasDistribution() ) {
5880 if ( n.getNodeData().getDistributions().size() != 1 ) {
5883 d = n.getNodeData().getDistribution( 0 );
5884 if ( d.getPoints().size() != 3 ) {
5887 if ( d.getPolygons().size() != 2 ) {
5890 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5893 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5896 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5899 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5902 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5905 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5908 Polygon p = d.getPolygons().get( 0 );
5909 if ( p.getPoints().size() != 3 ) {
5912 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5915 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5918 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5921 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5924 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5927 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5930 p = d.getPolygons().get( 1 );
5931 if ( p.getPoints().size() != 3 ) {
5934 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5937 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5940 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5944 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5945 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5946 if ( rt.length != 1 ) {
5949 final Phylogeny t1_rt = rt[ 0 ];
5950 n = t1_rt.getNode( "root node" );
5951 if ( !n.getNodeData().isHasDistribution() ) {
5954 if ( n.getNodeData().getDistributions().size() != 1 ) {
5957 d = n.getNodeData().getDistribution();
5958 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5961 if ( d.getPoints().size() != 1 ) {
5964 if ( d.getPolygons() != null ) {
5967 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5970 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5973 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5976 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5979 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5982 n = t1_rt.getNode( "node a" );
5983 if ( !n.getNodeData().isHasDistribution() ) {
5986 if ( n.getNodeData().getDistributions().size() != 2 ) {
5989 d = n.getNodeData().getDistribution( 1 );
5990 if ( !d.getDesc().equals( "San Diego" ) ) {
5993 if ( d.getPoints().size() != 1 ) {
5996 if ( d.getPolygons() != null ) {
5999 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6002 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6005 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6008 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6011 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6014 n = t1_rt.getNode( "node bb" );
6015 if ( !n.getNodeData().isHasDistribution() ) {
6018 if ( n.getNodeData().getDistributions().size() != 1 ) {
6021 d = n.getNodeData().getDistribution( 0 );
6022 if ( d.getPoints().size() != 3 ) {
6025 if ( d.getPolygons().size() != 2 ) {
6028 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6031 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6034 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6037 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6040 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6043 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6046 p = d.getPolygons().get( 0 );
6047 if ( p.getPoints().size() != 3 ) {
6050 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6053 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6056 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6059 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6062 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6065 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6068 p = d.getPolygons().get( 1 );
6069 if ( p.getPoints().size() != 3 ) {
6072 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6075 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6078 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6082 catch ( final Exception e ) {
6083 e.printStackTrace( System.out );
6089 private static boolean testPostOrderIterator() {
6091 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6092 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6093 PhylogenyNodeIterator it0;
6094 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
6097 for( it0.reset(); it0.hasNext(); ) {
6100 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6101 final PhylogenyNodeIterator it = t1.iteratorPostorder();
6102 if ( !it.next().getName().equals( "A" ) ) {
6105 if ( !it.next().getName().equals( "B" ) ) {
6108 if ( !it.next().getName().equals( "ab" ) ) {
6111 if ( !it.next().getName().equals( "C" ) ) {
6114 if ( !it.next().getName().equals( "D" ) ) {
6117 if ( !it.next().getName().equals( "cd" ) ) {
6120 if ( !it.next().getName().equals( "abcd" ) ) {
6123 if ( !it.next().getName().equals( "E" ) ) {
6126 if ( !it.next().getName().equals( "F" ) ) {
6129 if ( !it.next().getName().equals( "ef" ) ) {
6132 if ( !it.next().getName().equals( "G" ) ) {
6135 if ( !it.next().getName().equals( "H" ) ) {
6138 if ( !it.next().getName().equals( "gh" ) ) {
6141 if ( !it.next().getName().equals( "efgh" ) ) {
6144 if ( !it.next().getName().equals( "r" ) ) {
6147 if ( it.hasNext() ) {
6151 catch ( final Exception e ) {
6152 e.printStackTrace( System.out );
6158 private static boolean testPreOrderIterator() {
6160 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6161 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6162 PhylogenyNodeIterator it0;
6163 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
6166 for( it0.reset(); it0.hasNext(); ) {
6169 PhylogenyNodeIterator it = t0.iteratorPreorder();
6170 if ( !it.next().getName().equals( "r" ) ) {
6173 if ( !it.next().getName().equals( "ab" ) ) {
6176 if ( !it.next().getName().equals( "A" ) ) {
6179 if ( !it.next().getName().equals( "B" ) ) {
6182 if ( !it.next().getName().equals( "cd" ) ) {
6185 if ( !it.next().getName().equals( "C" ) ) {
6188 if ( !it.next().getName().equals( "D" ) ) {
6191 if ( it.hasNext() ) {
6194 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
6195 it = t1.iteratorPreorder();
6196 if ( !it.next().getName().equals( "r" ) ) {
6199 if ( !it.next().getName().equals( "abcd" ) ) {
6202 if ( !it.next().getName().equals( "ab" ) ) {
6205 if ( !it.next().getName().equals( "A" ) ) {
6208 if ( !it.next().getName().equals( "B" ) ) {
6211 if ( !it.next().getName().equals( "cd" ) ) {
6214 if ( !it.next().getName().equals( "C" ) ) {
6217 if ( !it.next().getName().equals( "D" ) ) {
6220 if ( !it.next().getName().equals( "efgh" ) ) {
6223 if ( !it.next().getName().equals( "ef" ) ) {
6226 if ( !it.next().getName().equals( "E" ) ) {
6229 if ( !it.next().getName().equals( "F" ) ) {
6232 if ( !it.next().getName().equals( "gh" ) ) {
6235 if ( !it.next().getName().equals( "G" ) ) {
6238 if ( !it.next().getName().equals( "H" ) ) {
6241 if ( it.hasNext() ) {
6245 catch ( final Exception e ) {
6246 e.printStackTrace( System.out );
6252 private static boolean testPropertiesMap() {
6254 final PropertiesMap pm = new PropertiesMap();
6255 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6256 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
6257 final Property p2 = new Property( "something:else",
6259 "improbable:research",
6262 pm.addProperty( p0 );
6263 pm.addProperty( p1 );
6264 pm.addProperty( p2 );
6265 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
6268 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
6271 if ( pm.getProperties().size() != 3 ) {
6274 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
6277 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6280 if ( pm.getProperties().size() != 3 ) {
6283 pm.removeProperty( "dimensions:diameter" );
6284 if ( pm.getProperties().size() != 2 ) {
6287 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
6290 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
6294 catch ( final Exception e ) {
6295 e.printStackTrace( System.out );
6301 private static boolean testReIdMethods() {
6303 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6304 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
6305 final int count = PhylogenyNode.getNodeCount();
6307 if ( p.getNode( "r" ).getId() != count ) {
6310 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
6313 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
6316 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
6319 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
6322 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
6325 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
6328 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
6331 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
6334 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
6337 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
6340 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
6343 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
6346 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
6349 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
6353 catch ( final Exception e ) {
6354 e.printStackTrace( System.out );
6360 private static boolean testRerooting() {
6362 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6363 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",
6364 new NHXParser() )[ 0 ];
6365 if ( !t1.isRooted() ) {
6368 t1.reRoot( t1.getNode( "D" ) );
6369 t1.reRoot( t1.getNode( "CD" ) );
6370 t1.reRoot( t1.getNode( "A" ) );
6371 t1.reRoot( t1.getNode( "B" ) );
6372 t1.reRoot( t1.getNode( "AB" ) );
6373 t1.reRoot( t1.getNode( "D" ) );
6374 t1.reRoot( t1.getNode( "C" ) );
6375 t1.reRoot( t1.getNode( "CD" ) );
6376 t1.reRoot( t1.getNode( "A" ) );
6377 t1.reRoot( t1.getNode( "B" ) );
6378 t1.reRoot( t1.getNode( "AB" ) );
6379 t1.reRoot( t1.getNode( "D" ) );
6380 t1.reRoot( t1.getNode( "D" ) );
6381 t1.reRoot( t1.getNode( "C" ) );
6382 t1.reRoot( t1.getNode( "A" ) );
6383 t1.reRoot( t1.getNode( "B" ) );
6384 t1.reRoot( t1.getNode( "AB" ) );
6385 t1.reRoot( t1.getNode( "C" ) );
6386 t1.reRoot( t1.getNode( "D" ) );
6387 t1.reRoot( t1.getNode( "CD" ) );
6388 t1.reRoot( t1.getNode( "D" ) );
6389 t1.reRoot( t1.getNode( "A" ) );
6390 t1.reRoot( t1.getNode( "B" ) );
6391 t1.reRoot( t1.getNode( "AB" ) );
6392 t1.reRoot( t1.getNode( "C" ) );
6393 t1.reRoot( t1.getNode( "D" ) );
6394 t1.reRoot( t1.getNode( "CD" ) );
6395 t1.reRoot( t1.getNode( "D" ) );
6396 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
6399 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
6402 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
6405 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
6408 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
6411 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
6414 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",
6415 new NHXParser() )[ 0 ];
6416 t2.reRoot( t2.getNode( "A" ) );
6417 t2.reRoot( t2.getNode( "D" ) );
6418 t2.reRoot( t2.getNode( "ABC" ) );
6419 t2.reRoot( t2.getNode( "A" ) );
6420 t2.reRoot( t2.getNode( "B" ) );
6421 t2.reRoot( t2.getNode( "D" ) );
6422 t2.reRoot( t2.getNode( "C" ) );
6423 t2.reRoot( t2.getNode( "ABC" ) );
6424 t2.reRoot( t2.getNode( "A" ) );
6425 t2.reRoot( t2.getNode( "B" ) );
6426 t2.reRoot( t2.getNode( "AB" ) );
6427 t2.reRoot( t2.getNode( "AB" ) );
6428 t2.reRoot( t2.getNode( "D" ) );
6429 t2.reRoot( t2.getNode( "C" ) );
6430 t2.reRoot( t2.getNode( "B" ) );
6431 t2.reRoot( t2.getNode( "AB" ) );
6432 t2.reRoot( t2.getNode( "D" ) );
6433 t2.reRoot( t2.getNode( "D" ) );
6434 t2.reRoot( t2.getNode( "ABC" ) );
6435 t2.reRoot( t2.getNode( "A" ) );
6436 t2.reRoot( t2.getNode( "B" ) );
6437 t2.reRoot( t2.getNode( "AB" ) );
6438 t2.reRoot( t2.getNode( "D" ) );
6439 t2.reRoot( t2.getNode( "C" ) );
6440 t2.reRoot( t2.getNode( "ABC" ) );
6441 t2.reRoot( t2.getNode( "A" ) );
6442 t2.reRoot( t2.getNode( "B" ) );
6443 t2.reRoot( t2.getNode( "AB" ) );
6444 t2.reRoot( t2.getNode( "D" ) );
6445 t2.reRoot( t2.getNode( "D" ) );
6446 t2.reRoot( t2.getNode( "C" ) );
6447 t2.reRoot( t2.getNode( "A" ) );
6448 t2.reRoot( t2.getNode( "B" ) );
6449 t2.reRoot( t2.getNode( "AB" ) );
6450 t2.reRoot( t2.getNode( "C" ) );
6451 t2.reRoot( t2.getNode( "D" ) );
6452 t2.reRoot( t2.getNode( "ABC" ) );
6453 t2.reRoot( t2.getNode( "D" ) );
6454 t2.reRoot( t2.getNode( "A" ) );
6455 t2.reRoot( t2.getNode( "B" ) );
6456 t2.reRoot( t2.getNode( "AB" ) );
6457 t2.reRoot( t2.getNode( "C" ) );
6458 t2.reRoot( t2.getNode( "D" ) );
6459 t2.reRoot( t2.getNode( "ABC" ) );
6460 t2.reRoot( t2.getNode( "D" ) );
6461 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6464 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6467 t2.reRoot( t2.getNode( "ABC" ) );
6468 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6471 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6474 t2.reRoot( t2.getNode( "AB" ) );
6475 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6478 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6481 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6484 t2.reRoot( t2.getNode( "AB" ) );
6485 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6488 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6491 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6494 t2.reRoot( t2.getNode( "D" ) );
6495 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6498 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6501 t2.reRoot( t2.getNode( "ABC" ) );
6502 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
6505 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
6508 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
6509 new NHXParser() )[ 0 ];
6510 t3.reRoot( t3.getNode( "B" ) );
6511 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6514 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6517 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6520 t3.reRoot( t3.getNode( "B" ) );
6521 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6524 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6527 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6530 t3.reRoot( t3.getRoot() );
6531 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6534 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
6537 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
6541 catch ( final Exception e ) {
6542 e.printStackTrace( System.out );
6548 private static boolean testSDIse() {
6550 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6551 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
6552 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
6553 gene1.setRooted( true );
6554 species1.setRooted( true );
6555 final SDI sdi = new SDI( gene1, species1 );
6556 if ( !gene1.getRoot().isDuplication() ) {
6559 final Phylogeny species2 = factory
6560 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6561 new NHXParser() )[ 0 ];
6562 final Phylogeny gene2 = factory
6563 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6564 new NHXParser() )[ 0 ];
6565 species2.setRooted( true );
6566 gene2.setRooted( true );
6567 final SDI sdi2 = new SDI( gene2, species2 );
6568 if ( sdi2.getDuplicationsSum() != 0 ) {
6571 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
6574 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
6577 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
6580 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
6583 if ( !gene2.getNode( "r" ).isSpeciation() ) {
6586 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
6589 final Phylogeny species3 = factory
6590 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6591 new NHXParser() )[ 0 ];
6592 final Phylogeny gene3 = factory
6593 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6594 new NHXParser() )[ 0 ];
6595 species3.setRooted( true );
6596 gene3.setRooted( true );
6597 final SDI sdi3 = new SDI( gene3, species3 );
6598 if ( sdi3.getDuplicationsSum() != 1 ) {
6601 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6604 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6607 final Phylogeny species4 = factory
6608 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6609 new NHXParser() )[ 0 ];
6610 final Phylogeny gene4 = factory
6611 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6612 new NHXParser() )[ 0 ];
6613 species4.setRooted( true );
6614 gene4.setRooted( true );
6615 final SDI sdi4 = new SDI( gene4, species4 );
6616 if ( sdi4.getDuplicationsSum() != 1 ) {
6619 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6622 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6625 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6628 if ( species4.getNumberOfExternalNodes() != 6 ) {
6631 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6634 final Phylogeny species5 = factory
6635 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6636 new NHXParser() )[ 0 ];
6637 final Phylogeny gene5 = factory
6638 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6639 new NHXParser() )[ 0 ];
6640 species5.setRooted( true );
6641 gene5.setRooted( true );
6642 final SDI sdi5 = new SDI( gene5, species5 );
6643 if ( sdi5.getDuplicationsSum() != 2 ) {
6646 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6649 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6652 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6655 if ( species5.getNumberOfExternalNodes() != 6 ) {
6658 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6661 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6662 // Conjecture for Comparing Molecular Phylogenies"
6663 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6664 final Phylogeny species6 = factory
6665 .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,"
6666 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6667 new NHXParser() )[ 0 ];
6668 final Phylogeny gene6 = factory
6669 .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,"
6670 + "((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,"
6671 + "(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;",
6672 new NHXParser() )[ 0 ];
6673 species6.setRooted( true );
6674 gene6.setRooted( true );
6675 final SDI sdi6 = new SDI( gene6, species6 );
6676 if ( sdi6.getDuplicationsSum() != 3 ) {
6679 if ( !gene6.getNode( "r" ).isDuplication() ) {
6682 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6685 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6688 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6691 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6694 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6697 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6700 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6703 sdi6.computeMappingCostL();
6704 if ( sdi6.computeMappingCostL() != 17 ) {
6707 if ( species6.getNumberOfExternalNodes() != 9 ) {
6710 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6713 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6714 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6715 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6716 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6717 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6718 species7.setRooted( true );
6719 final Phylogeny gene7_1 = Test
6720 .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])" );
6721 gene7_1.setRooted( true );
6722 final SDI sdi7 = new SDI( gene7_1, species7 );
6723 if ( sdi7.getDuplicationsSum() != 0 ) {
6726 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6729 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6732 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6735 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6738 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6741 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6744 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6747 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6750 final Phylogeny gene7_2 = Test
6751 .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])" );
6752 gene7_2.setRooted( true );
6753 final SDI sdi7_2 = new SDI( gene7_2, species7 );
6754 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6757 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6760 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6763 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6766 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6769 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6772 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6775 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6778 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6781 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6785 catch ( final Exception e ) {
6791 private static boolean testSDIunrooted() {
6793 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6794 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6795 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6796 final Iterator<PhylogenyBranch> iter = l.iterator();
6797 PhylogenyBranch br = iter.next();
6798 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6801 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6805 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6808 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6812 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6815 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6819 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6822 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6826 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6829 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6833 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6836 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6840 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6843 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6847 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6850 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6854 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6857 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6861 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6864 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6868 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6871 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6875 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6878 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6882 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6885 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6889 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6892 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6896 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6899 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6902 if ( iter.hasNext() ) {
6905 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6906 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6907 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6909 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6912 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6916 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6919 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6923 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6926 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6929 if ( iter1.hasNext() ) {
6932 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6933 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6934 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6936 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6939 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6943 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6946 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6950 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6953 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6956 if ( iter2.hasNext() ) {
6959 final Phylogeny species0 = factory
6960 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6961 new NHXParser() )[ 0 ];
6962 final Phylogeny gene1 = factory
6963 .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])",
6964 new NHXParser() )[ 0 ];
6965 species0.setRooted( true );
6966 gene1.setRooted( true );
6967 final SDIR sdi_unrooted = new SDIR();
6968 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6969 if ( sdi_unrooted.getCount() != 1 ) {
6972 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6975 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6978 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6981 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6984 final Phylogeny gene2 = factory
6985 .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])",
6986 new NHXParser() )[ 0 ];
6987 gene2.setRooted( true );
6988 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6989 if ( sdi_unrooted.getCount() != 1 ) {
6992 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6995 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6998 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7001 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7004 final Phylogeny species6 = factory
7005 .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,"
7006 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7007 new NHXParser() )[ 0 ];
7008 final Phylogeny gene6 = factory
7009 .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],"
7010 + "(((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],"
7011 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7012 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7013 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7014 new NHXParser() )[ 0 ];
7015 species6.setRooted( true );
7016 gene6.setRooted( true );
7017 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7018 if ( sdi_unrooted.getCount() != 1 ) {
7021 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7024 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7027 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7030 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7033 if ( !p6[ 0 ].getRoot().isDuplication() ) {
7036 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7039 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7042 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
7045 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7048 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
7051 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
7054 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7058 final Phylogeny species7 = factory
7059 .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,"
7060 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7061 new NHXParser() )[ 0 ];
7062 final Phylogeny gene7 = factory
7063 .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],"
7064 + "(((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],"
7065 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7066 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7067 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7068 new NHXParser() )[ 0 ];
7069 species7.setRooted( true );
7070 gene7.setRooted( true );
7071 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
7072 if ( sdi_unrooted.getCount() != 1 ) {
7075 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7078 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7081 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7084 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
7087 if ( !p7[ 0 ].getRoot().isDuplication() ) {
7090 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7093 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7096 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
7099 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7102 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
7105 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
7108 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7112 final Phylogeny species8 = factory
7113 .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,"
7114 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7115 new NHXParser() )[ 0 ];
7116 final Phylogeny gene8 = factory
7117 .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],"
7118 + "(((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],"
7119 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7120 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7121 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7122 new NHXParser() )[ 0 ];
7123 species8.setRooted( true );
7124 gene8.setRooted( true );
7125 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
7126 if ( sdi_unrooted.getCount() != 1 ) {
7129 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7132 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7135 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7138 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7141 if ( !p8[ 0 ].getRoot().isDuplication() ) {
7144 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7147 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7150 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
7153 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7156 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
7159 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
7162 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7167 catch ( final Exception e ) {
7168 e.printStackTrace( System.out );
7174 private static boolean testSplit() {
7176 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7177 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7178 //Archaeopteryx.createApplication( p0 );
7179 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7180 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7181 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7182 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7183 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7184 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7185 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7186 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7187 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7188 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7189 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
7190 // System.out.println( s0.toString() );
7192 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7193 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7194 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7195 if ( s0.match( query_nodes ) ) {
7198 query_nodes = new HashSet<PhylogenyNode>();
7199 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7201 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7202 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7203 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7205 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7206 if ( !s0.match( query_nodes ) ) {
7210 query_nodes = new HashSet<PhylogenyNode>();
7211 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7212 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7213 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7214 if ( !s0.match( query_nodes ) ) {
7218 query_nodes = new HashSet<PhylogenyNode>();
7219 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7220 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7223 if ( !s0.match( query_nodes ) ) {
7227 query_nodes = new HashSet<PhylogenyNode>();
7228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7230 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7232 if ( !s0.match( query_nodes ) ) {
7236 query_nodes = new HashSet<PhylogenyNode>();
7237 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7238 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7239 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7240 if ( !s0.match( query_nodes ) ) {
7244 query_nodes = new HashSet<PhylogenyNode>();
7245 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7246 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7247 if ( !s0.match( query_nodes ) ) {
7251 query_nodes = new HashSet<PhylogenyNode>();
7252 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7253 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7254 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7255 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7256 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7257 if ( !s0.match( query_nodes ) ) {
7261 query_nodes = new HashSet<PhylogenyNode>();
7262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7265 if ( !s0.match( query_nodes ) ) {
7269 query_nodes = new HashSet<PhylogenyNode>();
7270 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7271 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7273 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7274 if ( !s0.match( query_nodes ) ) {
7278 query_nodes = new HashSet<PhylogenyNode>();
7279 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7280 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7281 if ( s0.match( query_nodes ) ) {
7285 query_nodes = new HashSet<PhylogenyNode>();
7286 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7287 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7288 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7289 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7290 if ( s0.match( query_nodes ) ) {
7294 query_nodes = new HashSet<PhylogenyNode>();
7295 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7297 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7298 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7299 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7300 if ( s0.match( query_nodes ) ) {
7304 query_nodes = new HashSet<PhylogenyNode>();
7305 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7306 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7307 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7308 if ( s0.match( query_nodes ) ) {
7312 query_nodes = new HashSet<PhylogenyNode>();
7313 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7314 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7315 if ( s0.match( query_nodes ) ) {
7319 query_nodes = new HashSet<PhylogenyNode>();
7320 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7321 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7322 if ( s0.match( query_nodes ) ) {
7326 query_nodes = new HashSet<PhylogenyNode>();
7327 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7328 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7329 if ( s0.match( query_nodes ) ) {
7333 query_nodes = new HashSet<PhylogenyNode>();
7334 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7335 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7336 if ( s0.match( query_nodes ) ) {
7340 query_nodes = new HashSet<PhylogenyNode>();
7341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7342 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7343 if ( s0.match( query_nodes ) ) {
7347 query_nodes = new HashSet<PhylogenyNode>();
7348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7350 if ( s0.match( query_nodes ) ) {
7354 query_nodes = new HashSet<PhylogenyNode>();
7355 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7358 if ( s0.match( query_nodes ) ) {
7362 query_nodes = new HashSet<PhylogenyNode>();
7363 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7366 if ( s0.match( query_nodes ) ) {
7370 query_nodes = new HashSet<PhylogenyNode>();
7371 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7374 if ( s0.match( query_nodes ) ) {
7378 query_nodes = new HashSet<PhylogenyNode>();
7379 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7380 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7383 if ( s0.match( query_nodes ) ) {
7387 // query_nodes = new HashSet<PhylogenyNode>();
7388 // query_nodes.add( new PhylogenyNode( "X" ) );
7389 // query_nodes.add( new PhylogenyNode( "Y" ) );
7390 // query_nodes.add( new PhylogenyNode( "A" ) );
7391 // query_nodes.add( new PhylogenyNode( "B" ) );
7392 // query_nodes.add( new PhylogenyNode( "C" ) );
7393 // query_nodes.add( new PhylogenyNode( "D" ) );
7394 // query_nodes.add( new PhylogenyNode( "E" ) );
7395 // query_nodes.add( new PhylogenyNode( "F" ) );
7396 // query_nodes.add( new PhylogenyNode( "G" ) );
7397 // if ( !s0.match( query_nodes ) ) {
7400 // query_nodes = new HashSet<PhylogenyNode>();
7401 // query_nodes.add( new PhylogenyNode( "X" ) );
7402 // query_nodes.add( new PhylogenyNode( "Y" ) );
7403 // query_nodes.add( new PhylogenyNode( "A" ) );
7404 // query_nodes.add( new PhylogenyNode( "B" ) );
7405 // query_nodes.add( new PhylogenyNode( "C" ) );
7406 // if ( !s0.match( query_nodes ) ) {
7410 // query_nodes = new HashSet<PhylogenyNode>();
7411 // query_nodes.add( new PhylogenyNode( "X" ) );
7412 // query_nodes.add( new PhylogenyNode( "Y" ) );
7413 // query_nodes.add( new PhylogenyNode( "D" ) );
7414 // query_nodes.add( new PhylogenyNode( "E" ) );
7415 // query_nodes.add( new PhylogenyNode( "F" ) );
7416 // query_nodes.add( new PhylogenyNode( "G" ) );
7417 // if ( !s0.match( query_nodes ) ) {
7421 // query_nodes = new HashSet<PhylogenyNode>();
7422 // query_nodes.add( new PhylogenyNode( "X" ) );
7423 // query_nodes.add( new PhylogenyNode( "Y" ) );
7424 // query_nodes.add( new PhylogenyNode( "A" ) );
7425 // query_nodes.add( new PhylogenyNode( "B" ) );
7426 // query_nodes.add( new PhylogenyNode( "C" ) );
7427 // query_nodes.add( new PhylogenyNode( "D" ) );
7428 // if ( !s0.match( query_nodes ) ) {
7432 // query_nodes = new HashSet<PhylogenyNode>();
7433 // query_nodes.add( new PhylogenyNode( "X" ) );
7434 // query_nodes.add( new PhylogenyNode( "Y" ) );
7435 // query_nodes.add( new PhylogenyNode( "E" ) );
7436 // query_nodes.add( new PhylogenyNode( "F" ) );
7437 // query_nodes.add( new PhylogenyNode( "G" ) );
7438 // if ( !s0.match( query_nodes ) ) {
7442 // query_nodes = new HashSet<PhylogenyNode>();
7443 // query_nodes.add( new PhylogenyNode( "X" ) );
7444 // query_nodes.add( new PhylogenyNode( "Y" ) );
7445 // query_nodes.add( new PhylogenyNode( "F" ) );
7446 // query_nodes.add( new PhylogenyNode( "G" ) );
7447 // if ( !s0.match( query_nodes ) ) {
7451 query_nodes = new HashSet<PhylogenyNode>();
7452 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7453 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7454 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7455 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7456 if ( s0.match( query_nodes ) ) {
7460 query_nodes = new HashSet<PhylogenyNode>();
7461 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7462 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7463 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7464 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7465 if ( s0.match( query_nodes ) ) {
7468 ///////////////////////////
7470 query_nodes = new HashSet<PhylogenyNode>();
7471 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7472 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7473 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7474 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7475 if ( s0.match( query_nodes ) ) {
7479 query_nodes = new HashSet<PhylogenyNode>();
7480 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7481 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7482 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7484 if ( s0.match( query_nodes ) ) {
7488 query_nodes = new HashSet<PhylogenyNode>();
7489 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7490 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7491 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7493 if ( s0.match( query_nodes ) ) {
7497 query_nodes = new HashSet<PhylogenyNode>();
7498 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7499 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7500 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7501 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7502 if ( s0.match( query_nodes ) ) {
7506 query_nodes = new HashSet<PhylogenyNode>();
7507 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7508 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7509 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7510 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7511 if ( s0.match( query_nodes ) ) {
7515 query_nodes = new HashSet<PhylogenyNode>();
7516 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7517 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7518 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7519 if ( s0.match( query_nodes ) ) {
7523 query_nodes = new HashSet<PhylogenyNode>();
7524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7525 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7526 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7527 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7528 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7529 if ( s0.match( query_nodes ) ) {
7533 query_nodes = new HashSet<PhylogenyNode>();
7534 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7535 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7536 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7537 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7539 if ( s0.match( query_nodes ) ) {
7543 query_nodes = new HashSet<PhylogenyNode>();
7544 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7545 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7549 if ( s0.match( query_nodes ) ) {
7553 query_nodes = new HashSet<PhylogenyNode>();
7554 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
7555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
7556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7560 if ( s0.match( query_nodes ) ) {
7564 catch ( final Exception e ) {
7565 e.printStackTrace();
7571 private static boolean testSplitStrict() {
7573 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7574 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
7575 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
7576 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7577 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7578 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7579 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7580 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7581 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7582 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7583 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
7584 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
7585 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7586 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7587 if ( s0.match( query_nodes ) ) {
7590 query_nodes = new HashSet<PhylogenyNode>();
7591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7593 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7594 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7595 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7596 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7598 if ( !s0.match( query_nodes ) ) {
7602 query_nodes = new HashSet<PhylogenyNode>();
7603 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7604 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7606 if ( !s0.match( query_nodes ) ) {
7610 query_nodes = new HashSet<PhylogenyNode>();
7611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7612 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7615 if ( !s0.match( query_nodes ) ) {
7619 query_nodes = new HashSet<PhylogenyNode>();
7620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7624 if ( !s0.match( query_nodes ) ) {
7628 query_nodes = new HashSet<PhylogenyNode>();
7629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7632 if ( !s0.match( query_nodes ) ) {
7636 query_nodes = new HashSet<PhylogenyNode>();
7637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7638 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7639 if ( !s0.match( query_nodes ) ) {
7643 query_nodes = new HashSet<PhylogenyNode>();
7644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7645 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7646 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7649 if ( !s0.match( query_nodes ) ) {
7653 query_nodes = new HashSet<PhylogenyNode>();
7654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7657 if ( !s0.match( query_nodes ) ) {
7661 query_nodes = new HashSet<PhylogenyNode>();
7662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7665 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7666 if ( !s0.match( query_nodes ) ) {
7670 query_nodes = new HashSet<PhylogenyNode>();
7671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7673 if ( s0.match( query_nodes ) ) {
7677 query_nodes = new HashSet<PhylogenyNode>();
7678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7679 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7680 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7682 if ( s0.match( query_nodes ) ) {
7686 query_nodes = new HashSet<PhylogenyNode>();
7687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7690 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7691 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7692 if ( s0.match( query_nodes ) ) {
7696 query_nodes = new HashSet<PhylogenyNode>();
7697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7698 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7700 if ( s0.match( query_nodes ) ) {
7704 query_nodes = new HashSet<PhylogenyNode>();
7705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7706 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7707 if ( s0.match( query_nodes ) ) {
7711 query_nodes = new HashSet<PhylogenyNode>();
7712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7713 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7714 if ( s0.match( query_nodes ) ) {
7718 query_nodes = new HashSet<PhylogenyNode>();
7719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7720 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7721 if ( s0.match( query_nodes ) ) {
7725 query_nodes = new HashSet<PhylogenyNode>();
7726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7727 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7728 if ( s0.match( query_nodes ) ) {
7732 query_nodes = new HashSet<PhylogenyNode>();
7733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7734 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7735 if ( s0.match( query_nodes ) ) {
7739 query_nodes = new HashSet<PhylogenyNode>();
7740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7742 if ( s0.match( query_nodes ) ) {
7746 query_nodes = new HashSet<PhylogenyNode>();
7747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7750 if ( s0.match( query_nodes ) ) {
7754 query_nodes = new HashSet<PhylogenyNode>();
7755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7756 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7757 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7758 if ( s0.match( query_nodes ) ) {
7762 query_nodes = new HashSet<PhylogenyNode>();
7763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7764 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7765 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7766 if ( s0.match( query_nodes ) ) {
7770 query_nodes = new HashSet<PhylogenyNode>();
7771 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7772 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7773 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7774 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7775 if ( s0.match( query_nodes ) ) {
7779 catch ( final Exception e ) {
7780 e.printStackTrace();
7786 private static boolean testSubtreeDeletion() {
7788 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7789 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7790 t1.deleteSubtree( t1.getNode( "A" ), false );
7791 if ( t1.getNumberOfExternalNodes() != 5 ) {
7794 t1.toNewHampshireX();
7795 t1.deleteSubtree( t1.getNode( "E" ), false );
7796 if ( t1.getNumberOfExternalNodes() != 4 ) {
7799 t1.toNewHampshireX();
7800 t1.deleteSubtree( t1.getNode( "F" ), false );
7801 if ( t1.getNumberOfExternalNodes() != 3 ) {
7804 t1.toNewHampshireX();
7805 t1.deleteSubtree( t1.getNode( "D" ), false );
7806 t1.toNewHampshireX();
7807 if ( t1.getNumberOfExternalNodes() != 3 ) {
7810 t1.deleteSubtree( t1.getNode( "def" ), false );
7811 t1.toNewHampshireX();
7812 if ( t1.getNumberOfExternalNodes() != 2 ) {
7815 t1.deleteSubtree( t1.getNode( "B" ), false );
7816 t1.toNewHampshireX();
7817 if ( t1.getNumberOfExternalNodes() != 1 ) {
7820 t1.deleteSubtree( t1.getNode( "C" ), false );
7821 t1.toNewHampshireX();
7822 if ( t1.getNumberOfExternalNodes() != 1 ) {
7825 t1.deleteSubtree( t1.getNode( "abc" ), false );
7826 t1.toNewHampshireX();
7827 if ( t1.getNumberOfExternalNodes() != 1 ) {
7830 t1.deleteSubtree( t1.getNode( "r" ), false );
7831 if ( t1.getNumberOfExternalNodes() != 0 ) {
7834 if ( !t1.isEmpty() ) {
7837 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7838 t2.deleteSubtree( t2.getNode( "A" ), false );
7839 t2.toNewHampshireX();
7840 if ( t2.getNumberOfExternalNodes() != 5 ) {
7843 t2.deleteSubtree( t2.getNode( "abc" ), false );
7844 t2.toNewHampshireX();
7845 if ( t2.getNumberOfExternalNodes() != 3 ) {
7848 t2.deleteSubtree( t2.getNode( "def" ), false );
7849 t2.toNewHampshireX();
7850 if ( t2.getNumberOfExternalNodes() != 1 ) {
7854 catch ( final Exception e ) {
7855 e.printStackTrace( System.out );
7861 private static boolean testSupportCount() {
7863 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7864 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7865 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7866 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7867 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7868 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7869 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7871 SupportCount.count( t0_1, phylogenies_1, true, false );
7872 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7873 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7874 + "(((((A,B),C),D),E),((F,G),X))"
7875 + "(((((A,Y),B),C),D),((F,G),E))"
7876 + "(((((A,B),C),D),E),(F,G))"
7877 + "(((((A,B),C),D),E),(F,G))"
7878 + "(((((A,B),C),D),E),(F,G))"
7879 + "(((((A,B),C),D),E),(F,G),Z)"
7880 + "(((((A,B),C),D),E),(F,G))"
7881 + "((((((A,B),C),D),E),F),G)"
7882 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7884 SupportCount.count( t0_2, phylogenies_2, true, false );
7885 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7886 while ( it.hasNext() ) {
7887 final PhylogenyNode n = it.next();
7888 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7892 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7893 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7894 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7895 SupportCount.count( t0_3, phylogenies_3, true, false );
7896 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7897 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7900 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7903 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7906 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7909 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7912 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7915 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7918 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7921 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7924 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7927 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7928 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7929 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7930 SupportCount.count( t0_4, phylogenies_4, true, false );
7931 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7932 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7935 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7938 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7941 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7944 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7947 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7950 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7953 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7956 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7959 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7962 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7963 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7964 double d = SupportCount.compare( b1, a, true, true, true );
7965 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7968 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7969 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7970 d = SupportCount.compare( b2, a, true, true, true );
7971 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7974 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7975 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7976 d = SupportCount.compare( b3, a, true, true, true );
7977 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7980 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7981 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7982 d = SupportCount.compare( b4, a, true, true, false );
7983 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7987 catch ( final Exception e ) {
7988 e.printStackTrace( System.out );
7994 private static boolean testSupportTransfer() {
7996 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7997 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)",
7998 new NHXParser() )[ 0 ];
7999 final Phylogeny p2 = factory
8000 .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 ];
8001 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8004 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8007 support_transfer.moveBranchLengthsToBootstrap( p1 );
8008 support_transfer.transferSupportValues( p1, p2 );
8009 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8012 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8015 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8018 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8021 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
8024 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
8027 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
8030 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
8034 catch ( final Exception e ) {
8035 e.printStackTrace( System.out );
8041 private static boolean testUniprotTaxonomySearch() {
8043 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
8045 if ( results.size() != 1 ) {
8048 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8051 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8054 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8057 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8060 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8064 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
8065 if ( results.size() != 1 ) {
8068 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8071 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8074 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8077 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8080 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8084 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
8085 if ( results.size() != 1 ) {
8088 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8091 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8094 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8097 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8100 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8104 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
8105 if ( results.size() != 1 ) {
8108 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8111 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8114 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8117 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8120 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8123 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
8126 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
8129 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
8130 .equals( "Nematostella vectensis" ) ) {
8131 System.out.println( results.get( 0 ).getLineage() );
8135 catch ( final IOException e ) {
8136 System.out.println();
8137 System.out.println( "the following might be due to absence internet connection:" );
8138 e.printStackTrace( System.out );
8141 catch ( final Exception e ) {
8147 private static boolean testEmblEntryRetrieval() {
8148 //The format for GenBank Accession numbers are:
8149 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
8150 //Protein: 3 letters + 5 numerals
8151 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
8152 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
8155 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
8158 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
8161 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
8164 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
8167 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
8170 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
8173 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
8176 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
8179 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
8182 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
8185 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
8188 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
8194 private static boolean testUniprotEntryRetrieval() {
8195 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
8198 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
8201 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
8204 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
8207 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
8210 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
8213 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
8216 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
8219 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
8222 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
8225 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
8228 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
8231 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
8235 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
8236 if ( !entry.getAccession().equals( "P12345" ) ) {
8239 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
8242 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
8245 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8248 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8252 catch ( final IOException e ) {
8253 System.out.println();
8254 System.out.println( "the following might be due to absence internet connection:" );
8255 e.printStackTrace( System.out );
8258 catch ( final Exception e ) {
8264 private static boolean testWabiTxSearch() {
8267 result = TxSearch.searchSimple( "nematostella" );
8268 result = TxSearch.getTxId( "nematostella" );
8269 if ( !result.equals( "45350" ) ) {
8272 result = TxSearch.getTxName( "45350" );
8273 if ( !result.equals( "Nematostella" ) ) {
8276 result = TxSearch.getTxId( "nematostella vectensis" );
8277 if ( !result.equals( "45351" ) ) {
8280 result = TxSearch.getTxName( "45351" );
8281 if ( !result.equals( "Nematostella vectensis" ) ) {
8284 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8285 if ( !result.equals( "536089" ) ) {
8288 result = TxSearch.getTxName( "536089" );
8289 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8292 final List<String> queries = new ArrayList<String>();
8293 queries.add( "Campylobacter coli" );
8294 queries.add( "Escherichia coli" );
8295 queries.add( "Arabidopsis" );
8296 queries.add( "Trichoplax" );
8297 queries.add( "Samanea saman" );
8298 queries.add( "Kluyveromyces marxianus" );
8299 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8300 queries.add( "Bornavirus parrot/PDD/2008" );
8301 final List<RANKS> ranks = new ArrayList<RANKS>();
8302 ranks.add( RANKS.SUPERKINGDOM );
8303 ranks.add( RANKS.KINGDOM );
8304 ranks.add( RANKS.FAMILY );
8305 ranks.add( RANKS.GENUS );
8306 ranks.add( RANKS.TRIBE );
8307 result = TxSearch.searchLineage( queries, ranks );
8308 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8309 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8311 catch ( final Exception e ) {
8312 System.out.println();
8313 System.out.println( "the following might be due to absence internet connection:" );
8314 e.printStackTrace( System.out );
8320 private static boolean testAminoAcidSequence() {
8322 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8323 if ( aa1.getLength() != 13 ) {
8326 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8329 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8332 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8335 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8336 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8339 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8340 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8343 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8344 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8348 catch ( final Exception e ) {
8349 e.printStackTrace();
8355 private static boolean testCreateBalancedPhylogeny() {
8357 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8358 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8361 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8364 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8365 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8368 if ( p1.getNumberOfExternalNodes() != 100 ) {
8372 catch ( final Exception e ) {
8373 e.printStackTrace();
8379 private static boolean testFastaParser() {
8381 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8384 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8387 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8388 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8391 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8394 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8397 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8400 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8403 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8407 catch ( final Exception e ) {
8408 e.printStackTrace();
8414 private static boolean testGeneralMsaParser() {
8416 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8417 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8418 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
8419 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8420 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8421 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8422 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8423 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8424 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8427 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8430 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8433 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8436 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8439 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8442 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8445 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8448 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
8451 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
8454 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
8457 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
8460 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8461 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8464 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8467 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8470 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8471 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8474 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8477 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8480 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8481 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8484 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8487 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8491 catch ( final Exception e ) {
8492 e.printStackTrace();
8498 private static boolean testMafft( final String path ) {
8500 final List<String> opts = new ArrayList<String>();
8501 opts.add( "--maxiterate" );
8503 opts.add( "--localpair" );
8504 opts.add( "--quiet" );
8506 final MsaInferrer mafft = Mafft.createInstance( path );
8507 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
8508 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8511 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
8515 catch ( final Exception e ) {
8516 e.printStackTrace( System.out );
8522 private static boolean testNextNodeWithCollapsing() {
8524 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8526 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8527 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8528 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8529 t0.getNode( "cd" ).setCollapse( true );
8530 t0.getNode( "cde" ).setCollapse( true );
8531 n = t0.getFirstExternalNode();
8532 while ( n != null ) {
8534 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8536 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8539 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8542 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8545 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8548 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8551 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8555 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8556 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8557 t1.getNode( "ab" ).setCollapse( true );
8558 t1.getNode( "cd" ).setCollapse( true );
8559 t1.getNode( "cde" ).setCollapse( true );
8560 n = t1.getNode( "ab" );
8561 ext = new ArrayList<PhylogenyNode>();
8562 while ( n != null ) {
8564 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8566 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8569 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8572 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8575 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8578 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8584 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8585 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8586 t2.getNode( "ab" ).setCollapse( true );
8587 t2.getNode( "cd" ).setCollapse( true );
8588 t2.getNode( "cde" ).setCollapse( true );
8589 t2.getNode( "c" ).setCollapse( true );
8590 t2.getNode( "d" ).setCollapse( true );
8591 t2.getNode( "e" ).setCollapse( true );
8592 t2.getNode( "gh" ).setCollapse( true );
8593 n = t2.getNode( "ab" );
8594 ext = new ArrayList<PhylogenyNode>();
8595 while ( n != null ) {
8597 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8599 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8602 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8605 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8608 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8614 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8615 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8616 t3.getNode( "ab" ).setCollapse( true );
8617 t3.getNode( "cd" ).setCollapse( true );
8618 t3.getNode( "cde" ).setCollapse( true );
8619 t3.getNode( "c" ).setCollapse( true );
8620 t3.getNode( "d" ).setCollapse( true );
8621 t3.getNode( "e" ).setCollapse( true );
8622 t3.getNode( "gh" ).setCollapse( true );
8623 t3.getNode( "fgh" ).setCollapse( true );
8624 n = t3.getNode( "ab" );
8625 ext = new ArrayList<PhylogenyNode>();
8626 while ( n != null ) {
8628 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8630 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8633 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8636 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8642 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8643 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8644 t4.getNode( "ab" ).setCollapse( true );
8645 t4.getNode( "cd" ).setCollapse( true );
8646 t4.getNode( "cde" ).setCollapse( true );
8647 t4.getNode( "c" ).setCollapse( true );
8648 t4.getNode( "d" ).setCollapse( true );
8649 t4.getNode( "e" ).setCollapse( true );
8650 t4.getNode( "gh" ).setCollapse( true );
8651 t4.getNode( "fgh" ).setCollapse( true );
8652 t4.getNode( "abcdefgh" ).setCollapse( true );
8653 n = t4.getNode( "abcdefgh" );
8654 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8659 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8660 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8662 n = t5.getFirstExternalNode();
8663 while ( n != null ) {
8665 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8667 if ( ext.size() != 8 ) {
8670 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8673 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8676 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8679 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8682 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8685 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8688 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8691 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8696 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8697 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8699 t6.getNode( "ab" ).setCollapse( true );
8700 n = t6.getNode( "ab" );
8701 while ( n != null ) {
8703 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8705 if ( ext.size() != 7 ) {
8708 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8711 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8714 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8717 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8720 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8723 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8726 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8731 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8732 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8734 t7.getNode( "cd" ).setCollapse( true );
8735 n = t7.getNode( "a" );
8736 while ( n != null ) {
8738 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8740 if ( ext.size() != 7 ) {
8743 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8746 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8749 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8752 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8755 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8758 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8761 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8766 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8767 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8769 t8.getNode( "cd" ).setCollapse( true );
8770 t8.getNode( "c" ).setCollapse( true );
8771 t8.getNode( "d" ).setCollapse( true );
8772 n = t8.getNode( "a" );
8773 while ( n != null ) {
8775 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8777 if ( ext.size() != 7 ) {
8780 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8783 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8786 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8787 System.out.println( "2 fail" );
8790 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8793 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8796 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8799 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8804 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8805 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8807 t9.getNode( "gh" ).setCollapse( true );
8808 n = t9.getNode( "a" );
8809 while ( n != null ) {
8811 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8813 if ( ext.size() != 7 ) {
8816 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8819 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8822 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8825 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8828 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8831 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8834 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8839 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8840 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8842 t10.getNode( "gh" ).setCollapse( true );
8843 t10.getNode( "g" ).setCollapse( true );
8844 t10.getNode( "h" ).setCollapse( true );
8845 n = t10.getNode( "a" );
8846 while ( n != null ) {
8848 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8850 if ( ext.size() != 7 ) {
8853 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8856 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8859 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8862 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8865 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8868 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8871 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8876 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8877 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8879 t11.getNode( "gh" ).setCollapse( true );
8880 t11.getNode( "fgh" ).setCollapse( true );
8881 n = t11.getNode( "a" );
8882 while ( n != null ) {
8884 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8886 if ( ext.size() != 6 ) {
8889 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8892 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8895 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8898 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8901 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8904 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8909 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8910 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8912 t12.getNode( "gh" ).setCollapse( true );
8913 t12.getNode( "fgh" ).setCollapse( true );
8914 t12.getNode( "g" ).setCollapse( true );
8915 t12.getNode( "h" ).setCollapse( true );
8916 t12.getNode( "f" ).setCollapse( true );
8917 n = t12.getNode( "a" );
8918 while ( n != null ) {
8920 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8922 if ( ext.size() != 6 ) {
8925 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8928 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8931 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8934 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8937 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8940 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8945 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8946 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8948 t13.getNode( "ab" ).setCollapse( true );
8949 t13.getNode( "b" ).setCollapse( true );
8950 t13.getNode( "fgh" ).setCollapse( true );
8951 t13.getNode( "gh" ).setCollapse( true );
8952 n = t13.getNode( "ab" );
8953 while ( n != null ) {
8955 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8957 if ( ext.size() != 5 ) {
8960 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8963 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8966 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8969 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8972 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8977 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8978 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8980 t14.getNode( "ab" ).setCollapse( true );
8981 t14.getNode( "a" ).setCollapse( true );
8982 t14.getNode( "fgh" ).setCollapse( true );
8983 t14.getNode( "gh" ).setCollapse( true );
8984 n = t14.getNode( "ab" );
8985 while ( n != null ) {
8987 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8989 if ( ext.size() != 5 ) {
8992 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8995 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8998 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9001 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9004 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9009 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" );
9010 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9012 t15.getNode( "ab" ).setCollapse( true );
9013 t15.getNode( "a" ).setCollapse( true );
9014 t15.getNode( "fgh" ).setCollapse( true );
9015 t15.getNode( "gh" ).setCollapse( true );
9016 n = t15.getNode( "ab" );
9017 while ( n != null ) {
9019 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9021 if ( ext.size() != 6 ) {
9024 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9027 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9030 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9033 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9036 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
9039 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9044 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" );
9045 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
9047 t16.getNode( "ab" ).setCollapse( true );
9048 t16.getNode( "a" ).setCollapse( true );
9049 t16.getNode( "fgh" ).setCollapse( true );
9050 t16.getNode( "gh" ).setCollapse( true );
9051 t16.getNode( "cd" ).setCollapse( true );
9052 t16.getNode( "cde" ).setCollapse( true );
9053 t16.getNode( "d" ).setCollapse( true );
9054 t16.getNode( "x" ).setCollapse( true );
9055 n = t16.getNode( "ab" );
9056 while ( n != null ) {
9058 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9060 if ( ext.size() != 4 ) {
9063 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9066 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9069 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
9072 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
9076 catch ( final Exception e ) {
9077 e.printStackTrace( System.out );
9083 private static boolean testMsaQualityMethod() {
9085 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
9086 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
9087 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
9088 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
9089 final List<Sequence> l = new ArrayList<Sequence>();
9094 final Msa msa = BasicMsa.createInstance( l );
9095 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
9098 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
9101 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
9104 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
9108 catch ( final Exception e ) {
9109 e.printStackTrace( System.out );
9115 private static boolean testSequenceIdParsing() {
9117 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
9118 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9119 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9121 System.out.println( "value =" + id.getValue() );
9122 System.out.println( "provider=" + id.getProvider() );
9127 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
9128 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9129 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9131 System.out.println( "value =" + id.getValue() );
9132 System.out.println( "provider=" + id.getProvider() );
9137 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
9138 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9139 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
9141 System.out.println( "value =" + id.getValue() );
9142 System.out.println( "provider=" + id.getProvider() );
9147 id = SequenceIdParser.parse( "gb_AAA96518_1" );
9148 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9149 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
9151 System.out.println( "value =" + id.getValue() );
9152 System.out.println( "provider=" + id.getProvider() );
9157 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
9158 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9159 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
9161 System.out.println( "value =" + id.getValue() );
9162 System.out.println( "provider=" + id.getProvider() );
9167 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
9168 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9169 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
9171 System.out.println( "value =" + id.getValue() );
9172 System.out.println( "provider=" + id.getProvider() );
9177 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
9178 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9179 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
9181 System.out.println( "value =" + id.getValue() );
9182 System.out.println( "provider=" + id.getProvider() );
9187 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
9188 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9189 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9191 System.out.println( "value =" + id.getValue() );
9192 System.out.println( "provider=" + id.getProvider() );
9197 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
9198 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9199 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
9201 System.out.println( "value =" + id.getValue() );
9202 System.out.println( "provider=" + id.getProvider() );
9207 id = SequenceIdParser.parse( "P4A123" );
9208 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9209 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9211 System.out.println( "value =" + id.getValue() );
9212 System.out.println( "provider=" + id.getProvider() );
9217 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
9218 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
9219 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
9221 System.out.println( "value =" + id.getValue() );
9222 System.out.println( "provider=" + id.getProvider() );
9227 id = SequenceIdParser.parse( "XP_12345" );
9229 System.out.println( "value =" + id.getValue() );
9230 System.out.println( "provider=" + id.getProvider() );
9233 // lcl_91970_unknown_
9235 catch ( final Exception e ) {
9236 e.printStackTrace( System.out );