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.nexus.NexusPhylogeniesParser2;
54 import org.forester.io.parsers.nhx.NHXParser;
55 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
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( "Nexus tree parsing iterating: " );
176 if ( Test.testNexusTreeParsingIterating() ) {
177 System.out.println( "OK." );
181 System.out.println( "failed." );
185 System.out.print( "Sequence id parsing: " );
186 if ( testSequenceIdParsing() ) {
187 System.out.println( "OK." );
191 System.out.println( "failed." );
194 System.out.print( "Hmmscan output parser: " );
195 if ( testHmmscanOutputParser() ) {
196 System.out.println( "OK." );
200 System.out.println( "failed." );
203 System.out.print( "Basic node methods: " );
204 if ( Test.testBasicNodeMethods() ) {
205 System.out.println( "OK." );
209 System.out.println( "failed." );
212 System.out.print( "Taxonomy code extraction: " );
213 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
214 System.out.println( "OK." );
218 System.out.println( "failed." );
221 System.out.print( "Taxonomy extraction (general): " );
222 if ( Test.testTaxonomyExtraction() ) {
223 System.out.println( "OK." );
227 System.out.println( "failed." );
230 System.out.print( "Basic node construction and parsing of NHX (node level): " );
231 if ( Test.testNHXNodeParsing() ) {
232 System.out.println( "OK." );
236 System.out.println( "failed." );
239 System.out.print( "NHX parsing iterating: " );
240 if ( Test.testNHParsingIter() ) {
241 System.out.println( "OK." );
245 System.out.println( "failed." );
248 System.out.print( "NH parsing: " );
249 if ( Test.testNHParsing() ) {
250 System.out.println( "OK." );
254 System.out.println( "failed." );
257 System.out.print( "Conversion to NHX (node level): " );
258 if ( Test.testNHXconversion() ) {
259 System.out.println( "OK." );
263 System.out.println( "failed." );
266 System.out.print( "NHX parsing: " );
267 if ( Test.testNHXParsing() ) {
268 System.out.println( "OK." );
272 System.out.println( "failed." );
275 System.out.print( "NHX parsing with quotes: " );
276 if ( Test.testNHXParsingQuotes() ) {
277 System.out.println( "OK." );
281 System.out.println( "failed." );
284 System.out.print( "NHX parsing (MrBayes): " );
285 if ( Test.testNHXParsingMB() ) {
286 System.out.println( "OK." );
290 System.out.println( "failed." );
293 System.out.print( "Nexus characters parsing: " );
294 if ( Test.testNexusCharactersParsing() ) {
295 System.out.println( "OK." );
299 System.out.println( "failed." );
302 System.out.print( "Nexus tree parsing: " );
303 if ( Test.testNexusTreeParsing() ) {
304 System.out.println( "OK." );
308 System.out.println( "failed." );
311 System.out.print( "Nexus tree parsing (translating): " );
312 if ( Test.testNexusTreeParsingTranslating() ) {
313 System.out.println( "OK." );
317 System.out.println( "failed." );
320 System.out.print( "Nexus matrix parsing: " );
321 if ( Test.testNexusMatrixParsing() ) {
322 System.out.println( "OK." );
326 System.out.println( "failed." );
329 System.out.print( "Basic phyloXML parsing: " );
330 if ( Test.testBasicPhyloXMLparsing() ) {
331 System.out.println( "OK." );
335 System.out.println( "failed." );
338 System.out.print( "Basic phyloXML parsing (validating against schema): " );
339 if ( testBasicPhyloXMLparsingValidating() ) {
340 System.out.println( "OK." );
344 System.out.println( "failed." );
347 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
348 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
349 System.out.println( "OK." );
353 System.out.println( "failed." );
356 System.out.print( "phyloXML Distribution Element: " );
357 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
358 System.out.println( "OK." );
362 System.out.println( "failed." );
365 System.out.print( "Tol XML parsing: " );
366 if ( Test.testBasicTolXMLparsing() ) {
367 System.out.println( "OK." );
371 System.out.println( "failed." );
374 System.out.print( "Copying of node data: " );
375 if ( Test.testCopyOfNodeData() ) {
376 System.out.println( "OK." );
380 System.out.println( "failed." );
383 System.out.print( "Basic tree methods: " );
384 if ( Test.testBasicTreeMethods() ) {
385 System.out.println( "OK." );
389 System.out.println( "failed." );
392 System.out.print( "Postorder Iterator: " );
393 if ( Test.testPostOrderIterator() ) {
394 System.out.println( "OK." );
398 System.out.println( "failed." );
401 System.out.print( "Preorder Iterator: " );
402 if ( Test.testPreOrderIterator() ) {
403 System.out.println( "OK." );
407 System.out.println( "failed." );
410 System.out.print( "Levelorder Iterator: " );
411 if ( Test.testLevelOrderIterator() ) {
412 System.out.println( "OK." );
416 System.out.println( "failed." );
419 System.out.print( "Re-id methods: " );
420 if ( Test.testReIdMethods() ) {
421 System.out.println( "OK." );
425 System.out.println( "failed." );
428 System.out.print( "Methods on last external nodes: " );
429 if ( Test.testLastExternalNodeMethods() ) {
430 System.out.println( "OK." );
434 System.out.println( "failed." );
437 System.out.print( "Methods on external nodes: " );
438 if ( Test.testExternalNodeRelatedMethods() ) {
439 System.out.println( "OK." );
443 System.out.println( "failed." );
446 System.out.print( "Deletion of external nodes: " );
447 if ( Test.testDeletionOfExternalNodes() ) {
448 System.out.println( "OK." );
452 System.out.println( "failed." );
455 System.out.print( "Subtree deletion: " );
456 if ( Test.testSubtreeDeletion() ) {
457 System.out.println( "OK." );
461 System.out.println( "failed." );
464 System.out.print( "Phylogeny branch: " );
465 if ( Test.testPhylogenyBranch() ) {
466 System.out.println( "OK." );
470 System.out.println( "failed." );
473 System.out.print( "Rerooting: " );
474 if ( Test.testRerooting() ) {
475 System.out.println( "OK." );
479 System.out.println( "failed." );
482 System.out.print( "Mipoint rooting: " );
483 if ( Test.testMidpointrooting() ) {
484 System.out.println( "OK." );
488 System.out.println( "failed." );
491 System.out.print( "Node removal: " );
492 if ( Test.testNodeRemoval() ) {
493 System.out.println( "OK." );
497 System.out.println( "failed." );
500 System.out.print( "Support count: " );
501 if ( Test.testSupportCount() ) {
502 System.out.println( "OK." );
506 System.out.println( "failed." );
509 System.out.print( "Support transfer: " );
510 if ( Test.testSupportTransfer() ) {
511 System.out.println( "OK." );
515 System.out.println( "failed." );
518 System.out.print( "Finding of LCA: " );
519 if ( Test.testGetLCA() ) {
520 System.out.println( "OK." );
524 System.out.println( "failed." );
527 System.out.print( "Finding of LCA 2: " );
528 if ( Test.testGetLCA2() ) {
529 System.out.println( "OK." );
533 System.out.println( "failed." );
536 System.out.print( "Calculation of distance between nodes: " );
537 if ( Test.testGetDistance() ) {
538 System.out.println( "OK." );
542 System.out.println( "failed." );
545 System.out.print( "Descriptive statistics: " );
546 if ( Test.testDescriptiveStatistics() ) {
547 System.out.println( "OK." );
551 System.out.println( "failed." );
554 System.out.print( "Data objects and methods: " );
555 if ( Test.testDataObjects() ) {
556 System.out.println( "OK." );
560 System.out.println( "failed." );
563 System.out.print( "Properties map: " );
564 if ( Test.testPropertiesMap() ) {
565 System.out.println( "OK." );
569 System.out.println( "failed." );
572 System.out.print( "SDIse: " );
573 if ( Test.testSDIse() ) {
574 System.out.println( "OK." );
578 System.out.println( "failed." );
581 System.out.print( "SDIunrooted: " );
582 if ( Test.testSDIunrooted() ) {
583 System.out.println( "OK." );
587 System.out.println( "failed." );
590 System.out.print( "GSDI: " );
591 if ( TestGSDI.test() ) {
592 System.out.println( "OK." );
596 System.out.println( "failed." );
599 System.out.print( "RIO: " );
600 if ( TestRIO.test() ) {
601 System.out.println( "OK." );
605 System.out.println( "failed." );
608 System.out.print( "Phylogeny reconstruction:" );
609 System.out.println();
610 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
611 System.out.println( "OK." );
615 System.out.println( "failed." );
618 System.out.print( "Analysis of domain architectures: " );
619 System.out.println();
620 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
621 System.out.println( "OK." );
625 System.out.println( "failed." );
628 System.out.print( "GO: " );
629 System.out.println();
630 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
631 System.out.println( "OK." );
635 System.out.println( "failed." );
638 System.out.print( "Modeling tools: " );
639 if ( TestPccx.test() ) {
640 System.out.println( "OK." );
644 System.out.println( "failed." );
647 System.out.print( "Split Matrix strict: " );
648 if ( Test.testSplitStrict() ) {
649 System.out.println( "OK." );
653 System.out.println( "failed." );
656 System.out.print( "Split Matrix: " );
657 if ( Test.testSplit() ) {
658 System.out.println( "OK." );
662 System.out.println( "failed." );
665 System.out.print( "Confidence Assessor: " );
666 if ( Test.testConfidenceAssessor() ) {
667 System.out.println( "OK." );
671 System.out.println( "failed." );
674 System.out.print( "Basic table: " );
675 if ( Test.testBasicTable() ) {
676 System.out.println( "OK." );
680 System.out.println( "failed." );
683 System.out.print( "General table: " );
684 if ( Test.testGeneralTable() ) {
685 System.out.println( "OK." );
689 System.out.println( "failed." );
692 System.out.print( "Amino acid sequence: " );
693 if ( Test.testAminoAcidSequence() ) {
694 System.out.println( "OK." );
698 System.out.println( "failed." );
701 System.out.print( "General MSA parser: " );
702 if ( Test.testGeneralMsaParser() ) {
703 System.out.println( "OK." );
707 System.out.println( "failed." );
710 System.out.print( "Fasta parser for msa: " );
711 if ( Test.testFastaParser() ) {
712 System.out.println( "OK." );
716 System.out.println( "failed." );
719 System.out.print( "Creation of balanced phylogeny: " );
720 if ( Test.testCreateBalancedPhylogeny() ) {
721 System.out.println( "OK." );
725 System.out.println( "failed." );
728 System.out.print( "EMBL Entry Retrieval: " );
729 if ( Test.testEmblEntryRetrieval() ) {
730 System.out.println( "OK." );
734 System.out.println( "failed." );
737 System.out.print( "Uniprot Entry Retrieval: " );
738 if ( Test.testUniprotEntryRetrieval() ) {
739 System.out.println( "OK." );
743 System.out.println( "failed." );
746 System.out.print( "Uniprot Taxonomy Search: " );
747 if ( Test.testUniprotTaxonomySearch() ) {
748 System.out.println( "OK." );
752 System.out.println( "failed." );
757 final String os = ForesterUtil.OS_NAME.toLowerCase();
758 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
759 path = "/usr/local/bin/mafft";
761 else if ( os.indexOf( "win" ) >= 0 ) {
762 path = "C:\\Program Files\\mafft-win\\mafft.bat";
765 path = "/home/czmasek/bin/mafft";
767 if ( !MsaInferrer.isInstalled( path ) ) {
770 if ( !MsaInferrer.isInstalled( path ) ) {
771 path = "/usr/local/bin/mafft";
773 if ( MsaInferrer.isInstalled( path ) ) {
774 System.out.print( "MAFFT (external program): " );
775 if ( Test.testMafft( path ) ) {
776 System.out.println( "OK." );
780 System.out.println( "failed [will not count towards failed tests]" );
784 System.out.print( "Next nodes with collapsed: " );
785 if ( Test.testNextNodeWithCollapsing() ) {
786 System.out.println( "OK." );
790 System.out.println( "failed." );
793 System.out.print( "Simple MSA quality: " );
794 if ( Test.testMsaQualityMethod() ) {
795 System.out.println( "OK." );
799 System.out.println( "failed." );
802 System.out.println();
803 final Runtime rt = java.lang.Runtime.getRuntime();
804 final long free_memory = rt.freeMemory() / 1000000;
805 final long total_memory = rt.totalMemory() / 1000000;
806 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
807 + free_memory + "MB, total memory: " + total_memory + "MB)" );
808 System.out.println();
809 System.out.println( "Successful tests: " + succeeded );
810 System.out.println( "Failed tests: " + failed );
811 System.out.println();
813 System.out.println( "OK." );
816 System.out.println( "Not OK." );
820 private static boolean testExtractTaxonomyCodeFromNodeName() {
822 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
825 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
828 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
831 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
832 .equals( "MOUSE" ) ) {
835 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
836 .equals( "MOUSE" ) ) {
839 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
840 .equals( "MOUSE" ) ) {
843 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
846 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
849 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
853 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
857 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
861 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
864 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
867 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
870 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
874 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
875 .equals( "MOUSE" ) ) {
878 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
879 .equals( "MOUSE" ) ) {
883 catch ( final Exception e ) {
884 e.printStackTrace( System.out );
890 private static boolean testBasicNodeMethods() {
892 if ( PhylogenyNode.getNodeCount() != 0 ) {
895 final PhylogenyNode n1 = new PhylogenyNode();
896 final PhylogenyNode n2 = PhylogenyNode
897 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
898 final PhylogenyNode n3 = PhylogenyNode
899 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
900 final PhylogenyNode n4 = PhylogenyNode
901 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
902 if ( n1.isHasAssignedEvent() ) {
905 if ( PhylogenyNode.getNodeCount() != 4 ) {
908 if ( n3.getIndicator() != 0 ) {
911 if ( n3.getNumberOfExternalNodes() != 1 ) {
914 if ( !n3.isExternal() ) {
917 if ( !n3.isRoot() ) {
920 if ( !n4.getName().equals( "n4" ) ) {
924 catch ( final Exception e ) {
925 e.printStackTrace( System.out );
931 private static boolean testBasicPhyloXMLparsing() {
933 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
934 final PhyloXmlParser xml_parser = new PhyloXmlParser();
935 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
937 if ( xml_parser.getErrorCount() > 0 ) {
938 System.out.println( xml_parser.getErrorMessages().toString() );
941 if ( phylogenies_0.length != 4 ) {
944 final Phylogeny t1 = phylogenies_0[ 0 ];
945 final Phylogeny t2 = phylogenies_0[ 1 ];
946 final Phylogeny t3 = phylogenies_0[ 2 ];
947 final Phylogeny t4 = phylogenies_0[ 3 ];
948 if ( t1.getNumberOfExternalNodes() != 1 ) {
951 if ( !t1.isRooted() ) {
954 if ( t1.isRerootable() ) {
957 if ( !t1.getType().equals( "gene_tree" ) ) {
960 if ( t2.getNumberOfExternalNodes() != 2 ) {
963 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
966 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
969 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
972 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
975 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
978 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
981 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
982 .startsWith( "actgtgggggt" ) ) {
985 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
986 .startsWith( "ctgtgatgcat" ) ) {
989 if ( t3.getNumberOfExternalNodes() != 4 ) {
992 if ( !t1.getName().equals( "t1" ) ) {
995 if ( !t2.getName().equals( "t2" ) ) {
998 if ( !t3.getName().equals( "t3" ) ) {
1001 if ( !t4.getName().equals( "t4" ) ) {
1004 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1007 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1010 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1013 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1014 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1017 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1020 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1023 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1026 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1027 .equals( "apoptosis" ) ) {
1030 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1031 .equals( "GO:0006915" ) ) {
1034 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1035 .equals( "UniProtKB" ) ) {
1038 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1039 .equals( "experimental" ) ) {
1042 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1043 .equals( "function" ) ) {
1046 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1047 .getValue() != 1 ) {
1050 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1051 .getType().equals( "ml" ) ) {
1054 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1055 .equals( "apoptosis" ) ) {
1058 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1059 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1062 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1063 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1066 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1067 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1070 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1071 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1074 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1075 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1078 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1079 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1082 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1083 .equals( "GO:0005829" ) ) {
1086 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1087 .equals( "intracellular organelle" ) ) {
1090 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1093 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1094 .equals( "UniProt link" ) ) ) {
1097 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1101 catch ( final Exception e ) {
1102 e.printStackTrace( System.out );
1108 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1110 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1111 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1112 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1113 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1116 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1118 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1120 if ( xml_parser.getErrorCount() > 0 ) {
1121 System.out.println( xml_parser.getErrorMessages().toString() );
1124 if ( phylogenies_0.length != 4 ) {
1127 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1128 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1129 if ( phylogenies_t1.length != 1 ) {
1132 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1133 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1136 if ( !t1_rt.isRooted() ) {
1139 if ( t1_rt.isRerootable() ) {
1142 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1145 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1146 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1147 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1148 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1151 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1154 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1157 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1160 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1161 .startsWith( "actgtgggggt" ) ) {
1164 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1165 .startsWith( "ctgtgatgcat" ) ) {
1168 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1169 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1170 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1171 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1172 if ( phylogenies_1.length != 1 ) {
1175 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1176 if ( !t3_rt.getName().equals( "t3" ) ) {
1179 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1182 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1185 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1188 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1191 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1192 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1195 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1198 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1201 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1202 .equals( "UniProtKB" ) ) {
1205 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1206 .equals( "apoptosis" ) ) {
1209 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1210 .equals( "GO:0006915" ) ) {
1213 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1214 .equals( "UniProtKB" ) ) {
1217 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1218 .equals( "experimental" ) ) {
1221 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1222 .equals( "function" ) ) {
1225 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1226 .getValue() != 1 ) {
1229 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1230 .getType().equals( "ml" ) ) {
1233 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1234 .equals( "apoptosis" ) ) {
1237 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1238 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1241 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1242 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1246 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1249 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1250 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1253 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1254 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1257 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1258 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1261 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1262 .equals( "GO:0005829" ) ) {
1265 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1266 .equals( "intracellular organelle" ) ) {
1269 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1272 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1273 .equals( "UniProt link" ) ) ) {
1276 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1279 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1282 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1283 .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." ) ) ) {
1286 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1289 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1292 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1295 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1298 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1299 .equals( "ncbi" ) ) {
1302 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1305 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1306 .getName().equals( "B" ) ) {
1309 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1310 .getFrom() != 21 ) {
1313 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1316 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1317 .getLength() != 24 ) {
1320 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1321 .getConfidence() != 2144 ) {
1324 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1325 .equals( "pfam" ) ) {
1328 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1331 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1334 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1337 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1340 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1341 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1344 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1347 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1350 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1353 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1356 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1359 if ( taxbb.getSynonyms().size() != 2 ) {
1362 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1365 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1368 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1371 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1374 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1377 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1378 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1382 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1385 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1388 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1391 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1394 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1397 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1400 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1404 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1407 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1408 .equalsIgnoreCase( "435" ) ) {
1411 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1414 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1415 .equalsIgnoreCase( "443.7" ) ) {
1418 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1421 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1424 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1425 .equalsIgnoreCase( "433" ) ) {
1429 catch ( final Exception e ) {
1430 e.printStackTrace( System.out );
1436 private static boolean testBasicPhyloXMLparsingValidating() {
1438 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1439 PhyloXmlParser xml_parser = null;
1441 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1443 catch ( final Exception e ) {
1444 // Do nothing -- means were not running from jar.
1446 if ( xml_parser == null ) {
1447 xml_parser = new PhyloXmlParser();
1448 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1449 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1452 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1455 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1457 if ( xml_parser.getErrorCount() > 0 ) {
1458 System.out.println( xml_parser.getErrorMessages().toString() );
1461 if ( phylogenies_0.length != 4 ) {
1464 final Phylogeny t1 = phylogenies_0[ 0 ];
1465 final Phylogeny t2 = phylogenies_0[ 1 ];
1466 final Phylogeny t3 = phylogenies_0[ 2 ];
1467 final Phylogeny t4 = phylogenies_0[ 3 ];
1468 if ( !t1.getName().equals( "t1" ) ) {
1471 if ( !t2.getName().equals( "t2" ) ) {
1474 if ( !t3.getName().equals( "t3" ) ) {
1477 if ( !t4.getName().equals( "t4" ) ) {
1480 if ( t1.getNumberOfExternalNodes() != 1 ) {
1483 if ( t2.getNumberOfExternalNodes() != 2 ) {
1486 if ( t3.getNumberOfExternalNodes() != 4 ) {
1489 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1490 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1491 if ( xml_parser.getErrorCount() > 0 ) {
1492 System.out.println( "errors:" );
1493 System.out.println( xml_parser.getErrorMessages().toString() );
1496 if ( phylogenies_1.length != 4 ) {
1499 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1501 if ( xml_parser.getErrorCount() > 0 ) {
1502 System.out.println( "errors:" );
1503 System.out.println( xml_parser.getErrorMessages().toString() );
1506 if ( phylogenies_2.length != 1 ) {
1509 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1512 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1514 if ( xml_parser.getErrorCount() > 0 ) {
1515 System.out.println( xml_parser.getErrorMessages().toString() );
1518 if ( phylogenies_3.length != 2 ) {
1521 final Phylogeny a = phylogenies_3[ 0 ];
1522 if ( !a.getName().equals( "tree 4" ) ) {
1525 if ( a.getNumberOfExternalNodes() != 3 ) {
1528 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1531 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1534 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1536 if ( xml_parser.getErrorCount() > 0 ) {
1537 System.out.println( xml_parser.getErrorMessages().toString() );
1540 if ( phylogenies_4.length != 1 ) {
1543 final Phylogeny s = phylogenies_4[ 0 ];
1544 if ( s.getNumberOfExternalNodes() != 6 ) {
1547 s.getNode( "first" );
1549 s.getNode( "\"<a'b&c'd\">\"" );
1550 s.getNode( "'''\"" );
1551 s.getNode( "\"\"\"" );
1552 s.getNode( "dick & doof" );
1554 catch ( final Exception e ) {
1555 e.printStackTrace( System.out );
1561 private static boolean testBasicTable() {
1563 final BasicTable<String> t0 = new BasicTable<String>();
1564 if ( t0.getNumberOfColumns() != 0 ) {
1567 if ( t0.getNumberOfRows() != 0 ) {
1570 t0.setValue( 3, 2, "23" );
1571 t0.setValue( 10, 1, "error" );
1572 t0.setValue( 10, 1, "110" );
1573 t0.setValue( 9, 1, "19" );
1574 t0.setValue( 1, 10, "101" );
1575 t0.setValue( 10, 10, "1010" );
1576 t0.setValue( 100, 10, "10100" );
1577 t0.setValue( 0, 0, "00" );
1578 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1581 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1584 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1587 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1590 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1593 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1596 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1599 if ( t0.getNumberOfColumns() != 101 ) {
1602 if ( t0.getNumberOfRows() != 11 ) {
1605 if ( t0.getValueAsString( 49, 4 ) != null ) {
1608 final String l = ForesterUtil.getLineSeparator();
1609 final StringBuffer source = new StringBuffer();
1610 source.append( "" + l );
1611 source.append( "# 1 1 1 1 1 1 1 1" + l );
1612 source.append( " 00 01 02 03" + l );
1613 source.append( " 10 11 12 13 " + l );
1614 source.append( "20 21 22 23 " + l );
1615 source.append( " 30 31 32 33" + l );
1616 source.append( "40 41 42 43" + l );
1617 source.append( " # 1 1 1 1 1 " + l );
1618 source.append( "50 51 52 53 54" + l );
1619 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1620 if ( t1.getNumberOfColumns() != 5 ) {
1623 if ( t1.getNumberOfRows() != 6 ) {
1626 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1629 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1632 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1635 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1638 final StringBuffer source1 = new StringBuffer();
1639 source1.append( "" + l );
1640 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1641 source1.append( " 00; 01 ;02;03" + l );
1642 source1.append( " 10; 11; 12; 13 " + l );
1643 source1.append( "20; 21; 22; 23 " + l );
1644 source1.append( " 30; 31; 32; 33" + l );
1645 source1.append( "40;41;42;43" + l );
1646 source1.append( " # 1 1 1 1 1 " + l );
1647 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1648 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1649 if ( t2.getNumberOfColumns() != 5 ) {
1652 if ( t2.getNumberOfRows() != 6 ) {
1655 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1658 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1661 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1664 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1667 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1670 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1673 final StringBuffer source2 = new StringBuffer();
1674 source2.append( "" + l );
1675 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1676 source2.append( " 00; 01 ;02;03" + l );
1677 source2.append( " 10; 11; 12; 13 " + l );
1678 source2.append( "20; 21; 22; 23 " + l );
1679 source2.append( " " + l );
1680 source2.append( " 30; 31; 32; 33" + l );
1681 source2.append( "40;41;42;43" + l );
1682 source2.append( " comment: 1 1 1 1 1 " + l );
1683 source2.append( ";;;50 ; 52; 53;;54 " + l );
1684 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1690 if ( tl.size() != 2 ) {
1693 final BasicTable<String> t3 = tl.get( 0 );
1694 final BasicTable<String> t4 = tl.get( 1 );
1695 if ( t3.getNumberOfColumns() != 4 ) {
1698 if ( t3.getNumberOfRows() != 3 ) {
1701 if ( t4.getNumberOfColumns() != 4 ) {
1704 if ( t4.getNumberOfRows() != 3 ) {
1707 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1710 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1714 catch ( final Exception e ) {
1715 e.printStackTrace( System.out );
1721 private static boolean testBasicTolXMLparsing() {
1723 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1724 final TolParser parser = new TolParser();
1725 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1726 if ( parser.getErrorCount() > 0 ) {
1727 System.out.println( parser.getErrorMessages().toString() );
1730 if ( phylogenies_0.length != 1 ) {
1733 final Phylogeny t1 = phylogenies_0[ 0 ];
1734 if ( t1.getNumberOfExternalNodes() != 5 ) {
1737 if ( !t1.isRooted() ) {
1740 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1743 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1746 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1749 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1752 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1753 if ( parser.getErrorCount() > 0 ) {
1754 System.out.println( parser.getErrorMessages().toString() );
1757 if ( phylogenies_1.length != 1 ) {
1760 final Phylogeny t2 = phylogenies_1[ 0 ];
1761 if ( t2.getNumberOfExternalNodes() != 664 ) {
1764 if ( !t2.isRooted() ) {
1767 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1770 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1773 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1776 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1779 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1782 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1783 .equals( "Aquifex" ) ) {
1786 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1787 if ( parser.getErrorCount() > 0 ) {
1788 System.out.println( parser.getErrorMessages().toString() );
1791 if ( phylogenies_2.length != 1 ) {
1794 final Phylogeny t3 = phylogenies_2[ 0 ];
1795 if ( t3.getNumberOfExternalNodes() != 184 ) {
1798 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1801 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1804 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1807 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1808 if ( parser.getErrorCount() > 0 ) {
1809 System.out.println( parser.getErrorMessages().toString() );
1812 if ( phylogenies_3.length != 1 ) {
1815 final Phylogeny t4 = phylogenies_3[ 0 ];
1816 if ( t4.getNumberOfExternalNodes() != 1 ) {
1819 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1822 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1825 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1828 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1829 if ( parser.getErrorCount() > 0 ) {
1830 System.out.println( parser.getErrorMessages().toString() );
1833 if ( phylogenies_4.length != 1 ) {
1836 final Phylogeny t5 = phylogenies_4[ 0 ];
1837 if ( t5.getNumberOfExternalNodes() != 13 ) {
1840 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1843 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1846 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1850 catch ( final Exception e ) {
1851 e.printStackTrace( System.out );
1857 private static boolean testBasicTreeMethods() {
1859 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1860 final Phylogeny t1 = factory.create();
1861 if ( !t1.isEmpty() ) {
1864 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1865 if ( t2.getNumberOfExternalNodes() != 4 ) {
1868 if ( t2.getHeight() != 8.5 ) {
1871 if ( !t2.isCompletelyBinary() ) {
1874 if ( t2.isEmpty() ) {
1877 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1878 if ( t3.getNumberOfExternalNodes() != 5 ) {
1881 if ( t3.getHeight() != 11 ) {
1884 if ( t3.isCompletelyBinary() ) {
1887 final PhylogenyNode n = t3.getNode( "ABC" );
1888 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 ];
1889 if ( t4.getNumberOfExternalNodes() != 9 ) {
1892 if ( t4.getHeight() != 11 ) {
1895 if ( t4.isCompletelyBinary() ) {
1898 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)" );
1899 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1900 if ( t5.getNumberOfExternalNodes() != 8 ) {
1903 if ( t5.getHeight() != 15 ) {
1906 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)" );
1907 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1908 if ( t6.getHeight() != 15 ) {
1911 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)" );
1912 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1913 if ( t7.getHeight() != 15 ) {
1916 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)" );
1917 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1918 if ( t8.getNumberOfExternalNodes() != 10 ) {
1921 if ( t8.getHeight() != 15 ) {
1924 final char[] a9 = new char[] { 'a' };
1925 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1926 if ( t9.getHeight() != 0 ) {
1929 final char[] a10 = new char[] { 'a', ':', '6' };
1930 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1931 if ( t10.getHeight() != 6 ) {
1935 catch ( final Exception e ) {
1936 e.printStackTrace( System.out );
1942 private static boolean testConfidenceAssessor() {
1944 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1945 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1946 final Phylogeny[] ev0 = factory
1947 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1949 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1950 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1953 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1956 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1957 final Phylogeny[] ev1 = factory
1958 .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)));",
1960 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1961 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1964 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1967 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1968 final Phylogeny[] ev_b = factory
1969 .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",
1971 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1972 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1975 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1979 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1980 final Phylogeny[] ev1x = factory
1981 .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)));",
1983 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1984 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1987 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1990 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1991 final Phylogeny[] ev_bx = factory
1992 .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",
1994 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1995 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1998 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2002 final Phylogeny[] t2 = factory
2003 .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);",
2005 final Phylogeny[] ev2 = factory
2006 .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);",
2008 for( final Phylogeny target : t2 ) {
2009 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2012 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2013 new NHXParser() )[ 0 ];
2014 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2015 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2016 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2019 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2022 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2026 catch ( final Exception e ) {
2027 e.printStackTrace();
2033 private static boolean testCopyOfNodeData() {
2035 final PhylogenyNode n1 = PhylogenyNode
2036 .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]" );
2037 final PhylogenyNode n2 = n1.copyNodeData();
2038 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2042 catch ( final Exception e ) {
2043 e.printStackTrace();
2049 private static boolean testDataObjects() {
2051 final Confidence s0 = new Confidence();
2052 final Confidence s1 = new Confidence();
2053 if ( !s0.isEqual( s1 ) ) {
2056 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2057 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2058 if ( s2.isEqual( s1 ) ) {
2061 if ( !s2.isEqual( s3 ) ) {
2064 final Confidence s4 = ( Confidence ) s3.copy();
2065 if ( !s4.isEqual( s3 ) ) {
2072 final Taxonomy t1 = new Taxonomy();
2073 final Taxonomy t2 = new Taxonomy();
2074 final Taxonomy t3 = new Taxonomy();
2075 final Taxonomy t4 = new Taxonomy();
2076 final Taxonomy t5 = new Taxonomy();
2077 t1.setIdentifier( new Identifier( "ecoli" ) );
2078 t1.setTaxonomyCode( "ECOLI" );
2079 t1.setScientificName( "E. coli" );
2080 t1.setCommonName( "coli" );
2081 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2082 if ( !t1.isEqual( t0 ) ) {
2085 t2.setIdentifier( new Identifier( "ecoli" ) );
2086 t2.setTaxonomyCode( "OTHER" );
2087 t2.setScientificName( "what" );
2088 t2.setCommonName( "something" );
2089 if ( !t1.isEqual( t2 ) ) {
2092 t2.setIdentifier( new Identifier( "nemve" ) );
2093 if ( t1.isEqual( t2 ) ) {
2096 t1.setIdentifier( null );
2097 t3.setTaxonomyCode( "ECOLI" );
2098 t3.setScientificName( "what" );
2099 t3.setCommonName( "something" );
2100 if ( !t1.isEqual( t3 ) ) {
2103 t1.setIdentifier( null );
2104 t1.setTaxonomyCode( "" );
2105 t4.setScientificName( "E. ColI" );
2106 t4.setCommonName( "something" );
2107 if ( !t1.isEqual( t4 ) ) {
2110 t4.setScientificName( "B. subtilis" );
2111 t4.setCommonName( "something" );
2112 if ( t1.isEqual( t4 ) ) {
2115 t1.setIdentifier( null );
2116 t1.setTaxonomyCode( "" );
2117 t1.setScientificName( "" );
2118 t5.setCommonName( "COLI" );
2119 if ( !t1.isEqual( t5 ) ) {
2122 t5.setCommonName( "vibrio" );
2123 if ( t1.isEqual( t5 ) ) {
2128 final Identifier id0 = new Identifier( "123", "pfam" );
2129 final Identifier id1 = ( Identifier ) id0.copy();
2130 if ( !id1.isEqual( id1 ) ) {
2133 if ( !id1.isEqual( id0 ) ) {
2136 if ( !id0.isEqual( id1 ) ) {
2143 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2144 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2145 if ( !pd1.isEqual( pd1 ) ) {
2148 if ( !pd1.isEqual( pd0 ) ) {
2153 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2154 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2155 if ( !pd3.isEqual( pd3 ) ) {
2158 if ( !pd2.isEqual( pd3 ) ) {
2161 if ( !pd0.isEqual( pd3 ) ) {
2166 // DomainArchitecture
2167 // ------------------
2168 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2169 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2170 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2171 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2172 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2173 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2178 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2179 if ( ds0.getNumberOfDomains() != 4 ) {
2182 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2183 if ( !ds0.isEqual( ds0 ) ) {
2186 if ( !ds0.isEqual( ds1 ) ) {
2189 if ( ds1.getNumberOfDomains() != 4 ) {
2192 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2197 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2198 if ( ds0.isEqual( ds2 ) ) {
2204 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2205 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2206 System.out.println( ds3.toNHX() );
2209 if ( ds3.getNumberOfDomains() != 3 ) {
2214 final Event e1 = new Event( Event.EventType.fusion );
2215 if ( e1.isDuplication() ) {
2218 if ( !e1.isFusion() ) {
2221 if ( !e1.asText().toString().equals( "fusion" ) ) {
2224 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2227 final Event e11 = new Event( Event.EventType.fusion );
2228 if ( !e11.isEqual( e1 ) ) {
2231 if ( !e11.toNHX().toString().equals( "" ) ) {
2234 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2235 if ( e2.isDuplication() ) {
2238 if ( !e2.isSpeciationOrDuplication() ) {
2241 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2244 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2247 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2250 if ( e11.isEqual( e2 ) ) {
2253 final Event e2c = ( Event ) e2.copy();
2254 if ( !e2c.isEqual( e2 ) ) {
2257 Event e3 = new Event( 1, 2, 3 );
2258 if ( e3.isDuplication() ) {
2261 if ( e3.isSpeciation() ) {
2264 if ( e3.isGeneLoss() ) {
2267 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2270 final Event e3c = ( Event ) e3.copy();
2271 final Event e3cc = ( Event ) e3c.copy();
2272 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2276 if ( !e3c.isEqual( e3cc ) ) {
2279 Event e4 = new Event( 1, 2, 3 );
2280 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2283 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2286 final Event e4c = ( Event ) e4.copy();
2288 final Event e4cc = ( Event ) e4c.copy();
2289 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2292 if ( !e4c.isEqual( e4cc ) ) {
2295 final Event e5 = new Event();
2296 if ( !e5.isUnassigned() ) {
2299 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2302 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2305 final Event e6 = new Event( 1, 0, 0 );
2306 if ( !e6.asText().toString().equals( "duplication" ) ) {
2309 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2312 final Event e7 = new Event( 0, 1, 0 );
2313 if ( !e7.asText().toString().equals( "speciation" ) ) {
2316 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2319 final Event e8 = new Event( 0, 0, 1 );
2320 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2323 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2327 catch ( final Exception e ) {
2328 e.printStackTrace( System.out );
2334 private static boolean testDeletionOfExternalNodes() {
2336 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2337 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2338 final PhylogenyWriter w = new PhylogenyWriter();
2339 if ( t0.isEmpty() ) {
2342 if ( t0.getNumberOfExternalNodes() != 1 ) {
2345 t0.deleteSubtree( t0.getNode( "A" ), false );
2346 if ( t0.getNumberOfExternalNodes() != 0 ) {
2349 if ( !t0.isEmpty() ) {
2352 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2353 if ( t1.getNumberOfExternalNodes() != 2 ) {
2356 t1.deleteSubtree( t1.getNode( "A" ), false );
2357 if ( t1.getNumberOfExternalNodes() != 1 ) {
2360 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2363 t1.deleteSubtree( t1.getNode( "B" ), false );
2364 if ( t1.getNumberOfExternalNodes() != 1 ) {
2367 t1.deleteSubtree( t1.getNode( "r" ), false );
2368 if ( !t1.isEmpty() ) {
2371 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2372 if ( t2.getNumberOfExternalNodes() != 3 ) {
2375 t2.deleteSubtree( t2.getNode( "B" ), false );
2376 if ( t2.getNumberOfExternalNodes() != 2 ) {
2379 t2.toNewHampshireX();
2380 PhylogenyNode n = t2.getNode( "A" );
2381 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2384 t2.deleteSubtree( t2.getNode( "A" ), false );
2385 if ( t2.getNumberOfExternalNodes() != 2 ) {
2388 t2.deleteSubtree( t2.getNode( "C" ), true );
2389 if ( t2.getNumberOfExternalNodes() != 1 ) {
2392 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2393 if ( t3.getNumberOfExternalNodes() != 4 ) {
2396 t3.deleteSubtree( t3.getNode( "B" ), true );
2397 if ( t3.getNumberOfExternalNodes() != 3 ) {
2400 n = t3.getNode( "A" );
2401 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2404 n = n.getNextExternalNode();
2405 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2408 t3.deleteSubtree( t3.getNode( "A" ), true );
2409 if ( t3.getNumberOfExternalNodes() != 2 ) {
2412 n = t3.getNode( "C" );
2413 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2416 t3.deleteSubtree( t3.getNode( "C" ), true );
2417 if ( t3.getNumberOfExternalNodes() != 1 ) {
2420 t3.deleteSubtree( t3.getNode( "D" ), true );
2421 if ( t3.getNumberOfExternalNodes() != 0 ) {
2424 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2425 if ( t4.getNumberOfExternalNodes() != 6 ) {
2428 t4.deleteSubtree( t4.getNode( "B2" ), true );
2429 if ( t4.getNumberOfExternalNodes() != 5 ) {
2432 String s = w.toNewHampshire( t4, false, true ).toString();
2433 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2436 t4.deleteSubtree( t4.getNode( "B11" ), true );
2437 if ( t4.getNumberOfExternalNodes() != 4 ) {
2440 t4.deleteSubtree( t4.getNode( "C" ), true );
2441 if ( t4.getNumberOfExternalNodes() != 3 ) {
2444 n = t4.getNode( "A" );
2445 n = n.getNextExternalNode();
2446 if ( !n.getName().equals( "B12" ) ) {
2449 n = n.getNextExternalNode();
2450 if ( !n.getName().equals( "D" ) ) {
2453 s = w.toNewHampshire( t4, false, true ).toString();
2454 if ( !s.equals( "((A,B12),D);" ) ) {
2457 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2458 t5.deleteSubtree( t5.getNode( "A" ), true );
2459 if ( t5.getNumberOfExternalNodes() != 5 ) {
2462 s = w.toNewHampshire( t5, false, true ).toString();
2463 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2466 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2467 t6.deleteSubtree( t6.getNode( "B11" ), true );
2468 if ( t6.getNumberOfExternalNodes() != 5 ) {
2471 s = w.toNewHampshire( t6, false, false ).toString();
2472 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2475 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2476 t7.deleteSubtree( t7.getNode( "B12" ), true );
2477 if ( t7.getNumberOfExternalNodes() != 5 ) {
2480 s = w.toNewHampshire( t7, false, true ).toString();
2481 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2484 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2485 t8.deleteSubtree( t8.getNode( "B2" ), true );
2486 if ( t8.getNumberOfExternalNodes() != 5 ) {
2489 s = w.toNewHampshire( t8, false, false ).toString();
2490 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2493 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2494 t9.deleteSubtree( t9.getNode( "C" ), true );
2495 if ( t9.getNumberOfExternalNodes() != 5 ) {
2498 s = w.toNewHampshire( t9, false, true ).toString();
2499 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2502 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2503 t10.deleteSubtree( t10.getNode( "D" ), true );
2504 if ( t10.getNumberOfExternalNodes() != 5 ) {
2507 s = w.toNewHampshire( t10, false, true ).toString();
2508 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2511 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2512 t11.deleteSubtree( t11.getNode( "A" ), true );
2513 if ( t11.getNumberOfExternalNodes() != 2 ) {
2516 s = w.toNewHampshire( t11, false, true ).toString();
2517 if ( !s.equals( "(B,C);" ) ) {
2520 t11.deleteSubtree( t11.getNode( "C" ), true );
2521 if ( t11.getNumberOfExternalNodes() != 1 ) {
2524 s = w.toNewHampshire( t11, false, false ).toString();
2525 if ( !s.equals( "B;" ) ) {
2528 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2529 t12.deleteSubtree( t12.getNode( "B2" ), true );
2530 if ( t12.getNumberOfExternalNodes() != 8 ) {
2533 s = w.toNewHampshire( t12, false, true ).toString();
2534 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2537 t12.deleteSubtree( t12.getNode( "B3" ), true );
2538 if ( t12.getNumberOfExternalNodes() != 7 ) {
2541 s = w.toNewHampshire( t12, false, true ).toString();
2542 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2545 t12.deleteSubtree( t12.getNode( "C3" ), true );
2546 if ( t12.getNumberOfExternalNodes() != 6 ) {
2549 s = w.toNewHampshire( t12, false, true ).toString();
2550 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2553 t12.deleteSubtree( t12.getNode( "A1" ), true );
2554 if ( t12.getNumberOfExternalNodes() != 5 ) {
2557 s = w.toNewHampshire( t12, false, true ).toString();
2558 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2561 t12.deleteSubtree( t12.getNode( "B1" ), true );
2562 if ( t12.getNumberOfExternalNodes() != 4 ) {
2565 s = w.toNewHampshire( t12, false, true ).toString();
2566 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2569 t12.deleteSubtree( t12.getNode( "A3" ), true );
2570 if ( t12.getNumberOfExternalNodes() != 3 ) {
2573 s = w.toNewHampshire( t12, false, true ).toString();
2574 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2577 t12.deleteSubtree( t12.getNode( "A2" ), true );
2578 if ( t12.getNumberOfExternalNodes() != 2 ) {
2581 s = w.toNewHampshire( t12, false, true ).toString();
2582 if ( !s.equals( "(C1,C2);" ) ) {
2585 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2586 t13.deleteSubtree( t13.getNode( "D" ), true );
2587 if ( t13.getNumberOfExternalNodes() != 4 ) {
2590 s = w.toNewHampshire( t13, false, true ).toString();
2591 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2594 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2595 t14.deleteSubtree( t14.getNode( "E" ), true );
2596 if ( t14.getNumberOfExternalNodes() != 5 ) {
2599 s = w.toNewHampshire( t14, false, true ).toString();
2600 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2603 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2604 t15.deleteSubtree( t15.getNode( "B2" ), true );
2605 if ( t15.getNumberOfExternalNodes() != 11 ) {
2608 t15.deleteSubtree( t15.getNode( "B1" ), true );
2609 if ( t15.getNumberOfExternalNodes() != 10 ) {
2612 t15.deleteSubtree( t15.getNode( "B3" ), true );
2613 if ( t15.getNumberOfExternalNodes() != 9 ) {
2616 t15.deleteSubtree( t15.getNode( "B4" ), true );
2617 if ( t15.getNumberOfExternalNodes() != 8 ) {
2620 t15.deleteSubtree( t15.getNode( "A1" ), true );
2621 if ( t15.getNumberOfExternalNodes() != 7 ) {
2624 t15.deleteSubtree( t15.getNode( "C4" ), true );
2625 if ( t15.getNumberOfExternalNodes() != 6 ) {
2629 catch ( final Exception e ) {
2630 e.printStackTrace( System.out );
2636 private static boolean testDescriptiveStatistics() {
2638 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2639 dss1.addValue( 82 );
2640 dss1.addValue( 78 );
2641 dss1.addValue( 70 );
2642 dss1.addValue( 58 );
2643 dss1.addValue( 42 );
2644 if ( dss1.getN() != 5 ) {
2647 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2650 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2653 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2656 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2659 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2662 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2665 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2668 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2671 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2674 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2677 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2680 dss1.addValue( 123 );
2681 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2684 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2687 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2690 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2691 dss2.addValue( -1.85 );
2692 dss2.addValue( 57.5 );
2693 dss2.addValue( 92.78 );
2694 dss2.addValue( 57.78 );
2695 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2698 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2701 final double[] a = dss2.getDataAsDoubleArray();
2702 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2705 dss2.addValue( -100 );
2706 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2709 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2712 final double[] ds = new double[ 14 ];
2727 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2728 if ( bins.length != 4 ) {
2731 if ( bins[ 0 ] != 2 ) {
2734 if ( bins[ 1 ] != 3 ) {
2737 if ( bins[ 2 ] != 4 ) {
2740 if ( bins[ 3 ] != 5 ) {
2743 final double[] ds1 = new double[ 9 ];
2753 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2754 if ( bins1.length != 4 ) {
2757 if ( bins1[ 0 ] != 2 ) {
2760 if ( bins1[ 1 ] != 3 ) {
2763 if ( bins1[ 2 ] != 0 ) {
2766 if ( bins1[ 3 ] != 4 ) {
2769 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2770 if ( bins1_1.length != 3 ) {
2773 if ( bins1_1[ 0 ] != 3 ) {
2776 if ( bins1_1[ 1 ] != 2 ) {
2779 if ( bins1_1[ 2 ] != 4 ) {
2782 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2783 if ( bins1_2.length != 3 ) {
2786 if ( bins1_2[ 0 ] != 2 ) {
2789 if ( bins1_2[ 1 ] != 2 ) {
2792 if ( bins1_2[ 2 ] != 2 ) {
2795 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2809 dss3.addValue( 10 );
2810 dss3.addValue( 10 );
2811 dss3.addValue( 10 );
2812 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2813 histo.toStringBuffer( 10, '=', 40, 5 );
2814 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2816 catch ( final Exception e ) {
2817 e.printStackTrace( System.out );
2823 private static boolean testDir( final String file ) {
2825 final File f = new File( file );
2826 if ( !f.exists() ) {
2829 if ( !f.isDirectory() ) {
2832 if ( !f.canRead() ) {
2836 catch ( final Exception e ) {
2842 private static boolean testExternalNodeRelatedMethods() {
2844 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2845 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2846 PhylogenyNode n = t1.getNode( "A" );
2847 n = n.getNextExternalNode();
2848 if ( !n.getName().equals( "B" ) ) {
2851 n = n.getNextExternalNode();
2852 if ( !n.getName().equals( "C" ) ) {
2855 n = n.getNextExternalNode();
2856 if ( !n.getName().equals( "D" ) ) {
2859 n = t1.getNode( "B" );
2860 while ( !n.isLastExternalNode() ) {
2861 n = n.getNextExternalNode();
2863 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2864 n = t2.getNode( "A" );
2865 n = n.getNextExternalNode();
2866 if ( !n.getName().equals( "B" ) ) {
2869 n = n.getNextExternalNode();
2870 if ( !n.getName().equals( "C" ) ) {
2873 n = n.getNextExternalNode();
2874 if ( !n.getName().equals( "D" ) ) {
2877 n = t2.getNode( "B" );
2878 while ( !n.isLastExternalNode() ) {
2879 n = n.getNextExternalNode();
2881 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2882 n = t3.getNode( "A" );
2883 n = n.getNextExternalNode();
2884 if ( !n.getName().equals( "B" ) ) {
2887 n = n.getNextExternalNode();
2888 if ( !n.getName().equals( "C" ) ) {
2891 n = n.getNextExternalNode();
2892 if ( !n.getName().equals( "D" ) ) {
2895 n = n.getNextExternalNode();
2896 if ( !n.getName().equals( "E" ) ) {
2899 n = n.getNextExternalNode();
2900 if ( !n.getName().equals( "F" ) ) {
2903 n = n.getNextExternalNode();
2904 if ( !n.getName().equals( "G" ) ) {
2907 n = n.getNextExternalNode();
2908 if ( !n.getName().equals( "H" ) ) {
2911 n = t3.getNode( "B" );
2912 while ( !n.isLastExternalNode() ) {
2913 n = n.getNextExternalNode();
2915 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2916 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2917 final PhylogenyNode node = iter.next();
2919 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2920 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2921 final PhylogenyNode node = iter.next();
2923 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2924 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2925 if ( !iter.next().getName().equals( "A" ) ) {
2928 if ( !iter.next().getName().equals( "B" ) ) {
2931 if ( !iter.next().getName().equals( "C" ) ) {
2934 if ( !iter.next().getName().equals( "D" ) ) {
2937 if ( !iter.next().getName().equals( "E" ) ) {
2940 if ( !iter.next().getName().equals( "F" ) ) {
2943 if ( iter.hasNext() ) {
2947 catch ( final Exception e ) {
2948 e.printStackTrace( System.out );
2954 private static boolean testGeneralTable() {
2956 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2957 t0.setValue( 3, 2, "23" );
2958 t0.setValue( 10, 1, "error" );
2959 t0.setValue( 10, 1, "110" );
2960 t0.setValue( 9, 1, "19" );
2961 t0.setValue( 1, 10, "101" );
2962 t0.setValue( 10, 10, "1010" );
2963 t0.setValue( 100, 10, "10100" );
2964 t0.setValue( 0, 0, "00" );
2965 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2968 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2971 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2974 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2977 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2980 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2983 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2986 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2989 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2992 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2993 t1.setValue( "3", "2", "23" );
2994 t1.setValue( "10", "1", "error" );
2995 t1.setValue( "10", "1", "110" );
2996 t1.setValue( "9", "1", "19" );
2997 t1.setValue( "1", "10", "101" );
2998 t1.setValue( "10", "10", "1010" );
2999 t1.setValue( "100", "10", "10100" );
3000 t1.setValue( "0", "0", "00" );
3001 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3002 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3005 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3008 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3011 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3014 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3017 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3020 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3023 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3026 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3029 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3033 catch ( final Exception e ) {
3034 e.printStackTrace( System.out );
3040 private static boolean testGetDistance() {
3042 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3043 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",
3044 new NHXParser() )[ 0 ];
3045 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3048 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3051 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3054 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3057 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3060 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3063 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3066 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3069 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3072 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3075 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3078 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3081 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3084 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3087 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3090 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3093 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3096 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3099 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3102 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3105 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3108 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3111 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3114 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3117 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3120 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3123 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3126 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3129 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3132 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3135 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3138 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",
3139 new NHXParser() )[ 0 ];
3140 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3143 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3146 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3149 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3152 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3155 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3158 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3161 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3164 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3167 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3170 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3174 catch ( final Exception e ) {
3175 e.printStackTrace( System.out );
3181 private static boolean testGetLCA() {
3183 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3184 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3185 new NHXParser() )[ 0 ];
3186 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3187 if ( !A.getName().equals( "A" ) ) {
3190 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3191 if ( !gh.getName().equals( "gh" ) ) {
3194 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3195 if ( !ab.getName().equals( "ab" ) ) {
3198 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3199 if ( !ab2.getName().equals( "ab" ) ) {
3202 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3203 if ( !gh2.getName().equals( "gh" ) ) {
3206 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3207 if ( !gh3.getName().equals( "gh" ) ) {
3210 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3211 if ( !abc.getName().equals( "abc" ) ) {
3214 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3215 if ( !abc2.getName().equals( "abc" ) ) {
3218 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3219 if ( !abcd.getName().equals( "abcd" ) ) {
3222 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3223 if ( !abcd2.getName().equals( "abcd" ) ) {
3226 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3227 if ( !abcdef.getName().equals( "abcdef" ) ) {
3230 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3231 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3234 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3235 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3238 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3239 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3242 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3243 if ( !abcde.getName().equals( "abcde" ) ) {
3246 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3247 if ( !abcde2.getName().equals( "abcde" ) ) {
3250 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3251 if ( !r.getName().equals( "abcdefgh" ) ) {
3254 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3255 if ( !r2.getName().equals( "abcdefgh" ) ) {
3258 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3259 if ( !r3.getName().equals( "abcdefgh" ) ) {
3262 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3263 if ( !abcde3.getName().equals( "abcde" ) ) {
3266 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3267 if ( !abcde4.getName().equals( "abcde" ) ) {
3270 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3271 if ( !ab3.getName().equals( "ab" ) ) {
3274 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3275 if ( !ab4.getName().equals( "ab" ) ) {
3278 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3279 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3280 if ( !cd.getName().equals( "cd" ) ) {
3283 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3284 if ( !cd2.getName().equals( "cd" ) ) {
3287 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3288 if ( !cde.getName().equals( "cde" ) ) {
3291 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3292 if ( !cde2.getName().equals( "cde" ) ) {
3295 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3296 if ( !cdef.getName().equals( "cdef" ) ) {
3299 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3300 if ( !cdef2.getName().equals( "cdef" ) ) {
3303 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3304 if ( !cdef3.getName().equals( "cdef" ) ) {
3307 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3308 if ( !rt.getName().equals( "r" ) ) {
3311 final Phylogeny p3 = factory
3312 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3313 new NHXParser() )[ 0 ];
3314 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3315 if ( !bc_3.getName().equals( "bc" ) ) {
3318 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3319 if ( !ac_3.getName().equals( "abc" ) ) {
3322 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3323 if ( !ad_3.getName().equals( "abcde" ) ) {
3326 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3327 if ( !af_3.getName().equals( "abcdef" ) ) {
3330 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3331 if ( !ag_3.getName().equals( "" ) ) {
3334 if ( !ag_3.isRoot() ) {
3337 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3338 if ( !al_3.getName().equals( "" ) ) {
3341 if ( !al_3.isRoot() ) {
3344 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3345 if ( !kl_3.getName().equals( "" ) ) {
3348 if ( !kl_3.isRoot() ) {
3351 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3352 if ( !fl_3.getName().equals( "" ) ) {
3355 if ( !fl_3.isRoot() ) {
3358 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3359 if ( !gk_3.getName().equals( "ghijk" ) ) {
3362 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3363 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3364 if ( !r_4.getName().equals( "r" ) ) {
3367 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3368 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3369 if ( !r_5.getName().equals( "root" ) ) {
3372 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3373 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3374 if ( !r_6.getName().equals( "rot" ) ) {
3377 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3378 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3379 if ( !r_7.getName().equals( "rott" ) ) {
3383 catch ( final Exception e ) {
3384 e.printStackTrace( System.out );
3390 private static boolean testGetLCA2() {
3392 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3393 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3394 PhylogenyMethods.preOrderReId( p_a );
3395 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3396 p_a.getNode( "a" ) );
3397 if ( !p_a_1.getName().equals( "a" ) ) {
3400 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3401 PhylogenyMethods.preOrderReId( p_b );
3402 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3403 p_b.getNode( "a" ) );
3404 if ( !p_b_1.getName().equals( "b" ) ) {
3407 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3408 p_b.getNode( "b" ) );
3409 if ( !p_b_2.getName().equals( "b" ) ) {
3412 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3413 PhylogenyMethods.preOrderReId( p_c );
3414 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3415 p_c.getNode( "a" ) );
3416 if ( !p_c_1.getName().equals( "b" ) ) {
3419 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3420 p_c.getNode( "c" ) );
3421 if ( !p_c_2.getName().equals( "c" ) ) {
3422 System.out.println( p_c_2.getName() );
3426 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3427 p_c.getNode( "b" ) );
3428 if ( !p_c_3.getName().equals( "b" ) ) {
3431 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3432 p_c.getNode( "a" ) );
3433 if ( !p_c_4.getName().equals( "c" ) ) {
3436 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3437 new NHXParser() )[ 0 ];
3438 PhylogenyMethods.preOrderReId( p1 );
3439 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3440 p1.getNode( "A" ) );
3441 if ( !A.getName().equals( "A" ) ) {
3444 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3445 p1.getNode( "gh" ) );
3446 if ( !gh.getName().equals( "gh" ) ) {
3449 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3450 p1.getNode( "B" ) );
3451 if ( !ab.getName().equals( "ab" ) ) {
3454 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3455 p1.getNode( "A" ) );
3456 if ( !ab2.getName().equals( "ab" ) ) {
3459 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3460 p1.getNode( "G" ) );
3461 if ( !gh2.getName().equals( "gh" ) ) {
3464 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3465 p1.getNode( "H" ) );
3466 if ( !gh3.getName().equals( "gh" ) ) {
3469 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3470 p1.getNode( "A" ) );
3471 if ( !abc.getName().equals( "abc" ) ) {
3474 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3475 p1.getNode( "C" ) );
3476 if ( !abc2.getName().equals( "abc" ) ) {
3479 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3480 p1.getNode( "D" ) );
3481 if ( !abcd.getName().equals( "abcd" ) ) {
3484 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3485 p1.getNode( "A" ) );
3486 if ( !abcd2.getName().equals( "abcd" ) ) {
3489 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3490 p1.getNode( "F" ) );
3491 if ( !abcdef.getName().equals( "abcdef" ) ) {
3494 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3495 p1.getNode( "A" ) );
3496 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3499 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3500 p1.getNode( "F" ) );
3501 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3504 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3505 p1.getNode( "ab" ) );
3506 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3509 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3510 p1.getNode( "E" ) );
3511 if ( !abcde.getName().equals( "abcde" ) ) {
3514 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3515 p1.getNode( "A" ) );
3516 if ( !abcde2.getName().equals( "abcde" ) ) {
3519 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3520 p1.getNode( "abcdefgh" ) );
3521 if ( !r.getName().equals( "abcdefgh" ) ) {
3524 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3525 p1.getNode( "H" ) );
3526 if ( !r2.getName().equals( "abcdefgh" ) ) {
3529 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3530 p1.getNode( "A" ) );
3531 if ( !r3.getName().equals( "abcdefgh" ) ) {
3534 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3535 p1.getNode( "abcde" ) );
3536 if ( !abcde3.getName().equals( "abcde" ) ) {
3539 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3540 p1.getNode( "E" ) );
3541 if ( !abcde4.getName().equals( "abcde" ) ) {
3544 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3545 p1.getNode( "B" ) );
3546 if ( !ab3.getName().equals( "ab" ) ) {
3549 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3550 p1.getNode( "ab" ) );
3551 if ( !ab4.getName().equals( "ab" ) ) {
3554 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3555 PhylogenyMethods.preOrderReId( p2 );
3556 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3557 p2.getNode( "d" ) );
3558 if ( !cd.getName().equals( "cd" ) ) {
3561 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3562 p2.getNode( "c" ) );
3563 if ( !cd2.getName().equals( "cd" ) ) {
3566 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3567 p2.getNode( "e" ) );
3568 if ( !cde.getName().equals( "cde" ) ) {
3571 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3572 p2.getNode( "c" ) );
3573 if ( !cde2.getName().equals( "cde" ) ) {
3576 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3577 p2.getNode( "f" ) );
3578 if ( !cdef.getName().equals( "cdef" ) ) {
3581 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3582 p2.getNode( "f" ) );
3583 if ( !cdef2.getName().equals( "cdef" ) ) {
3586 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3587 p2.getNode( "d" ) );
3588 if ( !cdef3.getName().equals( "cdef" ) ) {
3591 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3592 p2.getNode( "a" ) );
3593 if ( !rt.getName().equals( "r" ) ) {
3596 final Phylogeny p3 = factory
3597 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3598 new NHXParser() )[ 0 ];
3599 PhylogenyMethods.preOrderReId( p3 );
3600 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3601 p3.getNode( "c" ) );
3602 if ( !bc_3.getName().equals( "bc" ) ) {
3605 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3606 p3.getNode( "c" ) );
3607 if ( !ac_3.getName().equals( "abc" ) ) {
3610 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3611 p3.getNode( "d" ) );
3612 if ( !ad_3.getName().equals( "abcde" ) ) {
3615 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3616 p3.getNode( "f" ) );
3617 if ( !af_3.getName().equals( "abcdef" ) ) {
3620 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3621 p3.getNode( "g" ) );
3622 if ( !ag_3.getName().equals( "" ) ) {
3625 if ( !ag_3.isRoot() ) {
3628 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3629 p3.getNode( "l" ) );
3630 if ( !al_3.getName().equals( "" ) ) {
3633 if ( !al_3.isRoot() ) {
3636 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3637 p3.getNode( "l" ) );
3638 if ( !kl_3.getName().equals( "" ) ) {
3641 if ( !kl_3.isRoot() ) {
3644 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3645 p3.getNode( "l" ) );
3646 if ( !fl_3.getName().equals( "" ) ) {
3649 if ( !fl_3.isRoot() ) {
3652 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3653 p3.getNode( "k" ) );
3654 if ( !gk_3.getName().equals( "ghijk" ) ) {
3657 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3658 PhylogenyMethods.preOrderReId( p4 );
3659 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3660 p4.getNode( "c" ) );
3661 if ( !r_4.getName().equals( "r" ) ) {
3664 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3665 PhylogenyMethods.preOrderReId( p5 );
3666 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3667 p5.getNode( "c" ) );
3668 if ( !r_5.getName().equals( "root" ) ) {
3671 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3672 PhylogenyMethods.preOrderReId( p6 );
3673 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3674 p6.getNode( "a" ) );
3675 if ( !r_6.getName().equals( "rot" ) ) {
3678 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3679 PhylogenyMethods.preOrderReId( p7 );
3680 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3681 p7.getNode( "e" ) );
3682 if ( !r_7.getName().equals( "rott" ) ) {
3685 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3686 p7.getNode( "a" ) );
3687 if ( !r_71.getName().equals( "rott" ) ) {
3690 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3691 p7.getNode( "rott" ) );
3692 if ( !r_72.getName().equals( "rott" ) ) {
3695 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3696 p7.getNode( "a" ) );
3697 if ( !r_73.getName().equals( "rott" ) ) {
3700 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3701 p7.getNode( "rott" ) );
3702 if ( !r_74.getName().equals( "rott" ) ) {
3705 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3706 p7.getNode( "e" ) );
3707 if ( !r_75.getName().equals( "e" ) ) {
3711 catch ( final Exception e ) {
3712 e.printStackTrace( System.out );
3718 private static boolean testHmmscanOutputParser() {
3719 final String test_dir = Test.PATH_TO_TEST_DATA;
3721 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3722 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3724 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3725 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3726 final List<Protein> proteins = parser2.parse();
3727 if ( parser2.getProteinsEncountered() != 4 ) {
3730 if ( proteins.size() != 4 ) {
3733 if ( parser2.getDomainsEncountered() != 69 ) {
3736 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3739 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3742 final Protein p1 = proteins.get( 0 );
3743 if ( p1.getNumberOfProteinDomains() != 15 ) {
3746 if ( p1.getLength() != 850 ) {
3749 final Protein p2 = proteins.get( 1 );
3750 if ( p2.getNumberOfProteinDomains() != 51 ) {
3753 if ( p2.getLength() != 1291 ) {
3756 final Protein p3 = proteins.get( 2 );
3757 if ( p3.getNumberOfProteinDomains() != 2 ) {
3760 final Protein p4 = proteins.get( 3 );
3761 if ( p4.getNumberOfProteinDomains() != 1 ) {
3764 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3767 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3770 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3773 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3776 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3779 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3782 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3785 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3788 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3792 catch ( final Exception e ) {
3793 e.printStackTrace( System.out );
3799 private static boolean testLastExternalNodeMethods() {
3801 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3802 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3803 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3804 final PhylogenyNode n1 = t0.getNode( "A" );
3805 if ( n1.isLastExternalNode() ) {
3808 final PhylogenyNode n2 = t0.getNode( "B" );
3809 if ( n2.isLastExternalNode() ) {
3812 final PhylogenyNode n3 = t0.getNode( "C" );
3813 if ( n3.isLastExternalNode() ) {
3816 final PhylogenyNode n4 = t0.getNode( "D" );
3817 if ( !n4.isLastExternalNode() ) {
3821 catch ( final Exception e ) {
3822 e.printStackTrace( System.out );
3828 private static boolean testLevelOrderIterator() {
3830 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3831 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3832 PhylogenyNodeIterator it0;
3833 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3836 for( it0.reset(); it0.hasNext(); ) {
3839 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3840 if ( !it.next().getName().equals( "r" ) ) {
3843 if ( !it.next().getName().equals( "ab" ) ) {
3846 if ( !it.next().getName().equals( "cd" ) ) {
3849 if ( !it.next().getName().equals( "A" ) ) {
3852 if ( !it.next().getName().equals( "B" ) ) {
3855 if ( !it.next().getName().equals( "C" ) ) {
3858 if ( !it.next().getName().equals( "D" ) ) {
3861 if ( it.hasNext() ) {
3864 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",
3865 new NHXParser() )[ 0 ];
3866 PhylogenyNodeIterator it2;
3867 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3870 for( it2.reset(); it2.hasNext(); ) {
3873 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3874 if ( !it3.next().getName().equals( "r" ) ) {
3877 if ( !it3.next().getName().equals( "abc" ) ) {
3880 if ( !it3.next().getName().equals( "defg" ) ) {
3883 if ( !it3.next().getName().equals( "A" ) ) {
3886 if ( !it3.next().getName().equals( "B" ) ) {
3889 if ( !it3.next().getName().equals( "C" ) ) {
3892 if ( !it3.next().getName().equals( "D" ) ) {
3895 if ( !it3.next().getName().equals( "E" ) ) {
3898 if ( !it3.next().getName().equals( "F" ) ) {
3901 if ( !it3.next().getName().equals( "G" ) ) {
3904 if ( !it3.next().getName().equals( "1" ) ) {
3907 if ( !it3.next().getName().equals( "2" ) ) {
3910 if ( !it3.next().getName().equals( "3" ) ) {
3913 if ( !it3.next().getName().equals( "4" ) ) {
3916 if ( !it3.next().getName().equals( "5" ) ) {
3919 if ( !it3.next().getName().equals( "6" ) ) {
3922 if ( !it3.next().getName().equals( "f1" ) ) {
3925 if ( !it3.next().getName().equals( "f2" ) ) {
3928 if ( !it3.next().getName().equals( "f3" ) ) {
3931 if ( !it3.next().getName().equals( "a" ) ) {
3934 if ( !it3.next().getName().equals( "b" ) ) {
3937 if ( !it3.next().getName().equals( "f21" ) ) {
3940 if ( !it3.next().getName().equals( "X" ) ) {
3943 if ( !it3.next().getName().equals( "Y" ) ) {
3946 if ( !it3.next().getName().equals( "Z" ) ) {
3949 if ( it3.hasNext() ) {
3952 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3953 PhylogenyNodeIterator it4;
3954 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3957 for( it4.reset(); it4.hasNext(); ) {
3960 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3961 if ( !it5.next().getName().equals( "r" ) ) {
3964 if ( !it5.next().getName().equals( "A" ) ) {
3967 if ( !it5.next().getName().equals( "B" ) ) {
3970 if ( !it5.next().getName().equals( "C" ) ) {
3973 if ( !it5.next().getName().equals( "D" ) ) {
3976 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3977 PhylogenyNodeIterator it6;
3978 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3981 for( it6.reset(); it6.hasNext(); ) {
3984 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3985 if ( !it7.next().getName().equals( "A" ) ) {
3988 if ( it.hasNext() ) {
3992 catch ( final Exception e ) {
3993 e.printStackTrace( System.out );
3999 private static boolean testNodeRemoval() {
4001 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4002 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
4003 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
4004 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
4007 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
4008 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
4009 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4012 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4013 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4014 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4018 catch ( final Exception e ) {
4019 e.printStackTrace( System.out );
4025 private static boolean testMidpointrooting() {
4027 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4028 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4029 PhylogenyMethods.midpointRoot( t0 );
4030 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4033 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4036 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4040 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",
4041 new NHXParser() )[ 0 ];
4042 if ( !t1.isRooted() ) {
4045 PhylogenyMethods.midpointRoot( t1 );
4046 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4049 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4052 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4055 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4058 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4061 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4064 t1.reRoot( t1.getNode( "A" ) );
4065 PhylogenyMethods.midpointRoot( t1 );
4066 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4069 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4072 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4075 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4078 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4082 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4086 catch ( final Exception e ) {
4087 e.printStackTrace( System.out );
4093 private static boolean testNexusCharactersParsing() {
4095 final NexusCharactersParser parser = new NexusCharactersParser();
4096 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4098 String[] labels = parser.getCharStateLabels();
4099 if ( labels.length != 7 ) {
4102 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4105 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4108 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4111 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4114 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4117 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4120 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4123 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4125 labels = parser.getCharStateLabels();
4126 if ( labels.length != 7 ) {
4129 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4132 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4135 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4138 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4141 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4144 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4147 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4151 catch ( final Exception e ) {
4152 e.printStackTrace( System.out );
4158 private static boolean testNexusMatrixParsing() {
4160 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4161 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4163 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4164 if ( m.getNumberOfCharacters() != 9 ) {
4167 if ( m.getNumberOfIdentifiers() != 5 ) {
4170 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4173 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4176 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4179 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4182 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4185 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4188 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4191 // if ( labels.length != 7 ) {
4194 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4197 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4200 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4203 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4206 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4209 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4212 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4215 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4217 // labels = parser.getCharStateLabels();
4218 // if ( labels.length != 7 ) {
4221 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4224 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4227 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4230 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4233 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4236 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4239 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4243 catch ( final Exception e ) {
4244 e.printStackTrace( System.out );
4250 private static boolean testNexusTreeParsing() {
4252 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4253 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4254 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4255 if ( phylogenies.length != 1 ) {
4258 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4261 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4265 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4266 if ( phylogenies.length != 1 ) {
4269 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4272 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4276 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4277 if ( phylogenies.length != 1 ) {
4280 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4283 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4286 if ( phylogenies[ 0 ].isRooted() ) {
4290 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4291 if ( phylogenies.length != 18 ) {
4294 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4297 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4300 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4303 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4306 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4309 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4312 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4315 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4318 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4321 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4324 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4327 if ( phylogenies[ 8 ].isRooted() ) {
4330 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4333 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4336 if ( !phylogenies[ 9 ].isRooted() ) {
4339 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4342 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4345 if ( !phylogenies[ 10 ].isRooted() ) {
4348 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4351 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4354 if ( phylogenies[ 11 ].isRooted() ) {
4357 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4360 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4363 if ( !phylogenies[ 12 ].isRooted() ) {
4366 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4369 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4372 if ( !phylogenies[ 13 ].isRooted() ) {
4375 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4378 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4381 if ( !phylogenies[ 14 ].isRooted() ) {
4384 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4387 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4390 if ( phylogenies[ 15 ].isRooted() ) {
4393 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4396 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4399 if ( !phylogenies[ 16 ].isRooted() ) {
4402 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4405 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4408 if ( phylogenies[ 17 ].isRooted() ) {
4411 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4415 catch ( final Exception e ) {
4416 e.printStackTrace( System.out );
4422 private static boolean testNexusTreeParsingIterating() {
4424 final NexusPhylogeniesParser2 p = new NexusPhylogeniesParser2();
4425 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
4426 if ( !p.hasNext() ) {
4429 Phylogeny phy = p.next();
4430 if ( phy == null ) {
4433 if ( phy.getNumberOfExternalNodes() != 25 ) {
4436 if ( !phy.getName().equals( "" ) ) {
4439 if ( p.hasNext() ) {
4443 if ( phy != null ) {
4448 if ( !p.hasNext() ) {
4452 if ( phy == null ) {
4455 if ( phy.getNumberOfExternalNodes() != 25 ) {
4458 if ( !phy.getName().equals( "" ) ) {
4461 if ( p.hasNext() ) {
4465 if ( phy != null ) {
4469 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
4470 if ( !p.hasNext() ) {
4474 if ( phy == null ) {
4477 if ( phy.getNumberOfExternalNodes() != 10 ) {
4480 if ( !phy.getName().equals( "name" ) ) {
4483 if ( p.hasNext() ) {
4487 if ( phy != null ) {
4492 if ( !p.hasNext() ) {
4496 if ( phy == null ) {
4499 if ( phy.getNumberOfExternalNodes() != 10 ) {
4502 if ( !phy.getName().equals( "name" ) ) {
4505 if ( p.hasNext() ) {
4509 if ( phy != null ) {
4513 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
4514 if ( !p.hasNext() ) {
4518 if ( phy == null ) {
4521 if ( phy.getNumberOfExternalNodes() != 3 ) {
4524 if ( !phy.getName().equals( "" ) ) {
4527 if ( phy.isRooted() ) {
4530 if ( p.hasNext() ) {
4534 if ( phy != null ) {
4539 if ( !p.hasNext() ) {
4543 if ( phy == null ) {
4546 if ( phy.getNumberOfExternalNodes() != 3 ) {
4549 if ( !phy.getName().equals( "" ) ) {
4552 if ( p.hasNext() ) {
4556 if ( phy != null ) {
4560 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
4561 // if ( phylogenies.length != 18 ) {
4565 if ( !p.hasNext() ) {
4569 if ( phy == null ) {
4572 if ( phy.getNumberOfExternalNodes() != 10 ) {
4575 if ( !phy.getName().equals( "tree 0" ) ) {
4579 if ( !p.hasNext() ) {
4583 if ( phy == null ) {
4586 if ( phy.getNumberOfExternalNodes() != 10 ) {
4589 if ( !phy.getName().equals( "tree 1" ) ) {
4593 if ( !p.hasNext() ) {
4597 if ( phy == null ) {
4600 if ( phy.getNumberOfExternalNodes() != 3 ) {
4603 if ( !phy.getName().equals( "" ) ) {
4606 if ( phy.isRooted() ) {
4610 if ( !p.hasNext() ) {
4614 if ( phy == null ) {
4617 if ( phy.getNumberOfExternalNodes() != 4 ) {
4620 if ( !phy.getName().equals( "" ) ) {
4623 if ( !phy.isRooted() ) {
4627 if ( !p.hasNext() ) {
4631 if ( phy == null ) {
4634 if ( phy.getNumberOfExternalNodes() != 5 ) {
4635 System.out.println( phy.getNumberOfExternalNodes() );
4638 if ( !phy.getName().equals( "" ) ) {
4641 if ( !phy.isRooted() ) {
4645 if ( !p.hasNext() ) {
4649 if ( phy == null ) {
4652 if ( phy.getNumberOfExternalNodes() != 3 ) {
4655 if ( !phy.getName().equals( "" ) ) {
4658 if ( phy.isRooted() ) {
4662 if ( !p.hasNext() ) {
4666 if ( phy == null ) {
4669 if ( phy.getNumberOfExternalNodes() != 2 ) {
4672 if ( !phy.getName().equals( "" ) ) {
4675 if ( !phy.isRooted() ) {
4679 if ( !p.hasNext() ) {
4683 if ( phy.getNumberOfExternalNodes() != 3 ) {
4686 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4689 if ( !phy.isRooted() ) {
4693 if ( !p.hasNext() ) {
4697 if ( phy.getNumberOfExternalNodes() != 3 ) {
4700 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
4703 if ( !phy.getName().equals( "tree 8" ) ) {
4707 if ( !p.hasNext() ) {
4711 if ( phy.getNumberOfExternalNodes() != 3 ) {
4714 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
4717 if ( !phy.getName().equals( "tree 9" ) ) {
4721 if ( !p.hasNext() ) {
4725 if ( phy.getNumberOfExternalNodes() != 3 ) {
4728 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4731 if ( !phy.getName().equals( "tree 10" ) ) {
4734 if ( !phy.isRooted() ) {
4738 if ( !p.hasNext() ) {
4742 if ( phy.getNumberOfExternalNodes() != 3 ) {
4745 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
4748 if ( !phy.getName().equals( "tree 11" ) ) {
4751 if ( phy.isRooted() ) {
4755 if ( !p.hasNext() ) {
4759 if ( phy.getNumberOfExternalNodes() != 3 ) {
4762 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
4765 if ( !phy.getName().equals( "tree 12" ) ) {
4768 if ( !phy.isRooted() ) {
4772 if ( !p.hasNext() ) {
4776 if ( phy.getNumberOfExternalNodes() != 3 ) {
4779 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4782 if ( !phy.getName().equals( "tree 13" ) ) {
4785 if ( !phy.isRooted() ) {
4789 if ( !p.hasNext() ) {
4793 if ( phy.getNumberOfExternalNodes() != 10 ) {
4794 System.out.println( phy.getNumberOfExternalNodes() );
4799 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4800 System.out.println( phy.toNewHampshire() );
4803 if ( !phy.getName().equals( "tree 14" ) ) {
4806 if ( !phy.isRooted() ) {
4810 if ( !p.hasNext() ) {
4814 if ( phy.getNumberOfExternalNodes() != 10 ) {
4815 System.out.println( phy.getNumberOfExternalNodes() );
4820 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4821 System.out.println( phy.toNewHampshire() );
4824 if ( !phy.getName().equals( "tree 15" ) ) {
4827 if ( phy.isRooted() ) {
4831 if ( !p.hasNext() ) {
4835 if ( phy.getNumberOfExternalNodes() != 10 ) {
4836 System.out.println( phy.getNumberOfExternalNodes() );
4841 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4842 System.out.println( phy.toNewHampshire() );
4845 if ( !phy.getName().equals( "tree 16" ) ) {
4848 if ( !phy.isRooted() ) {
4852 if ( !p.hasNext() ) {
4856 if ( phy.getNumberOfExternalNodes() != 10 ) {
4857 System.out.println( phy.getNumberOfExternalNodes() );
4862 .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
4863 System.out.println( phy.toNewHampshire() );
4866 if ( !phy.getName().equals( "tree 17" ) ) {
4869 if ( phy.isRooted() ) {
4873 if ( p.hasNext() ) {
4877 if ( phy != null ) {
4882 if ( !p.hasNext() ) {
4886 if ( phy == null ) {
4889 if ( phy.getNumberOfExternalNodes() != 10 ) {
4892 if ( !phy.getName().equals( "tree 0" ) ) {
4896 if ( !p.hasNext() ) {
4900 if ( phy == null ) {
4903 if ( phy.getNumberOfExternalNodes() != 10 ) {
4906 if ( !phy.getName().equals( "tree 1" ) ) {
4910 if ( !p.hasNext() ) {
4914 if ( phy == null ) {
4917 if ( phy.getNumberOfExternalNodes() != 3 ) {
4920 if ( !phy.getName().equals( "" ) ) {
4923 if ( phy.isRooted() ) {
4927 if ( !p.hasNext() ) {
4931 if ( phy == null ) {
4934 if ( phy.getNumberOfExternalNodes() != 4 ) {
4937 if ( !phy.getName().equals( "" ) ) {
4940 if ( !phy.isRooted() ) {
4944 if ( !p.hasNext() ) {
4948 if ( phy == null ) {
4951 if ( phy.getNumberOfExternalNodes() != 5 ) {
4952 System.out.println( phy.getNumberOfExternalNodes() );
4955 if ( !phy.getName().equals( "" ) ) {
4958 if ( !phy.isRooted() ) {
4962 if ( !p.hasNext() ) {
4966 if ( phy == null ) {
4969 if ( phy.getNumberOfExternalNodes() != 3 ) {
4972 if ( !phy.getName().equals( "" ) ) {
4975 if ( phy.isRooted() ) {
4979 catch ( final Exception e ) {
4980 e.printStackTrace( System.out );
4986 private static boolean testNexusTreeParsingTranslating() {
4988 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4989 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4990 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4991 if ( phylogenies.length != 1 ) {
4994 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4997 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5000 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5003 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5006 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5007 .equals( "Aranaeus" ) ) {
5011 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
5012 if ( phylogenies.length != 3 ) {
5015 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5018 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5021 if ( phylogenies[ 0 ].isRooted() ) {
5024 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5027 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5030 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5031 .equals( "Aranaeus" ) ) {
5034 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
5037 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
5040 if ( phylogenies[ 1 ].isRooted() ) {
5043 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5046 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5049 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5050 .equals( "Aranaeus" ) ) {
5053 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
5056 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
5059 if ( !phylogenies[ 2 ].isRooted() ) {
5062 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5065 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5068 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5069 .equals( "Aranaeus" ) ) {
5073 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
5074 if ( phylogenies.length != 3 ) {
5077 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5080 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5083 if ( phylogenies[ 0 ].isRooted() ) {
5086 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5089 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5092 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5093 .equals( "Aranaeus" ) ) {
5096 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
5099 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
5102 if ( phylogenies[ 1 ].isRooted() ) {
5105 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5108 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5111 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5112 .equals( "Aranaeus" ) ) {
5115 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
5118 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
5121 if ( !phylogenies[ 2 ].isRooted() ) {
5124 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5127 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5130 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5131 .equals( "Aranaeus" ) ) {
5135 catch ( final Exception e ) {
5136 e.printStackTrace( System.out );
5142 private static boolean testNHParsing() {
5144 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5145 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
5146 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
5149 final NHXParser nhxp = new NHXParser();
5150 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
5151 nhxp.setReplaceUnderscores( true );
5152 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
5153 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
5156 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
5159 final Phylogeny p1b = factory
5160 .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 ",
5161 new NHXParser() )[ 0 ];
5162 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
5165 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
5168 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
5169 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
5170 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
5171 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
5172 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
5173 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
5174 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
5175 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
5176 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
5177 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
5178 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
5179 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
5180 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
5182 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
5185 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
5188 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
5191 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
5194 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
5195 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
5196 final String p16_S = "((A,B),C)";
5197 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
5198 if ( p16.length != 1 ) {
5201 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
5204 final String p17_S = "(C,(A,B))";
5205 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
5206 if ( p17.length != 1 ) {
5209 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
5212 final String p18_S = "((A,B),(C,D))";
5213 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
5214 if ( p18.length != 1 ) {
5217 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
5220 final String p19_S = "(((A,B),C),D)";
5221 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
5222 if ( p19.length != 1 ) {
5225 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
5228 final String p20_S = "(A,(B,(C,D)))";
5229 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
5230 if ( p20.length != 1 ) {
5233 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
5236 final String p21_S = "(A,(B,(C,(D,E))))";
5237 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
5238 if ( p21.length != 1 ) {
5241 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
5244 final String p22_S = "((((A,B),C),D),E)";
5245 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
5246 if ( p22.length != 1 ) {
5249 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
5252 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5253 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
5254 if ( p23.length != 1 ) {
5255 System.out.println( "xl=" + p23.length );
5259 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
5262 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5263 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
5264 if ( p24.length != 1 ) {
5267 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
5270 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5271 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5272 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
5273 if ( p241.length != 2 ) {
5276 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
5279 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
5282 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
5283 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
5284 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
5285 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
5286 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
5287 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
5288 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
5289 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
5290 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
5291 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
5294 final String p26_S = "(A,B)ab";
5295 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
5296 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
5299 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5300 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
5301 if ( p27s.length != 1 ) {
5302 System.out.println( "xxl=" + p27s.length );
5306 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
5307 System.out.println( p27s[ 0 ].toNewHampshireX() );
5311 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
5313 if ( p27.length != 1 ) {
5314 System.out.println( "yl=" + p27.length );
5318 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
5319 System.out.println( p27[ 0 ].toNewHampshireX() );
5323 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5324 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5325 final String p28_S3 = "(A,B)ab";
5326 final String p28_S4 = "((((A,B),C),D),;E;)";
5327 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
5329 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
5332 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
5335 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
5338 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
5341 if ( p28.length != 4 ) {
5344 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";
5345 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
5346 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
5349 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";
5350 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
5351 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
5354 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
5355 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
5356 if ( ( p32.length != 0 ) ) {
5359 final String p33_S = "A";
5360 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
5361 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
5364 final String p34_S = "B;";
5365 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
5366 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
5369 final String p35_S = "B:0.2";
5370 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
5371 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
5374 final String p36_S = "(A)";
5375 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
5376 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
5379 final String p37_S = "((A))";
5380 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
5381 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
5384 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
5385 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
5386 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
5389 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
5390 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
5391 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
5394 final String p40_S = "(A,B,C)";
5395 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
5396 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
5399 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
5400 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
5401 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
5404 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
5405 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
5406 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
5409 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)";
5410 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
5411 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
5414 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)))";
5415 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
5416 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
5419 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
5420 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
5421 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
5424 final String p46_S = "";
5425 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
5426 if ( p46.length != 0 ) {
5429 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
5430 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5433 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5434 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5437 final Phylogeny p49 = factory
5438 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
5439 new NHXParser() )[ 0 ];
5440 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5443 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5444 if ( p50.getNode( "A" ) == null ) {
5447 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
5448 .equals( "((A,B)ab:2.0[88],C);" ) ) {
5451 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
5454 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
5455 .equals( "((A,B)88:2.0,C);" ) ) {
5458 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5459 if ( p51.getNode( "A(A" ) == null ) {
5462 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5463 if ( p52.getNode( "A(A" ) == null ) {
5466 final Phylogeny p53 = factory
5467 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
5468 new NHXParser() )[ 0 ];
5469 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
5473 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
5474 if ( p54.getNode( "A" ) == null ) {
5477 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
5478 .equals( "((A,B)[88],C);" ) ) {
5482 catch ( final Exception e ) {
5483 e.printStackTrace( System.out );
5489 private static boolean testNHParsingIter() {
5491 final String p0_str = "(A,B);";
5492 final NHXParser p = new NHXParser();
5493 p.setSource( p0_str );
5494 if ( !p.hasNext() ) {
5497 final Phylogeny p0 = p.next();
5498 if ( !p0.toNewHampshire().equals( p0_str ) ) {
5499 System.out.println( p0.toNewHampshire() );
5502 if ( p.hasNext() ) {
5505 if ( p.next() != null ) {
5509 final String p00_str = "(A,B)root;";
5510 p.setSource( p00_str );
5511 final Phylogeny p00 = p.next();
5512 if ( !p00.toNewHampshire().equals( p00_str ) ) {
5513 System.out.println( p00.toNewHampshire() );
5517 final String p000_str = "A;";
5518 p.setSource( p000_str );
5519 final Phylogeny p000 = p.next();
5520 if ( !p000.toNewHampshire().equals( p000_str ) ) {
5521 System.out.println( p000.toNewHampshire() );
5525 final String p0000_str = "A";
5526 p.setSource( p0000_str );
5527 final Phylogeny p0000 = p.next();
5528 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
5529 System.out.println( p0000.toNewHampshire() );
5533 p.setSource( "(A)" );
5534 final Phylogeny p00000 = p.next();
5535 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
5536 System.out.println( p00000.toNewHampshire() );
5540 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
5541 p.setSource( p1_str );
5542 if ( !p.hasNext() ) {
5545 final Phylogeny p1_0 = p.next();
5546 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
5547 System.out.println( p1_0.toNewHampshire() );
5550 if ( !p.hasNext() ) {
5553 final Phylogeny p1_1 = p.next();
5554 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
5555 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
5558 if ( !p.hasNext() ) {
5561 final Phylogeny p1_2 = p.next();
5562 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
5563 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
5566 if ( !p.hasNext() ) {
5569 final Phylogeny p1_3 = p.next();
5570 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
5571 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
5574 if ( p.hasNext() ) {
5577 if ( p.next() != null ) {
5581 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
5582 p.setSource( p2_str );
5583 if ( !p.hasNext() ) {
5586 Phylogeny p2_0 = p.next();
5587 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5588 System.out.println( p2_0.toNewHampshire() );
5591 if ( !p.hasNext() ) {
5594 Phylogeny p2_1 = p.next();
5595 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5596 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5599 if ( !p.hasNext() ) {
5602 Phylogeny p2_2 = p.next();
5603 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5604 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5607 if ( !p.hasNext() ) {
5610 Phylogeny p2_3 = p.next();
5611 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5612 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5615 if ( !p.hasNext() ) {
5618 Phylogeny p2_4 = p.next();
5619 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5620 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5623 if ( p.hasNext() ) {
5626 if ( p.next() != null ) {
5631 if ( !p.hasNext() ) {
5635 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5636 System.out.println( p2_0.toNewHampshire() );
5639 if ( !p.hasNext() ) {
5643 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5644 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5647 if ( !p.hasNext() ) {
5651 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5652 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5655 if ( !p.hasNext() ) {
5659 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5660 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5663 if ( !p.hasNext() ) {
5667 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5668 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5671 if ( p.hasNext() ) {
5674 if ( p.next() != null ) {
5678 final String p3_str = "((A,B),C)abc";
5679 p.setSource( p3_str );
5680 if ( !p.hasNext() ) {
5683 final Phylogeny p3_0 = p.next();
5684 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
5687 if ( p.hasNext() ) {
5690 if ( p.next() != null ) {
5694 final String p4_str = "((A,B)ab,C)abc";
5695 p.setSource( p4_str );
5696 if ( !p.hasNext() ) {
5699 final Phylogeny p4_0 = p.next();
5700 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
5703 if ( p.hasNext() ) {
5706 if ( p.next() != null ) {
5710 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
5711 p.setSource( p5_str );
5712 if ( !p.hasNext() ) {
5715 final Phylogeny p5_0 = p.next();
5716 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
5719 if ( p.hasNext() ) {
5722 if ( p.next() != null ) {
5726 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5727 p.setSource( p6_str );
5728 if ( !p.hasNext() ) {
5731 Phylogeny p6_0 = p.next();
5732 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5735 if ( p.hasNext() ) {
5738 if ( p.next() != null ) {
5742 if ( !p.hasNext() ) {
5746 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5749 if ( p.hasNext() ) {
5752 if ( p.next() != null ) {
5756 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5757 p.setSource( p7_str );
5758 if ( !p.hasNext() ) {
5761 Phylogeny p7_0 = p.next();
5762 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5765 if ( p.hasNext() ) {
5768 if ( p.next() != null ) {
5772 if ( !p.hasNext() ) {
5776 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5779 if ( p.hasNext() ) {
5782 if ( p.next() != null ) {
5786 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
5787 p.setSource( p8_str );
5788 if ( !p.hasNext() ) {
5791 Phylogeny p8_0 = p.next();
5792 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5795 if ( !p.hasNext() ) {
5798 if ( !p.hasNext() ) {
5801 Phylogeny p8_1 = p.next();
5802 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5805 if ( p.hasNext() ) {
5808 if ( p.next() != null ) {
5812 if ( !p.hasNext() ) {
5816 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5819 if ( !p.hasNext() ) {
5823 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5826 if ( p.hasNext() ) {
5829 if ( p.next() != null ) {
5835 if ( p.hasNext() ) {
5839 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
5840 if ( !p.hasNext() ) {
5843 Phylogeny p_27 = p.next();
5844 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5845 System.out.println( p_27.toNewHampshireX() );
5849 if ( p.hasNext() ) {
5852 if ( p.next() != null ) {
5856 if ( !p.hasNext() ) {
5860 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5861 System.out.println( p_27.toNewHampshireX() );
5865 if ( p.hasNext() ) {
5868 if ( p.next() != null ) {
5872 catch ( final Exception e ) {
5873 e.printStackTrace( System.out );
5879 private static boolean testNHXconversion() {
5881 final PhylogenyNode n1 = new PhylogenyNode();
5882 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5883 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5884 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5885 final PhylogenyNode n5 = PhylogenyNode
5886 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
5887 final PhylogenyNode n6 = PhylogenyNode
5888 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
5889 if ( !n1.toNewHampshireX().equals( "" ) ) {
5892 if ( !n2.toNewHampshireX().equals( "" ) ) {
5895 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
5898 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
5901 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
5904 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
5908 catch ( final Exception e ) {
5909 e.printStackTrace( System.out );
5915 private static boolean testTaxonomyExtraction() {
5917 final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
5918 NHXParser.TAXONOMY_EXTRACTION.YES );
5919 if ( n0.getNodeData().isHasTaxonomy() ) {
5922 final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
5923 NHXParser.TAXONOMY_EXTRACTION.YES );
5924 if ( n1.getNodeData().isHasTaxonomy() ) {
5925 System.out.println( n1.toString() );
5928 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
5929 NHXParser.TAXONOMY_EXTRACTION.YES );
5930 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5931 System.out.println( n2.toString() );
5934 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
5935 NHXParser.TAXONOMY_EXTRACTION.YES );
5936 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5937 System.out.println( n3.toString() );
5940 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
5941 NHXParser.TAXONOMY_EXTRACTION.YES );
5942 if ( n4.getNodeData().isHasTaxonomy() ) {
5943 System.out.println( n4.toString() );
5946 final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
5947 NHXParser.TAXONOMY_EXTRACTION.YES );
5948 if ( n5.getNodeData().isHasTaxonomy() ) {
5949 System.out.println( n5.toString() );
5952 final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
5953 NHXParser.TAXONOMY_EXTRACTION.YES );
5954 if ( n6.getNodeData().isHasTaxonomy() ) {
5955 System.out.println( n6.toString() );
5958 final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
5959 NHXParser.TAXONOMY_EXTRACTION.YES );
5960 if ( n7.getNodeData().isHasTaxonomy() ) {
5961 System.out.println( n7.toString() );
5964 final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
5965 NHXParser.TAXONOMY_EXTRACTION.YES );
5966 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5967 System.out.println( n8.toString() );
5970 final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
5971 NHXParser.TAXONOMY_EXTRACTION.YES );
5972 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5973 System.out.println( n9.toString() );
5976 final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
5977 NHXParser.TAXONOMY_EXTRACTION.YES );
5978 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
5979 System.out.println( n10.toString() );
5982 final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
5983 NHXParser.TAXONOMY_EXTRACTION.YES );
5984 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
5985 System.out.println( n11.toString() );
5988 final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
5989 NHXParser.TAXONOMY_EXTRACTION.YES );
5990 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
5991 System.out.println( n12.toString() );
5994 final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
5995 NHXParser.TAXONOMY_EXTRACTION.YES );
5996 if ( n13.getNodeData().isHasTaxonomy() ) {
5997 System.out.println( n13.toString() );
6000 final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
6001 NHXParser.TAXONOMY_EXTRACTION.YES );
6002 if ( n14.getNodeData().isHasTaxonomy() ) {
6003 System.out.println( n14.toString() );
6006 final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
6007 NHXParser.TAXONOMY_EXTRACTION.YES );
6008 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
6009 System.out.println( n15.toString() );
6012 final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
6013 NHXParser.TAXONOMY_EXTRACTION.YES );
6014 if ( n16.getNodeData().isHasTaxonomy() ) {
6015 System.out.println( n16.toString() );
6018 final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
6019 NHXParser.TAXONOMY_EXTRACTION.YES );
6020 if ( n17.getNodeData().isHasTaxonomy() ) {
6021 System.out.println( n17.toString() );
6025 catch ( final Exception e ) {
6026 e.printStackTrace( System.out );
6032 private static boolean testNHXNodeParsing() {
6034 final PhylogenyNode n1 = new PhylogenyNode();
6035 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
6036 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
6037 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
6038 final PhylogenyNode n5 = PhylogenyNode
6039 .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]" );
6040 if ( !n3.getName().equals( "n3" ) ) {
6043 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6046 if ( n3.isDuplication() ) {
6049 if ( n3.isHasAssignedEvent() ) {
6052 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
6055 if ( !n4.getName().equals( "n4" ) ) {
6058 if ( n4.getDistanceToParent() != 0.01 ) {
6061 if ( !n5.getName().equals( "n5" ) ) {
6064 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
6067 if ( n5.getDistanceToParent() != 0.1 ) {
6070 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
6073 if ( !n5.isDuplication() ) {
6076 if ( !n5.isHasAssignedEvent() ) {
6079 final PhylogenyNode n8 = PhylogenyNode
6080 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6081 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
6084 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
6087 final PhylogenyNode n9 = PhylogenyNode
6088 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6089 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
6092 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
6095 final PhylogenyNode n10 = PhylogenyNode
6096 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6097 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
6100 final PhylogenyNode n20 = PhylogenyNode
6101 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6102 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
6105 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
6108 final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
6109 NHXParser.TAXONOMY_EXTRACTION.YES );
6110 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
6113 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
6116 final PhylogenyNode n20xx = PhylogenyNode
6117 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6118 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
6121 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
6124 final PhylogenyNode n20xxx = PhylogenyNode
6125 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6126 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
6129 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
6132 final PhylogenyNode n20xxxx = PhylogenyNode
6133 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6134 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
6137 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
6140 final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
6141 NHXParser.TAXONOMY_EXTRACTION.YES );
6142 if ( !n21.getName().equals( "n21_PIG" ) ) {
6145 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
6148 final PhylogenyNode n21x = PhylogenyNode
6149 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6150 if ( !n21x.getName().equals( "n21_PIG" ) ) {
6153 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
6156 final PhylogenyNode n22 = PhylogenyNode
6157 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6158 if ( !n22.getName().equals( "n22/PIG" ) ) {
6161 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
6164 final PhylogenyNode n23 = PhylogenyNode
6165 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6166 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
6169 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
6172 final PhylogenyNode a = PhylogenyNode
6173 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6174 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
6177 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
6180 final PhylogenyNode b = PhylogenyNode
6181 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6182 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
6185 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
6188 final PhylogenyNode c = PhylogenyNode
6189 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
6190 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6191 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
6194 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
6197 final PhylogenyNode c1 = PhylogenyNode
6198 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
6199 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6200 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
6203 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
6206 final PhylogenyNode c2 = PhylogenyNode
6207 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
6208 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6209 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
6212 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
6215 final PhylogenyNode d = PhylogenyNode
6216 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6217 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
6220 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
6223 final PhylogenyNode e = PhylogenyNode
6224 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6225 if ( !e.getName().equals( "n10_RAT1" ) ) {
6228 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
6231 final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
6232 NHXParser.TAXONOMY_EXTRACTION.YES );
6233 if ( !e2.getName().equals( "n10_RAT1" ) ) {
6236 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
6239 final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
6240 NHXParser.TAXONOMY_EXTRACTION.YES );
6241 if ( !e3.getName().equals( "n10_RAT~" ) ) {
6244 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
6247 final PhylogenyNode n11 = PhylogenyNode
6248 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
6249 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6250 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
6253 if ( n11.getDistanceToParent() != 0.4 ) {
6256 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
6259 final PhylogenyNode n12 = PhylogenyNode
6260 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
6261 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6262 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
6265 if ( n12.getDistanceToParent() != 0.4 ) {
6268 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
6271 final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
6272 NHXParser.TAXONOMY_EXTRACTION.YES );
6273 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
6276 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
6279 final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
6280 NHXParser.TAXONOMY_EXTRACTION.YES );
6281 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
6284 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
6287 if ( n1.getName().compareTo( "" ) != 0 ) {
6290 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
6293 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6296 if ( n2.getName().compareTo( "" ) != 0 ) {
6299 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
6302 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6305 final PhylogenyNode n00 = PhylogenyNode
6306 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
6307 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
6310 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
6313 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
6314 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
6317 final PhylogenyNode n13 = PhylogenyNode
6318 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6319 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
6322 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
6325 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
6328 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6331 final PhylogenyNode n14 = PhylogenyNode
6332 .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6333 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
6336 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
6339 final PhylogenyNode n15 = PhylogenyNode
6340 .createInstanceFromNhxString( "something_wicked[123]",
6341 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6342 if ( !n15.getName().equals( "something_wicked" ) ) {
6345 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
6348 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
6351 final PhylogenyNode n16 = PhylogenyNode
6352 .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6353 if ( !n16.getName().equals( "something_wicked2" ) ) {
6356 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
6359 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
6362 final PhylogenyNode n17 = PhylogenyNode
6363 .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6364 if ( !n17.getName().equals( "something_wicked3" ) ) {
6367 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
6370 final PhylogenyNode n18 = PhylogenyNode
6371 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
6372 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
6375 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
6378 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
6381 final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
6382 NHXParser.TAXONOMY_EXTRACTION.YES );
6383 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
6386 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6389 final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
6390 NHXParser.TAXONOMY_EXTRACTION.YES );
6391 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
6394 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6397 final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
6398 NHXParser.TAXONOMY_EXTRACTION.YES );
6399 if ( n31.getNodeData().isHasTaxonomy() ) {
6402 final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
6403 NHXParser.TAXONOMY_EXTRACTION.YES );
6404 if ( n32.getNodeData().isHasTaxonomy() ) {
6408 catch ( final Exception e ) {
6409 e.printStackTrace( System.out );
6415 private static boolean testNHXParsing() {
6417 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6418 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
6419 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
6422 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]";
6423 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
6424 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6427 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]";
6428 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
6429 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
6432 final Phylogeny[] p3 = factory
6433 .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]",
6435 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6438 final Phylogeny[] p4 = factory
6439 .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(]",
6441 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6444 final Phylogeny[] p5 = factory
6445 .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(((]",
6447 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6450 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)";
6451 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)";
6452 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
6453 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
6456 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)))";
6457 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)))";
6458 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
6459 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
6462 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]) ))[,,, ])))))))";
6463 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
6464 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
6465 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
6468 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
6469 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
6472 final Phylogeny p10 = factory
6473 .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]",
6474 new NHXParser() )[ 0 ];
6475 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
6479 catch ( final Exception e ) {
6480 e.printStackTrace( System.out );
6486 private static boolean testNHXParsingQuotes() {
6488 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6489 final NHXParser p = new NHXParser();
6490 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
6491 if ( phylogenies_0.length != 5 ) {
6494 final Phylogeny phy = phylogenies_0[ 4 ];
6495 if ( phy.getNumberOfExternalNodes() != 7 ) {
6498 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
6501 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
6504 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
6505 .getScientificName().equals( "hsapiens" ) ) {
6508 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
6511 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
6514 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
6517 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
6520 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
6523 final NHXParser p1p = new NHXParser();
6524 p1p.setIgnoreQuotes( true );
6525 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
6526 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
6529 final NHXParser p2p = new NHXParser();
6530 p1p.setIgnoreQuotes( false );
6531 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
6532 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
6535 final NHXParser p3p = new NHXParser();
6536 p3p.setIgnoreQuotes( false );
6537 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
6538 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
6541 final NHXParser p4p = new NHXParser();
6542 p4p.setIgnoreQuotes( false );
6543 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
6544 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
6547 final Phylogeny p10 = factory
6548 .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]",
6549 new NHXParser() )[ 0 ];
6550 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]";
6551 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
6554 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
6555 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
6559 final Phylogeny p12 = factory
6560 .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]",
6561 new NHXParser() )[ 0 ];
6562 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]";
6563 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
6566 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
6567 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
6570 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;";
6571 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
6574 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
6575 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
6579 catch ( final Exception e ) {
6580 e.printStackTrace( System.out );
6586 private static boolean testNHXParsingMB() {
6588 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6589 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
6590 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6591 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6592 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6593 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6594 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6595 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6596 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6597 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
6598 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
6601 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
6604 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
6605 0.1100000000000000e+00 ) ) {
6608 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
6611 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
6614 final Phylogeny p2 = factory
6615 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
6616 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6617 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6618 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6619 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6620 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6621 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6622 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6623 + "7.369400000000000e-02}])",
6624 new NHXParser() )[ 0 ];
6625 if ( p2.getNode( "1" ) == null ) {
6628 if ( p2.getNode( "2" ) == null ) {
6632 catch ( final Exception e ) {
6633 e.printStackTrace( System.out );
6640 private static boolean testPhylogenyBranch() {
6642 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
6643 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
6644 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
6645 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
6646 if ( !a1b1.equals( a1b1 ) ) {
6649 if ( !a1b1.equals( b1a1 ) ) {
6652 if ( !b1a1.equals( a1b1 ) ) {
6655 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
6656 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
6657 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
6658 if ( a1_b1.equals( b1_a1 ) ) {
6661 if ( a1_b1.equals( a1_b1_ ) ) {
6664 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
6665 if ( !a1_b1.equals( b1_a1_ ) ) {
6668 if ( a1_b1_.equals( b1_a1_ ) ) {
6671 if ( !a1_b1_.equals( b1_a1 ) ) {
6675 catch ( final Exception e ) {
6676 e.printStackTrace( System.out );
6682 private static boolean testPhyloXMLparsingOfDistributionElement() {
6684 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6685 PhyloXmlParser xml_parser = null;
6687 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
6689 catch ( final Exception e ) {
6690 // Do nothing -- means were not running from jar.
6692 if ( xml_parser == null ) {
6693 xml_parser = new PhyloXmlParser();
6694 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
6695 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
6698 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
6701 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
6703 if ( xml_parser.getErrorCount() > 0 ) {
6704 System.out.println( xml_parser.getErrorMessages().toString() );
6707 if ( phylogenies_0.length != 1 ) {
6710 final Phylogeny t1 = phylogenies_0[ 0 ];
6711 PhylogenyNode n = null;
6712 Distribution d = null;
6713 n = t1.getNode( "root node" );
6714 if ( !n.getNodeData().isHasDistribution() ) {
6717 if ( n.getNodeData().getDistributions().size() != 1 ) {
6720 d = n.getNodeData().getDistribution();
6721 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6724 if ( d.getPoints().size() != 1 ) {
6727 if ( d.getPolygons() != null ) {
6730 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6733 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6736 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6739 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6742 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6745 n = t1.getNode( "node a" );
6746 if ( !n.getNodeData().isHasDistribution() ) {
6749 if ( n.getNodeData().getDistributions().size() != 2 ) {
6752 d = n.getNodeData().getDistribution( 1 );
6753 if ( !d.getDesc().equals( "San Diego" ) ) {
6756 if ( d.getPoints().size() != 1 ) {
6759 if ( d.getPolygons() != null ) {
6762 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6765 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6768 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6771 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6774 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6777 n = t1.getNode( "node bb" );
6778 if ( !n.getNodeData().isHasDistribution() ) {
6781 if ( n.getNodeData().getDistributions().size() != 1 ) {
6784 d = n.getNodeData().getDistribution( 0 );
6785 if ( d.getPoints().size() != 3 ) {
6788 if ( d.getPolygons().size() != 2 ) {
6791 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6794 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6797 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6800 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6803 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6806 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6809 Polygon p = d.getPolygons().get( 0 );
6810 if ( p.getPoints().size() != 3 ) {
6813 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6816 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6819 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6822 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6825 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6828 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6831 p = d.getPolygons().get( 1 );
6832 if ( p.getPoints().size() != 3 ) {
6835 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6838 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6841 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6845 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
6846 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
6847 if ( rt.length != 1 ) {
6850 final Phylogeny t1_rt = rt[ 0 ];
6851 n = t1_rt.getNode( "root node" );
6852 if ( !n.getNodeData().isHasDistribution() ) {
6855 if ( n.getNodeData().getDistributions().size() != 1 ) {
6858 d = n.getNodeData().getDistribution();
6859 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6862 if ( d.getPoints().size() != 1 ) {
6865 if ( d.getPolygons() != null ) {
6868 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6871 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6874 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6877 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6880 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6883 n = t1_rt.getNode( "node a" );
6884 if ( !n.getNodeData().isHasDistribution() ) {
6887 if ( n.getNodeData().getDistributions().size() != 2 ) {
6890 d = n.getNodeData().getDistribution( 1 );
6891 if ( !d.getDesc().equals( "San Diego" ) ) {
6894 if ( d.getPoints().size() != 1 ) {
6897 if ( d.getPolygons() != null ) {
6900 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6903 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6906 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6909 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6912 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6915 n = t1_rt.getNode( "node bb" );
6916 if ( !n.getNodeData().isHasDistribution() ) {
6919 if ( n.getNodeData().getDistributions().size() != 1 ) {
6922 d = n.getNodeData().getDistribution( 0 );
6923 if ( d.getPoints().size() != 3 ) {
6926 if ( d.getPolygons().size() != 2 ) {
6929 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6932 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6935 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6938 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6941 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6944 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6947 p = d.getPolygons().get( 0 );
6948 if ( p.getPoints().size() != 3 ) {
6951 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6954 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6957 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6960 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6963 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6966 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6969 p = d.getPolygons().get( 1 );
6970 if ( p.getPoints().size() != 3 ) {
6973 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6976 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6979 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6983 catch ( final Exception e ) {
6984 e.printStackTrace( System.out );
6990 private static boolean testPostOrderIterator() {
6992 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6993 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
6994 PhylogenyNodeIterator it0;
6995 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
6998 for( it0.reset(); it0.hasNext(); ) {
7001 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
7002 final PhylogenyNodeIterator it = t1.iteratorPostorder();
7003 if ( !it.next().getName().equals( "A" ) ) {
7006 if ( !it.next().getName().equals( "B" ) ) {
7009 if ( !it.next().getName().equals( "ab" ) ) {
7012 if ( !it.next().getName().equals( "C" ) ) {
7015 if ( !it.next().getName().equals( "D" ) ) {
7018 if ( !it.next().getName().equals( "cd" ) ) {
7021 if ( !it.next().getName().equals( "abcd" ) ) {
7024 if ( !it.next().getName().equals( "E" ) ) {
7027 if ( !it.next().getName().equals( "F" ) ) {
7030 if ( !it.next().getName().equals( "ef" ) ) {
7033 if ( !it.next().getName().equals( "G" ) ) {
7036 if ( !it.next().getName().equals( "H" ) ) {
7039 if ( !it.next().getName().equals( "gh" ) ) {
7042 if ( !it.next().getName().equals( "efgh" ) ) {
7045 if ( !it.next().getName().equals( "r" ) ) {
7048 if ( it.hasNext() ) {
7052 catch ( final Exception e ) {
7053 e.printStackTrace( System.out );
7059 private static boolean testPreOrderIterator() {
7061 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7062 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
7063 PhylogenyNodeIterator it0;
7064 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
7067 for( it0.reset(); it0.hasNext(); ) {
7070 PhylogenyNodeIterator it = t0.iteratorPreorder();
7071 if ( !it.next().getName().equals( "r" ) ) {
7074 if ( !it.next().getName().equals( "ab" ) ) {
7077 if ( !it.next().getName().equals( "A" ) ) {
7080 if ( !it.next().getName().equals( "B" ) ) {
7083 if ( !it.next().getName().equals( "cd" ) ) {
7086 if ( !it.next().getName().equals( "C" ) ) {
7089 if ( !it.next().getName().equals( "D" ) ) {
7092 if ( it.hasNext() ) {
7095 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
7096 it = t1.iteratorPreorder();
7097 if ( !it.next().getName().equals( "r" ) ) {
7100 if ( !it.next().getName().equals( "abcd" ) ) {
7103 if ( !it.next().getName().equals( "ab" ) ) {
7106 if ( !it.next().getName().equals( "A" ) ) {
7109 if ( !it.next().getName().equals( "B" ) ) {
7112 if ( !it.next().getName().equals( "cd" ) ) {
7115 if ( !it.next().getName().equals( "C" ) ) {
7118 if ( !it.next().getName().equals( "D" ) ) {
7121 if ( !it.next().getName().equals( "efgh" ) ) {
7124 if ( !it.next().getName().equals( "ef" ) ) {
7127 if ( !it.next().getName().equals( "E" ) ) {
7130 if ( !it.next().getName().equals( "F" ) ) {
7133 if ( !it.next().getName().equals( "gh" ) ) {
7136 if ( !it.next().getName().equals( "G" ) ) {
7139 if ( !it.next().getName().equals( "H" ) ) {
7142 if ( it.hasNext() ) {
7146 catch ( final Exception e ) {
7147 e.printStackTrace( System.out );
7153 private static boolean testPropertiesMap() {
7155 final PropertiesMap pm = new PropertiesMap();
7156 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
7157 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
7158 final Property p2 = new Property( "something:else",
7160 "improbable:research",
7163 pm.addProperty( p0 );
7164 pm.addProperty( p1 );
7165 pm.addProperty( p2 );
7166 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
7169 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
7172 if ( pm.getProperties().size() != 3 ) {
7175 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
7178 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
7181 if ( pm.getProperties().size() != 3 ) {
7184 pm.removeProperty( "dimensions:diameter" );
7185 if ( pm.getProperties().size() != 2 ) {
7188 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
7191 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
7195 catch ( final Exception e ) {
7196 e.printStackTrace( System.out );
7202 private static boolean testReIdMethods() {
7204 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7205 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
7206 final int count = PhylogenyNode.getNodeCount();
7208 if ( p.getNode( "r" ).getId() != count ) {
7211 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
7214 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
7217 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
7220 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
7223 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
7226 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
7229 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
7232 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
7235 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
7238 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
7241 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
7244 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
7247 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
7250 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
7254 catch ( final Exception e ) {
7255 e.printStackTrace( System.out );
7261 private static boolean testRerooting() {
7263 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7264 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",
7265 new NHXParser() )[ 0 ];
7266 if ( !t1.isRooted() ) {
7269 t1.reRoot( t1.getNode( "D" ) );
7270 t1.reRoot( t1.getNode( "CD" ) );
7271 t1.reRoot( t1.getNode( "A" ) );
7272 t1.reRoot( t1.getNode( "B" ) );
7273 t1.reRoot( t1.getNode( "AB" ) );
7274 t1.reRoot( t1.getNode( "D" ) );
7275 t1.reRoot( t1.getNode( "C" ) );
7276 t1.reRoot( t1.getNode( "CD" ) );
7277 t1.reRoot( t1.getNode( "A" ) );
7278 t1.reRoot( t1.getNode( "B" ) );
7279 t1.reRoot( t1.getNode( "AB" ) );
7280 t1.reRoot( t1.getNode( "D" ) );
7281 t1.reRoot( t1.getNode( "D" ) );
7282 t1.reRoot( t1.getNode( "C" ) );
7283 t1.reRoot( t1.getNode( "A" ) );
7284 t1.reRoot( t1.getNode( "B" ) );
7285 t1.reRoot( t1.getNode( "AB" ) );
7286 t1.reRoot( t1.getNode( "C" ) );
7287 t1.reRoot( t1.getNode( "D" ) );
7288 t1.reRoot( t1.getNode( "CD" ) );
7289 t1.reRoot( t1.getNode( "D" ) );
7290 t1.reRoot( t1.getNode( "A" ) );
7291 t1.reRoot( t1.getNode( "B" ) );
7292 t1.reRoot( t1.getNode( "AB" ) );
7293 t1.reRoot( t1.getNode( "C" ) );
7294 t1.reRoot( t1.getNode( "D" ) );
7295 t1.reRoot( t1.getNode( "CD" ) );
7296 t1.reRoot( t1.getNode( "D" ) );
7297 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
7300 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
7303 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
7306 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
7309 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
7312 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
7315 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",
7316 new NHXParser() )[ 0 ];
7317 t2.reRoot( t2.getNode( "A" ) );
7318 t2.reRoot( t2.getNode( "D" ) );
7319 t2.reRoot( t2.getNode( "ABC" ) );
7320 t2.reRoot( t2.getNode( "A" ) );
7321 t2.reRoot( t2.getNode( "B" ) );
7322 t2.reRoot( t2.getNode( "D" ) );
7323 t2.reRoot( t2.getNode( "C" ) );
7324 t2.reRoot( t2.getNode( "ABC" ) );
7325 t2.reRoot( t2.getNode( "A" ) );
7326 t2.reRoot( t2.getNode( "B" ) );
7327 t2.reRoot( t2.getNode( "AB" ) );
7328 t2.reRoot( t2.getNode( "AB" ) );
7329 t2.reRoot( t2.getNode( "D" ) );
7330 t2.reRoot( t2.getNode( "C" ) );
7331 t2.reRoot( t2.getNode( "B" ) );
7332 t2.reRoot( t2.getNode( "AB" ) );
7333 t2.reRoot( t2.getNode( "D" ) );
7334 t2.reRoot( t2.getNode( "D" ) );
7335 t2.reRoot( t2.getNode( "ABC" ) );
7336 t2.reRoot( t2.getNode( "A" ) );
7337 t2.reRoot( t2.getNode( "B" ) );
7338 t2.reRoot( t2.getNode( "AB" ) );
7339 t2.reRoot( t2.getNode( "D" ) );
7340 t2.reRoot( t2.getNode( "C" ) );
7341 t2.reRoot( t2.getNode( "ABC" ) );
7342 t2.reRoot( t2.getNode( "A" ) );
7343 t2.reRoot( t2.getNode( "B" ) );
7344 t2.reRoot( t2.getNode( "AB" ) );
7345 t2.reRoot( t2.getNode( "D" ) );
7346 t2.reRoot( t2.getNode( "D" ) );
7347 t2.reRoot( t2.getNode( "C" ) );
7348 t2.reRoot( t2.getNode( "A" ) );
7349 t2.reRoot( t2.getNode( "B" ) );
7350 t2.reRoot( t2.getNode( "AB" ) );
7351 t2.reRoot( t2.getNode( "C" ) );
7352 t2.reRoot( t2.getNode( "D" ) );
7353 t2.reRoot( t2.getNode( "ABC" ) );
7354 t2.reRoot( t2.getNode( "D" ) );
7355 t2.reRoot( t2.getNode( "A" ) );
7356 t2.reRoot( t2.getNode( "B" ) );
7357 t2.reRoot( t2.getNode( "AB" ) );
7358 t2.reRoot( t2.getNode( "C" ) );
7359 t2.reRoot( t2.getNode( "D" ) );
7360 t2.reRoot( t2.getNode( "ABC" ) );
7361 t2.reRoot( t2.getNode( "D" ) );
7362 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7365 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7368 t2.reRoot( t2.getNode( "ABC" ) );
7369 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7372 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7375 t2.reRoot( t2.getNode( "AB" ) );
7376 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7379 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7382 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7385 t2.reRoot( t2.getNode( "AB" ) );
7386 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7389 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7392 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7395 t2.reRoot( t2.getNode( "D" ) );
7396 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7399 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7402 t2.reRoot( t2.getNode( "ABC" ) );
7403 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7406 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7409 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
7410 new NHXParser() )[ 0 ];
7411 t3.reRoot( t3.getNode( "B" ) );
7412 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7415 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7418 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7421 t3.reRoot( t3.getNode( "B" ) );
7422 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7425 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7428 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7431 t3.reRoot( t3.getRoot() );
7432 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7435 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7438 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7442 catch ( final Exception e ) {
7443 e.printStackTrace( System.out );
7449 private static boolean testSDIse() {
7451 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7452 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
7453 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
7454 gene1.setRooted( true );
7455 species1.setRooted( true );
7456 final SDI sdi = new SDI( gene1, species1 );
7457 if ( !gene1.getRoot().isDuplication() ) {
7460 final Phylogeny species2 = factory
7461 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7462 new NHXParser() )[ 0 ];
7463 final Phylogeny gene2 = factory
7464 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7465 new NHXParser() )[ 0 ];
7466 species2.setRooted( true );
7467 gene2.setRooted( true );
7468 final SDI sdi2 = new SDI( gene2, species2 );
7469 if ( sdi2.getDuplicationsSum() != 0 ) {
7472 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
7475 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
7478 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
7481 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
7484 if ( !gene2.getNode( "r" ).isSpeciation() ) {
7487 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
7490 final Phylogeny species3 = factory
7491 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7492 new NHXParser() )[ 0 ];
7493 final Phylogeny gene3 = factory
7494 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7495 new NHXParser() )[ 0 ];
7496 species3.setRooted( true );
7497 gene3.setRooted( true );
7498 final SDI sdi3 = new SDI( gene3, species3 );
7499 if ( sdi3.getDuplicationsSum() != 1 ) {
7502 if ( !gene3.getNode( "aa" ).isDuplication() ) {
7505 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
7508 final Phylogeny species4 = factory
7509 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7510 new NHXParser() )[ 0 ];
7511 final Phylogeny gene4 = factory
7512 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7513 new NHXParser() )[ 0 ];
7514 species4.setRooted( true );
7515 gene4.setRooted( true );
7516 final SDI sdi4 = new SDI( gene4, species4 );
7517 if ( sdi4.getDuplicationsSum() != 1 ) {
7520 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
7523 if ( !gene4.getNode( "abc" ).isDuplication() ) {
7526 if ( gene4.getNode( "abcd" ).isDuplication() ) {
7529 if ( species4.getNumberOfExternalNodes() != 6 ) {
7532 if ( gene4.getNumberOfExternalNodes() != 6 ) {
7535 final Phylogeny species5 = factory
7536 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7537 new NHXParser() )[ 0 ];
7538 final Phylogeny gene5 = factory
7539 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7540 new NHXParser() )[ 0 ];
7541 species5.setRooted( true );
7542 gene5.setRooted( true );
7543 final SDI sdi5 = new SDI( gene5, species5 );
7544 if ( sdi5.getDuplicationsSum() != 2 ) {
7547 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
7550 if ( !gene5.getNode( "adc" ).isDuplication() ) {
7553 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
7556 if ( species5.getNumberOfExternalNodes() != 6 ) {
7559 if ( gene5.getNumberOfExternalNodes() != 6 ) {
7562 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
7563 // Conjecture for Comparing Molecular Phylogenies"
7564 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
7565 final Phylogeny species6 = factory
7566 .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,"
7567 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7568 new NHXParser() )[ 0 ];
7569 final Phylogeny gene6 = factory
7570 .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,"
7571 + "((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,"
7572 + "(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;",
7573 new NHXParser() )[ 0 ];
7574 species6.setRooted( true );
7575 gene6.setRooted( true );
7576 final SDI sdi6 = new SDI( gene6, species6 );
7577 if ( sdi6.getDuplicationsSum() != 3 ) {
7580 if ( !gene6.getNode( "r" ).isDuplication() ) {
7583 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
7586 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
7589 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
7592 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
7595 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
7598 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
7601 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
7604 sdi6.computeMappingCostL();
7605 if ( sdi6.computeMappingCostL() != 17 ) {
7608 if ( species6.getNumberOfExternalNodes() != 9 ) {
7611 if ( gene6.getNumberOfExternalNodes() != 9 ) {
7614 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
7615 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
7616 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
7617 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
7618 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
7619 species7.setRooted( true );
7620 final Phylogeny gene7_1 = Test
7621 .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])" );
7622 gene7_1.setRooted( true );
7623 final SDI sdi7 = new SDI( gene7_1, species7 );
7624 if ( sdi7.getDuplicationsSum() != 0 ) {
7627 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
7630 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
7633 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
7636 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
7639 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
7642 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
7645 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
7648 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
7651 final Phylogeny gene7_2 = Test
7652 .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])" );
7653 gene7_2.setRooted( true );
7654 final SDI sdi7_2 = new SDI( gene7_2, species7 );
7655 if ( sdi7_2.getDuplicationsSum() != 1 ) {
7658 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
7661 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
7664 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
7667 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
7670 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
7673 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
7676 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
7679 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
7682 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
7686 catch ( final Exception e ) {
7692 private static boolean testSDIunrooted() {
7694 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7695 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
7696 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
7697 final Iterator<PhylogenyBranch> iter = l.iterator();
7698 PhylogenyBranch br = iter.next();
7699 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
7702 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
7706 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7709 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7713 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
7716 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
7720 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7723 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7727 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7730 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7734 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7737 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7741 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7744 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7748 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7751 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7755 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7758 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7762 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7765 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7769 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7772 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7776 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
7779 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
7783 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7786 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7790 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
7793 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
7797 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
7800 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
7803 if ( iter.hasNext() ) {
7806 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
7807 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
7808 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
7810 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7813 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7817 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7820 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7824 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7827 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7830 if ( iter1.hasNext() ) {
7833 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
7834 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
7835 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
7837 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7840 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7844 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7847 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7851 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7854 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7857 if ( iter2.hasNext() ) {
7860 final Phylogeny species0 = factory
7861 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7862 new NHXParser() )[ 0 ];
7863 final Phylogeny gene1 = factory
7864 .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])",
7865 new NHXParser() )[ 0 ];
7866 species0.setRooted( true );
7867 gene1.setRooted( true );
7868 final SDIR sdi_unrooted = new SDIR();
7869 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
7870 if ( sdi_unrooted.getCount() != 1 ) {
7873 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
7876 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
7879 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
7882 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7885 final Phylogeny gene2 = factory
7886 .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])",
7887 new NHXParser() )[ 0 ];
7888 gene2.setRooted( true );
7889 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
7890 if ( sdi_unrooted.getCount() != 1 ) {
7893 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7896 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7899 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7902 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7905 final Phylogeny species6 = factory
7906 .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,"
7907 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7908 new NHXParser() )[ 0 ];
7909 final Phylogeny gene6 = factory
7910 .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],"
7911 + "(((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],"
7912 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7913 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7914 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7915 new NHXParser() )[ 0 ];
7916 species6.setRooted( true );
7917 gene6.setRooted( true );
7918 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7919 if ( sdi_unrooted.getCount() != 1 ) {
7922 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7925 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7928 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7931 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7934 if ( !p6[ 0 ].getRoot().isDuplication() ) {
7937 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7940 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7943 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
7946 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
7949 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
7952 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
7955 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
7959 final Phylogeny species7 = factory
7960 .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,"
7961 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7962 new NHXParser() )[ 0 ];
7963 final Phylogeny gene7 = factory
7964 .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],"
7965 + "(((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],"
7966 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7967 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7968 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7969 new NHXParser() )[ 0 ];
7970 species7.setRooted( true );
7971 gene7.setRooted( true );
7972 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
7973 if ( sdi_unrooted.getCount() != 1 ) {
7976 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7979 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
7982 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7985 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
7988 if ( !p7[ 0 ].getRoot().isDuplication() ) {
7991 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
7994 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
7997 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
8000 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8003 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
8006 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
8009 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8013 final Phylogeny species8 = factory
8014 .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,"
8015 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
8016 new NHXParser() )[ 0 ];
8017 final Phylogeny gene8 = factory
8018 .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],"
8019 + "(((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],"
8020 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
8021 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
8022 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
8023 new NHXParser() )[ 0 ];
8024 species8.setRooted( true );
8025 gene8.setRooted( true );
8026 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
8027 if ( sdi_unrooted.getCount() != 1 ) {
8030 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
8033 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
8036 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
8039 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
8042 if ( !p8[ 0 ].getRoot().isDuplication() ) {
8045 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
8048 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
8051 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
8054 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8057 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
8060 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
8063 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8068 catch ( final Exception e ) {
8069 e.printStackTrace( System.out );
8075 private static boolean testSplit() {
8077 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8078 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
8079 //Archaeopteryx.createApplication( p0 );
8080 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
8081 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8082 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8083 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8084 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8085 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8086 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8087 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8088 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8089 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8090 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
8091 // System.out.println( s0.toString() );
8093 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
8094 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8096 if ( s0.match( query_nodes ) ) {
8099 query_nodes = new HashSet<PhylogenyNode>();
8100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8105 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8106 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8107 if ( !s0.match( query_nodes ) ) {
8111 query_nodes = new HashSet<PhylogenyNode>();
8112 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8113 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8114 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8115 if ( !s0.match( query_nodes ) ) {
8119 query_nodes = new HashSet<PhylogenyNode>();
8120 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8121 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8122 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8123 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8124 if ( !s0.match( query_nodes ) ) {
8128 query_nodes = new HashSet<PhylogenyNode>();
8129 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8130 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8133 if ( !s0.match( query_nodes ) ) {
8137 query_nodes = new HashSet<PhylogenyNode>();
8138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8140 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8141 if ( !s0.match( query_nodes ) ) {
8145 query_nodes = new HashSet<PhylogenyNode>();
8146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8147 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8148 if ( !s0.match( query_nodes ) ) {
8152 query_nodes = new HashSet<PhylogenyNode>();
8153 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8156 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8157 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8158 if ( !s0.match( query_nodes ) ) {
8162 query_nodes = new HashSet<PhylogenyNode>();
8163 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8164 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8165 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8166 if ( !s0.match( query_nodes ) ) {
8170 query_nodes = new HashSet<PhylogenyNode>();
8171 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8172 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8173 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8174 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8175 if ( !s0.match( query_nodes ) ) {
8179 query_nodes = new HashSet<PhylogenyNode>();
8180 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8182 if ( s0.match( query_nodes ) ) {
8186 query_nodes = new HashSet<PhylogenyNode>();
8187 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8188 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8190 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8191 if ( s0.match( query_nodes ) ) {
8195 query_nodes = new HashSet<PhylogenyNode>();
8196 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8197 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8199 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8200 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8201 if ( s0.match( query_nodes ) ) {
8205 query_nodes = new HashSet<PhylogenyNode>();
8206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8208 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8209 if ( s0.match( query_nodes ) ) {
8213 query_nodes = new HashSet<PhylogenyNode>();
8214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8216 if ( s0.match( query_nodes ) ) {
8220 query_nodes = new HashSet<PhylogenyNode>();
8221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8223 if ( s0.match( query_nodes ) ) {
8227 query_nodes = new HashSet<PhylogenyNode>();
8228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8230 if ( s0.match( query_nodes ) ) {
8234 query_nodes = new HashSet<PhylogenyNode>();
8235 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8236 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8237 if ( s0.match( query_nodes ) ) {
8241 query_nodes = new HashSet<PhylogenyNode>();
8242 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8243 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8244 if ( s0.match( query_nodes ) ) {
8248 query_nodes = new HashSet<PhylogenyNode>();
8249 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8250 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8251 if ( s0.match( query_nodes ) ) {
8255 query_nodes = new HashSet<PhylogenyNode>();
8256 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8257 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8258 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8259 if ( s0.match( query_nodes ) ) {
8263 query_nodes = new HashSet<PhylogenyNode>();
8264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8265 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8266 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8267 if ( s0.match( query_nodes ) ) {
8271 query_nodes = new HashSet<PhylogenyNode>();
8272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8273 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8274 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8275 if ( s0.match( query_nodes ) ) {
8279 query_nodes = new HashSet<PhylogenyNode>();
8280 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8281 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8282 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8283 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8284 if ( s0.match( query_nodes ) ) {
8288 // query_nodes = new HashSet<PhylogenyNode>();
8289 // query_nodes.add( new PhylogenyNode( "X" ) );
8290 // query_nodes.add( new PhylogenyNode( "Y" ) );
8291 // query_nodes.add( new PhylogenyNode( "A" ) );
8292 // query_nodes.add( new PhylogenyNode( "B" ) );
8293 // query_nodes.add( new PhylogenyNode( "C" ) );
8294 // query_nodes.add( new PhylogenyNode( "D" ) );
8295 // query_nodes.add( new PhylogenyNode( "E" ) );
8296 // query_nodes.add( new PhylogenyNode( "F" ) );
8297 // query_nodes.add( new PhylogenyNode( "G" ) );
8298 // if ( !s0.match( query_nodes ) ) {
8301 // query_nodes = new HashSet<PhylogenyNode>();
8302 // query_nodes.add( new PhylogenyNode( "X" ) );
8303 // query_nodes.add( new PhylogenyNode( "Y" ) );
8304 // query_nodes.add( new PhylogenyNode( "A" ) );
8305 // query_nodes.add( new PhylogenyNode( "B" ) );
8306 // query_nodes.add( new PhylogenyNode( "C" ) );
8307 // if ( !s0.match( query_nodes ) ) {
8311 // query_nodes = new HashSet<PhylogenyNode>();
8312 // query_nodes.add( new PhylogenyNode( "X" ) );
8313 // query_nodes.add( new PhylogenyNode( "Y" ) );
8314 // query_nodes.add( new PhylogenyNode( "D" ) );
8315 // query_nodes.add( new PhylogenyNode( "E" ) );
8316 // query_nodes.add( new PhylogenyNode( "F" ) );
8317 // query_nodes.add( new PhylogenyNode( "G" ) );
8318 // if ( !s0.match( query_nodes ) ) {
8322 // query_nodes = new HashSet<PhylogenyNode>();
8323 // query_nodes.add( new PhylogenyNode( "X" ) );
8324 // query_nodes.add( new PhylogenyNode( "Y" ) );
8325 // query_nodes.add( new PhylogenyNode( "A" ) );
8326 // query_nodes.add( new PhylogenyNode( "B" ) );
8327 // query_nodes.add( new PhylogenyNode( "C" ) );
8328 // query_nodes.add( new PhylogenyNode( "D" ) );
8329 // if ( !s0.match( query_nodes ) ) {
8333 // query_nodes = new HashSet<PhylogenyNode>();
8334 // query_nodes.add( new PhylogenyNode( "X" ) );
8335 // query_nodes.add( new PhylogenyNode( "Y" ) );
8336 // query_nodes.add( new PhylogenyNode( "E" ) );
8337 // query_nodes.add( new PhylogenyNode( "F" ) );
8338 // query_nodes.add( new PhylogenyNode( "G" ) );
8339 // if ( !s0.match( query_nodes ) ) {
8343 // query_nodes = new HashSet<PhylogenyNode>();
8344 // query_nodes.add( new PhylogenyNode( "X" ) );
8345 // query_nodes.add( new PhylogenyNode( "Y" ) );
8346 // query_nodes.add( new PhylogenyNode( "F" ) );
8347 // query_nodes.add( new PhylogenyNode( "G" ) );
8348 // if ( !s0.match( query_nodes ) ) {
8352 query_nodes = new HashSet<PhylogenyNode>();
8353 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8354 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8355 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8357 if ( s0.match( query_nodes ) ) {
8361 query_nodes = new HashSet<PhylogenyNode>();
8362 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8363 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8364 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8365 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8366 if ( s0.match( query_nodes ) ) {
8369 ///////////////////////////
8371 query_nodes = new HashSet<PhylogenyNode>();
8372 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8373 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8374 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8375 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8376 if ( s0.match( query_nodes ) ) {
8380 query_nodes = new HashSet<PhylogenyNode>();
8381 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8382 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8383 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8384 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8385 if ( s0.match( query_nodes ) ) {
8389 query_nodes = new HashSet<PhylogenyNode>();
8390 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8391 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8392 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8393 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8394 if ( s0.match( query_nodes ) ) {
8398 query_nodes = new HashSet<PhylogenyNode>();
8399 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8400 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8401 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8402 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8403 if ( s0.match( query_nodes ) ) {
8407 query_nodes = new HashSet<PhylogenyNode>();
8408 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8409 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8410 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8411 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8412 if ( s0.match( query_nodes ) ) {
8416 query_nodes = new HashSet<PhylogenyNode>();
8417 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8418 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8419 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8420 if ( s0.match( query_nodes ) ) {
8424 query_nodes = new HashSet<PhylogenyNode>();
8425 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8426 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8427 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8428 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8429 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8430 if ( s0.match( query_nodes ) ) {
8434 query_nodes = new HashSet<PhylogenyNode>();
8435 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8436 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8437 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8438 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8439 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8440 if ( s0.match( query_nodes ) ) {
8444 query_nodes = new HashSet<PhylogenyNode>();
8445 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8446 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8448 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8449 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8450 if ( s0.match( query_nodes ) ) {
8454 query_nodes = new HashSet<PhylogenyNode>();
8455 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8456 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8457 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8458 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8459 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8460 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8461 if ( s0.match( query_nodes ) ) {
8465 catch ( final Exception e ) {
8466 e.printStackTrace();
8472 private static boolean testSplitStrict() {
8474 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8475 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
8476 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
8477 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8478 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8479 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8480 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8481 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8482 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8483 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8484 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
8485 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
8486 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8487 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8488 if ( s0.match( query_nodes ) ) {
8491 query_nodes = new HashSet<PhylogenyNode>();
8492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8494 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8495 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8496 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8497 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8498 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8499 if ( !s0.match( query_nodes ) ) {
8503 query_nodes = new HashSet<PhylogenyNode>();
8504 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8505 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8506 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8507 if ( !s0.match( query_nodes ) ) {
8511 query_nodes = new HashSet<PhylogenyNode>();
8512 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8513 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8514 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8515 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8516 if ( !s0.match( query_nodes ) ) {
8520 query_nodes = new HashSet<PhylogenyNode>();
8521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8523 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8525 if ( !s0.match( query_nodes ) ) {
8529 query_nodes = new HashSet<PhylogenyNode>();
8530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8533 if ( !s0.match( query_nodes ) ) {
8537 query_nodes = new HashSet<PhylogenyNode>();
8538 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8540 if ( !s0.match( query_nodes ) ) {
8544 query_nodes = new HashSet<PhylogenyNode>();
8545 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8546 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8549 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8550 if ( !s0.match( query_nodes ) ) {
8554 query_nodes = new HashSet<PhylogenyNode>();
8555 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8558 if ( !s0.match( query_nodes ) ) {
8562 query_nodes = new HashSet<PhylogenyNode>();
8563 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8564 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8567 if ( !s0.match( query_nodes ) ) {
8571 query_nodes = new HashSet<PhylogenyNode>();
8572 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8573 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8574 if ( s0.match( query_nodes ) ) {
8578 query_nodes = new HashSet<PhylogenyNode>();
8579 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8583 if ( s0.match( query_nodes ) ) {
8587 query_nodes = new HashSet<PhylogenyNode>();
8588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8593 if ( s0.match( query_nodes ) ) {
8597 query_nodes = new HashSet<PhylogenyNode>();
8598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8601 if ( s0.match( query_nodes ) ) {
8605 query_nodes = new HashSet<PhylogenyNode>();
8606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8608 if ( s0.match( query_nodes ) ) {
8612 query_nodes = new HashSet<PhylogenyNode>();
8613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8615 if ( s0.match( query_nodes ) ) {
8619 query_nodes = new HashSet<PhylogenyNode>();
8620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8622 if ( s0.match( query_nodes ) ) {
8626 query_nodes = new HashSet<PhylogenyNode>();
8627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8629 if ( s0.match( query_nodes ) ) {
8633 query_nodes = new HashSet<PhylogenyNode>();
8634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8636 if ( s0.match( query_nodes ) ) {
8640 query_nodes = new HashSet<PhylogenyNode>();
8641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8643 if ( s0.match( query_nodes ) ) {
8647 query_nodes = new HashSet<PhylogenyNode>();
8648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8651 if ( s0.match( query_nodes ) ) {
8655 query_nodes = new HashSet<PhylogenyNode>();
8656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8658 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8659 if ( s0.match( query_nodes ) ) {
8663 query_nodes = new HashSet<PhylogenyNode>();
8664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8665 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8667 if ( s0.match( query_nodes ) ) {
8671 query_nodes = new HashSet<PhylogenyNode>();
8672 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8676 if ( s0.match( query_nodes ) ) {
8680 catch ( final Exception e ) {
8681 e.printStackTrace();
8687 private static boolean testSubtreeDeletion() {
8689 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8690 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8691 t1.deleteSubtree( t1.getNode( "A" ), false );
8692 if ( t1.getNumberOfExternalNodes() != 5 ) {
8695 t1.toNewHampshireX();
8696 t1.deleteSubtree( t1.getNode( "E" ), false );
8697 if ( t1.getNumberOfExternalNodes() != 4 ) {
8700 t1.toNewHampshireX();
8701 t1.deleteSubtree( t1.getNode( "F" ), false );
8702 if ( t1.getNumberOfExternalNodes() != 3 ) {
8705 t1.toNewHampshireX();
8706 t1.deleteSubtree( t1.getNode( "D" ), false );
8707 t1.toNewHampshireX();
8708 if ( t1.getNumberOfExternalNodes() != 3 ) {
8711 t1.deleteSubtree( t1.getNode( "def" ), false );
8712 t1.toNewHampshireX();
8713 if ( t1.getNumberOfExternalNodes() != 2 ) {
8716 t1.deleteSubtree( t1.getNode( "B" ), false );
8717 t1.toNewHampshireX();
8718 if ( t1.getNumberOfExternalNodes() != 1 ) {
8721 t1.deleteSubtree( t1.getNode( "C" ), false );
8722 t1.toNewHampshireX();
8723 if ( t1.getNumberOfExternalNodes() != 1 ) {
8726 t1.deleteSubtree( t1.getNode( "abc" ), false );
8727 t1.toNewHampshireX();
8728 if ( t1.getNumberOfExternalNodes() != 1 ) {
8731 t1.deleteSubtree( t1.getNode( "r" ), false );
8732 if ( t1.getNumberOfExternalNodes() != 0 ) {
8735 if ( !t1.isEmpty() ) {
8738 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8739 t2.deleteSubtree( t2.getNode( "A" ), false );
8740 t2.toNewHampshireX();
8741 if ( t2.getNumberOfExternalNodes() != 5 ) {
8744 t2.deleteSubtree( t2.getNode( "abc" ), false );
8745 t2.toNewHampshireX();
8746 if ( t2.getNumberOfExternalNodes() != 3 ) {
8749 t2.deleteSubtree( t2.getNode( "def" ), false );
8750 t2.toNewHampshireX();
8751 if ( t2.getNumberOfExternalNodes() != 1 ) {
8755 catch ( final Exception e ) {
8756 e.printStackTrace( System.out );
8762 private static boolean testSupportCount() {
8764 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8765 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
8766 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
8767 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
8768 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
8769 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
8770 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
8772 SupportCount.count( t0_1, phylogenies_1, true, false );
8773 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
8774 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
8775 + "(((((A,B),C),D),E),((F,G),X))"
8776 + "(((((A,Y),B),C),D),((F,G),E))"
8777 + "(((((A,B),C),D),E),(F,G))"
8778 + "(((((A,B),C),D),E),(F,G))"
8779 + "(((((A,B),C),D),E),(F,G))"
8780 + "(((((A,B),C),D),E),(F,G),Z)"
8781 + "(((((A,B),C),D),E),(F,G))"
8782 + "((((((A,B),C),D),E),F),G)"
8783 + "(((((X,Y),F,G),E),((A,B),C)),D)",
8785 SupportCount.count( t0_2, phylogenies_2, true, false );
8786 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
8787 while ( it.hasNext() ) {
8788 final PhylogenyNode n = it.next();
8789 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
8793 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
8794 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
8795 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
8796 SupportCount.count( t0_3, phylogenies_3, true, false );
8797 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
8798 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
8801 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
8804 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
8807 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
8810 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
8813 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
8816 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
8819 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
8822 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
8825 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
8828 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8829 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
8830 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
8831 SupportCount.count( t0_4, phylogenies_4, true, false );
8832 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
8833 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
8836 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
8839 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
8842 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
8845 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
8848 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
8851 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
8854 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
8857 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
8860 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
8863 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8864 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8865 double d = SupportCount.compare( b1, a, true, true, true );
8866 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
8869 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8870 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8871 d = SupportCount.compare( b2, a, true, true, true );
8872 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
8875 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8876 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
8877 d = SupportCount.compare( b3, a, true, true, true );
8878 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
8881 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
8882 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
8883 d = SupportCount.compare( b4, a, true, true, false );
8884 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
8888 catch ( final Exception e ) {
8889 e.printStackTrace( System.out );
8895 private static boolean testSupportTransfer() {
8897 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8898 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)",
8899 new NHXParser() )[ 0 ];
8900 final Phylogeny p2 = factory
8901 .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 ];
8902 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8905 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8908 support_transfer.moveBranchLengthsToBootstrap( p1 );
8909 support_transfer.transferSupportValues( p1, p2 );
8910 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8913 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8916 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8919 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8922 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
8925 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
8928 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
8931 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
8935 catch ( final Exception e ) {
8936 e.printStackTrace( System.out );
8942 private static boolean testUniprotTaxonomySearch() {
8944 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
8946 if ( results.size() != 1 ) {
8949 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8952 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8955 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8958 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8961 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8965 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
8966 if ( results.size() != 1 ) {
8969 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8972 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8975 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8978 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
8981 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
8985 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
8986 if ( results.size() != 1 ) {
8989 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
8992 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
8995 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
8998 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9001 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9005 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
9006 if ( results.size() != 1 ) {
9009 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
9012 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
9015 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
9018 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9021 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9024 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
9027 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
9030 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
9031 .equals( "Nematostella vectensis" ) ) {
9032 System.out.println( results.get( 0 ).getLineage() );
9036 catch ( final IOException e ) {
9037 System.out.println();
9038 System.out.println( "the following might be due to absence internet connection:" );
9039 e.printStackTrace( System.out );
9042 catch ( final Exception e ) {
9048 private static boolean testEmblEntryRetrieval() {
9049 //The format for GenBank Accession numbers are:
9050 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
9051 //Protein: 3 letters + 5 numerals
9052 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
9053 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
9056 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
9059 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
9062 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
9065 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
9068 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
9071 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
9074 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
9077 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
9080 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
9083 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
9086 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
9089 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
9095 private static boolean testUniprotEntryRetrieval() {
9096 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
9099 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
9102 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
9105 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
9108 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
9111 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
9114 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
9117 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
9120 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
9123 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
9126 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
9129 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
9132 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
9136 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
9137 if ( !entry.getAccession().equals( "P12345" ) ) {
9140 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
9143 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
9146 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
9149 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
9153 catch ( final IOException e ) {
9154 System.out.println();
9155 System.out.println( "the following might be due to absence internet connection:" );
9156 e.printStackTrace( System.out );
9159 catch ( final Exception e ) {
9165 private static boolean testWabiTxSearch() {
9168 result = TxSearch.searchSimple( "nematostella" );
9169 result = TxSearch.getTxId( "nematostella" );
9170 if ( !result.equals( "45350" ) ) {
9173 result = TxSearch.getTxName( "45350" );
9174 if ( !result.equals( "Nematostella" ) ) {
9177 result = TxSearch.getTxId( "nematostella vectensis" );
9178 if ( !result.equals( "45351" ) ) {
9181 result = TxSearch.getTxName( "45351" );
9182 if ( !result.equals( "Nematostella vectensis" ) ) {
9185 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
9186 if ( !result.equals( "536089" ) ) {
9189 result = TxSearch.getTxName( "536089" );
9190 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
9193 final List<String> queries = new ArrayList<String>();
9194 queries.add( "Campylobacter coli" );
9195 queries.add( "Escherichia coli" );
9196 queries.add( "Arabidopsis" );
9197 queries.add( "Trichoplax" );
9198 queries.add( "Samanea saman" );
9199 queries.add( "Kluyveromyces marxianus" );
9200 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
9201 queries.add( "Bornavirus parrot/PDD/2008" );
9202 final List<RANKS> ranks = new ArrayList<RANKS>();
9203 ranks.add( RANKS.SUPERKINGDOM );
9204 ranks.add( RANKS.KINGDOM );
9205 ranks.add( RANKS.FAMILY );
9206 ranks.add( RANKS.GENUS );
9207 ranks.add( RANKS.TRIBE );
9208 result = TxSearch.searchLineage( queries, ranks );
9209 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
9210 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
9212 catch ( final Exception e ) {
9213 System.out.println();
9214 System.out.println( "the following might be due to absence internet connection:" );
9215 e.printStackTrace( System.out );
9221 private static boolean testAminoAcidSequence() {
9223 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
9224 if ( aa1.getLength() != 13 ) {
9227 if ( aa1.getResidueAt( 0 ) != 'A' ) {
9230 if ( aa1.getResidueAt( 2 ) != 'K' ) {
9233 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
9236 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
9237 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
9240 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
9241 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
9244 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
9245 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
9249 catch ( final Exception e ) {
9250 e.printStackTrace();
9256 private static boolean testCreateBalancedPhylogeny() {
9258 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
9259 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
9262 if ( p0.getNumberOfExternalNodes() != 15625 ) {
9265 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
9266 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
9269 if ( p1.getNumberOfExternalNodes() != 100 ) {
9273 catch ( final Exception e ) {
9274 e.printStackTrace();
9280 private static boolean testFastaParser() {
9282 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
9285 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
9288 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
9289 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
9292 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
9295 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
9298 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
9301 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
9304 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
9308 catch ( final Exception e ) {
9309 e.printStackTrace();
9315 private static boolean testGeneralMsaParser() {
9317 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
9318 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
9319 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
9320 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
9321 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
9322 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
9323 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
9324 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
9325 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9328 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9331 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9334 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9337 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9340 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9343 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9346 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9349 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9352 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9355 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9358 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9361 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
9362 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
9365 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
9368 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
9371 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
9372 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
9375 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
9378 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
9381 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
9382 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
9385 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
9388 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
9392 catch ( final Exception e ) {
9393 e.printStackTrace();
9399 private static boolean testMafft( final String path ) {
9401 final List<String> opts = new ArrayList<String>();
9402 opts.add( "--maxiterate" );
9404 opts.add( "--localpair" );
9405 opts.add( "--quiet" );
9407 final MsaInferrer mafft = Mafft.createInstance( path );
9408 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
9409 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
9412 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
9416 catch ( final Exception e ) {
9417 e.printStackTrace( System.out );
9423 private static boolean testNextNodeWithCollapsing() {
9425 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9427 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
9428 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9429 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
9430 t0.getNode( "cd" ).setCollapse( true );
9431 t0.getNode( "cde" ).setCollapse( true );
9432 n = t0.getFirstExternalNode();
9433 while ( n != null ) {
9435 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9437 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9440 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9443 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
9446 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
9449 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
9452 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
9456 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9457 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
9458 t1.getNode( "ab" ).setCollapse( true );
9459 t1.getNode( "cd" ).setCollapse( true );
9460 t1.getNode( "cde" ).setCollapse( true );
9461 n = t1.getNode( "ab" );
9462 ext = new ArrayList<PhylogenyNode>();
9463 while ( n != null ) {
9465 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9467 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9470 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9473 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
9476 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
9479 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
9485 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9486 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
9487 t2.getNode( "ab" ).setCollapse( true );
9488 t2.getNode( "cd" ).setCollapse( true );
9489 t2.getNode( "cde" ).setCollapse( true );
9490 t2.getNode( "c" ).setCollapse( true );
9491 t2.getNode( "d" ).setCollapse( true );
9492 t2.getNode( "e" ).setCollapse( true );
9493 t2.getNode( "gh" ).setCollapse( true );
9494 n = t2.getNode( "ab" );
9495 ext = new ArrayList<PhylogenyNode>();
9496 while ( n != null ) {
9498 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9500 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9503 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9506 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
9509 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
9515 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9516 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
9517 t3.getNode( "ab" ).setCollapse( true );
9518 t3.getNode( "cd" ).setCollapse( true );
9519 t3.getNode( "cde" ).setCollapse( true );
9520 t3.getNode( "c" ).setCollapse( true );
9521 t3.getNode( "d" ).setCollapse( true );
9522 t3.getNode( "e" ).setCollapse( true );
9523 t3.getNode( "gh" ).setCollapse( true );
9524 t3.getNode( "fgh" ).setCollapse( true );
9525 n = t3.getNode( "ab" );
9526 ext = new ArrayList<PhylogenyNode>();
9527 while ( n != null ) {
9529 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9531 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9534 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9537 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
9543 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9544 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
9545 t4.getNode( "ab" ).setCollapse( true );
9546 t4.getNode( "cd" ).setCollapse( true );
9547 t4.getNode( "cde" ).setCollapse( true );
9548 t4.getNode( "c" ).setCollapse( true );
9549 t4.getNode( "d" ).setCollapse( true );
9550 t4.getNode( "e" ).setCollapse( true );
9551 t4.getNode( "gh" ).setCollapse( true );
9552 t4.getNode( "fgh" ).setCollapse( true );
9553 t4.getNode( "abcdefgh" ).setCollapse( true );
9554 n = t4.getNode( "abcdefgh" );
9555 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
9560 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9561 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
9563 n = t5.getFirstExternalNode();
9564 while ( n != null ) {
9566 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9568 if ( ext.size() != 8 ) {
9571 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9574 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9577 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9580 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9583 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9586 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9589 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
9592 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
9597 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9598 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
9600 t6.getNode( "ab" ).setCollapse( true );
9601 n = t6.getNode( "ab" );
9602 while ( n != null ) {
9604 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9606 if ( ext.size() != 7 ) {
9609 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9612 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9615 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9618 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9621 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9624 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9627 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9632 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9633 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
9635 t7.getNode( "cd" ).setCollapse( true );
9636 n = t7.getNode( "a" );
9637 while ( n != null ) {
9639 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9641 if ( ext.size() != 7 ) {
9644 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9647 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9650 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9653 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9656 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9659 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9662 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9667 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9668 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
9670 t8.getNode( "cd" ).setCollapse( true );
9671 t8.getNode( "c" ).setCollapse( true );
9672 t8.getNode( "d" ).setCollapse( true );
9673 n = t8.getNode( "a" );
9674 while ( n != null ) {
9676 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9678 if ( ext.size() != 7 ) {
9681 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9684 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9687 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9688 System.out.println( "2 fail" );
9691 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9694 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9697 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9700 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9705 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9706 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
9708 t9.getNode( "gh" ).setCollapse( true );
9709 n = t9.getNode( "a" );
9710 while ( n != null ) {
9712 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9714 if ( ext.size() != 7 ) {
9717 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9720 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9723 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9726 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9729 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9732 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9735 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9740 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9741 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
9743 t10.getNode( "gh" ).setCollapse( true );
9744 t10.getNode( "g" ).setCollapse( true );
9745 t10.getNode( "h" ).setCollapse( true );
9746 n = t10.getNode( "a" );
9747 while ( n != null ) {
9749 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9751 if ( ext.size() != 7 ) {
9754 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9757 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9760 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9763 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9766 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9769 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9772 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9777 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9778 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
9780 t11.getNode( "gh" ).setCollapse( true );
9781 t11.getNode( "fgh" ).setCollapse( true );
9782 n = t11.getNode( "a" );
9783 while ( n != null ) {
9785 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9787 if ( ext.size() != 6 ) {
9790 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9793 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9796 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9799 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9802 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9805 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9810 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9811 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
9813 t12.getNode( "gh" ).setCollapse( true );
9814 t12.getNode( "fgh" ).setCollapse( true );
9815 t12.getNode( "g" ).setCollapse( true );
9816 t12.getNode( "h" ).setCollapse( true );
9817 t12.getNode( "f" ).setCollapse( true );
9818 n = t12.getNode( "a" );
9819 while ( n != null ) {
9821 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9823 if ( ext.size() != 6 ) {
9826 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9829 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9832 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9835 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9838 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9841 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9846 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9847 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
9849 t13.getNode( "ab" ).setCollapse( true );
9850 t13.getNode( "b" ).setCollapse( true );
9851 t13.getNode( "fgh" ).setCollapse( true );
9852 t13.getNode( "gh" ).setCollapse( true );
9853 n = t13.getNode( "ab" );
9854 while ( n != null ) {
9856 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9858 if ( ext.size() != 5 ) {
9861 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9864 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9867 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9870 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9873 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9878 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
9879 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
9881 t14.getNode( "ab" ).setCollapse( true );
9882 t14.getNode( "a" ).setCollapse( true );
9883 t14.getNode( "fgh" ).setCollapse( true );
9884 t14.getNode( "gh" ).setCollapse( true );
9885 n = t14.getNode( "ab" );
9886 while ( n != null ) {
9888 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9890 if ( ext.size() != 5 ) {
9893 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9896 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9899 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9902 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9905 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9910 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" );
9911 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9913 t15.getNode( "ab" ).setCollapse( true );
9914 t15.getNode( "a" ).setCollapse( true );
9915 t15.getNode( "fgh" ).setCollapse( true );
9916 t15.getNode( "gh" ).setCollapse( true );
9917 n = t15.getNode( "ab" );
9918 while ( n != null ) {
9920 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9922 if ( ext.size() != 6 ) {
9925 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9928 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9931 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9934 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9937 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
9940 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9945 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" );
9946 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
9948 t16.getNode( "ab" ).setCollapse( true );
9949 t16.getNode( "a" ).setCollapse( true );
9950 t16.getNode( "fgh" ).setCollapse( true );
9951 t16.getNode( "gh" ).setCollapse( true );
9952 t16.getNode( "cd" ).setCollapse( true );
9953 t16.getNode( "cde" ).setCollapse( true );
9954 t16.getNode( "d" ).setCollapse( true );
9955 t16.getNode( "x" ).setCollapse( true );
9956 n = t16.getNode( "ab" );
9957 while ( n != null ) {
9959 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9961 if ( ext.size() != 4 ) {
9964 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9967 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9970 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
9973 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
9977 catch ( final Exception e ) {
9978 e.printStackTrace( System.out );
9984 private static boolean testMsaQualityMethod() {
9986 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
9987 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
9988 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
9989 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
9990 final List<Sequence> l = new ArrayList<Sequence>();
9995 final Msa msa = BasicMsa.createInstance( l );
9996 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
9999 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
10002 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
10005 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
10009 catch ( final Exception e ) {
10010 e.printStackTrace( System.out );
10016 private static boolean testSequenceIdParsing() {
10018 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
10019 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10020 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10021 if ( id != null ) {
10022 System.out.println( "value =" + id.getValue() );
10023 System.out.println( "provider=" + id.getProvider() );
10028 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
10029 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10030 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10031 if ( id != null ) {
10032 System.out.println( "value =" + id.getValue() );
10033 System.out.println( "provider=" + id.getProvider() );
10038 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
10039 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10040 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10041 if ( id != null ) {
10042 System.out.println( "value =" + id.getValue() );
10043 System.out.println( "provider=" + id.getProvider() );
10048 id = SequenceIdParser.parse( "gb_AAA96518_1" );
10049 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10050 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
10051 if ( id != null ) {
10052 System.out.println( "value =" + id.getValue() );
10053 System.out.println( "provider=" + id.getProvider() );
10058 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
10059 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10060 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
10061 if ( id != null ) {
10062 System.out.println( "value =" + id.getValue() );
10063 System.out.println( "provider=" + id.getProvider() );
10068 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
10069 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10070 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
10071 if ( id != null ) {
10072 System.out.println( "value =" + id.getValue() );
10073 System.out.println( "provider=" + id.getProvider() );
10078 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
10079 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10080 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
10081 if ( id != null ) {
10082 System.out.println( "value =" + id.getValue() );
10083 System.out.println( "provider=" + id.getProvider() );
10088 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
10089 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10090 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
10091 if ( id != null ) {
10092 System.out.println( "value =" + id.getValue() );
10093 System.out.println( "provider=" + id.getProvider() );
10098 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
10099 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10100 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
10101 if ( id != null ) {
10102 System.out.println( "value =" + id.getValue() );
10103 System.out.println( "provider=" + id.getProvider() );
10108 id = SequenceIdParser.parse( "P4A123" );
10109 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10110 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
10111 if ( id != null ) {
10112 System.out.println( "value =" + id.getValue() );
10113 System.out.println( "provider=" + id.getProvider() );
10118 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
10119 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10120 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
10121 if ( id != null ) {
10122 System.out.println( "value =" + id.getValue() );
10123 System.out.println( "provider=" + id.getProvider() );
10128 id = SequenceIdParser.parse( "XP_12345" );
10129 if ( id != null ) {
10130 System.out.println( "value =" + id.getValue() );
10131 System.out.println( "provider=" + id.getProvider() );
10134 // lcl_91970_unknown_
10136 catch ( final Exception e ) {
10137 e.printStackTrace( System.out );