2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
55 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
56 import org.forester.io.parsers.tol.TolParser;
57 import org.forester.io.parsers.util.ParserUtils;
58 import org.forester.io.writers.PhylogenyWriter;
59 import org.forester.msa.BasicMsa;
60 import org.forester.msa.Mafft;
61 import org.forester.msa.Msa;
62 import org.forester.msa.MsaInferrer;
63 import org.forester.msa.MsaMethods;
64 import org.forester.pccx.TestPccx;
65 import org.forester.phylogeny.Phylogeny;
66 import org.forester.phylogeny.PhylogenyBranch;
67 import org.forester.phylogeny.PhylogenyMethods;
68 import org.forester.phylogeny.PhylogenyNode;
69 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
70 import org.forester.phylogeny.data.BinaryCharacters;
71 import org.forester.phylogeny.data.BranchWidth;
72 import org.forester.phylogeny.data.Confidence;
73 import org.forester.phylogeny.data.Distribution;
74 import org.forester.phylogeny.data.DomainArchitecture;
75 import org.forester.phylogeny.data.Event;
76 import org.forester.phylogeny.data.Identifier;
77 import org.forester.phylogeny.data.PhylogenyData;
78 import org.forester.phylogeny.data.PhylogenyDataUtil;
79 import org.forester.phylogeny.data.Polygon;
80 import org.forester.phylogeny.data.PropertiesMap;
81 import org.forester.phylogeny.data.Property;
82 import org.forester.phylogeny.data.Property.AppliesTo;
83 import org.forester.phylogeny.data.ProteinDomain;
84 import org.forester.phylogeny.data.Taxonomy;
85 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
86 import org.forester.phylogeny.factories.PhylogenyFactory;
87 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
88 import org.forester.protein.Protein;
89 import org.forester.rio.TestRIO;
90 import org.forester.sdi.SDI;
91 import org.forester.sdi.SDIR;
92 import org.forester.sdi.TestGSDI;
93 import org.forester.sequence.BasicSequence;
94 import org.forester.sequence.Sequence;
95 import org.forester.surfacing.TestSurfacing;
96 import org.forester.tools.ConfidenceAssessor;
97 import org.forester.tools.SupportCount;
98 import org.forester.tools.TreeSplitMatrix;
99 import org.forester.util.AsciiHistogram;
100 import org.forester.util.BasicDescriptiveStatistics;
101 import org.forester.util.BasicTable;
102 import org.forester.util.BasicTableParser;
103 import org.forester.util.DescriptiveStatistics;
104 import org.forester.util.ForesterConstants;
105 import org.forester.util.ForesterUtil;
106 import org.forester.util.GeneralTable;
107 import org.forester.util.SequenceIdParser;
108 import org.forester.ws.seqdb.SequenceDatabaseEntry;
109 import org.forester.ws.seqdb.SequenceDbWsTools;
110 import org.forester.ws.seqdb.UniProtTaxonomy;
111 import org.forester.ws.wabi.TxSearch;
112 import org.forester.ws.wabi.TxSearch.RANKS;
113 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
114 import org.forester.ws.wabi.TxSearch.TAX_RANK;
116 @SuppressWarnings( "unused")
117 public final class Test {
119 private final static double ZERO_DIFF = 1.0E-9;
120 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "test_data"
122 + ForesterUtil.getFileSeparator();
123 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
124 + ForesterUtil.getFileSeparator() + "resources"
125 + ForesterUtil.getFileSeparator();
126 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
127 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
130 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
131 + ForesterConstants.PHYLO_XML_VERSION + "/"
132 + ForesterConstants.PHYLO_XML_XSD;
134 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
135 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
139 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
140 return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
143 public static boolean isEqual( final double a, final double b ) {
144 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
147 public static void main( final String[] args ) {
148 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
149 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
151 Locale.setDefault( Locale.US );
152 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
155 System.out.print( "[Test if directory with files for testing exists/is readable: " );
156 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
157 System.out.println( "OK.]" );
160 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
161 System.out.println( "Testing aborted." );
164 System.out.print( "[Test if resources directory exists/is readable: " );
165 if ( testDir( PATH_TO_RESOURCES ) ) {
166 System.out.println( "OK.]" );
169 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
170 System.out.println( "Testing aborted." );
173 final long start_time = new Date().getTime();
174 System.out.print( "Sequence id parsing: " );
175 if ( testSequenceIdParsing() ) {
176 System.out.println( "OK." );
180 System.out.println( "failed." );
183 System.out.print( "Hmmscan output parser: " );
184 if ( testHmmscanOutputParser() ) {
185 System.out.println( "OK." );
189 System.out.println( "failed." );
192 System.out.print( "Basic node methods: " );
193 if ( Test.testBasicNodeMethods() ) {
194 System.out.println( "OK." );
198 System.out.println( "failed." );
201 System.out.print( "Taxonomy code extraction: " );
202 if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
203 System.out.println( "OK." );
207 System.out.println( "failed." );
210 System.out.print( "Taxonomy extraction (general): " );
211 if ( Test.testTaxonomyExtraction() ) {
212 System.out.println( "OK." );
216 System.out.println( "failed." );
219 System.out.print( "Basic node construction and parsing of NHX (node level): " );
220 if ( Test.testNHXNodeParsing() ) {
221 System.out.println( "OK." );
225 System.out.println( "failed." );
228 System.out.print( "NHX parsing iterating: " );
229 if ( Test.testNHParsingIter() ) {
230 System.out.println( "OK." );
234 System.out.println( "failed." );
237 System.out.print( "NH parsing: " );
238 if ( Test.testNHParsing() ) {
239 System.out.println( "OK." );
243 System.out.println( "failed." );
246 System.out.print( "Conversion to NHX (node level): " );
247 if ( Test.testNHXconversion() ) {
248 System.out.println( "OK." );
252 System.out.println( "failed." );
255 System.out.print( "NHX parsing: " );
256 if ( Test.testNHXParsing() ) {
257 System.out.println( "OK." );
261 System.out.println( "failed." );
264 System.out.print( "NHX parsing with quotes: " );
265 if ( Test.testNHXParsingQuotes() ) {
266 System.out.println( "OK." );
270 System.out.println( "failed." );
273 System.out.print( "NHX parsing (MrBayes): " );
274 if ( Test.testNHXParsingMB() ) {
275 System.out.println( "OK." );
279 System.out.println( "failed." );
282 System.out.print( "Nexus characters parsing: " );
283 if ( Test.testNexusCharactersParsing() ) {
284 System.out.println( "OK." );
288 System.out.println( "failed." );
291 System.out.print( "Nexus tree parsing iterating: " );
292 if ( Test.testNexusTreeParsingIterating() ) {
293 System.out.println( "OK." );
297 System.out.println( "failed." );
300 System.out.print( "Nexus tree parsing: " );
301 if ( Test.testNexusTreeParsing() ) {
302 System.out.println( "OK." );
306 System.out.println( "failed." );
309 System.out.print( "Nexus tree parsing (translating): " );
310 if ( Test.testNexusTreeParsingTranslating() ) {
311 System.out.println( "OK." );
315 System.out.println( "failed." );
318 System.out.print( "Nexus matrix parsing: " );
319 if ( Test.testNexusMatrixParsing() ) {
320 System.out.println( "OK." );
324 System.out.println( "failed." );
327 System.out.print( "Basic phyloXML parsing: " );
328 if ( Test.testBasicPhyloXMLparsing() ) {
329 System.out.println( "OK." );
333 System.out.println( "failed." );
336 System.out.print( "Basic phyloXML parsing (validating against schema): " );
337 if ( testBasicPhyloXMLparsingValidating() ) {
338 System.out.println( "OK." );
342 System.out.println( "failed." );
345 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
346 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
347 System.out.println( "OK." );
351 System.out.println( "failed." );
354 System.out.print( "phyloXML Distribution Element: " );
355 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
356 System.out.println( "OK." );
360 System.out.println( "failed." );
363 System.out.print( "Tol XML parsing: " );
364 if ( Test.testBasicTolXMLparsing() ) {
365 System.out.println( "OK." );
369 System.out.println( "failed." );
372 System.out.print( "Copying of node data: " );
373 if ( Test.testCopyOfNodeData() ) {
374 System.out.println( "OK." );
378 System.out.println( "failed." );
381 System.out.print( "Basic tree methods: " );
382 if ( Test.testBasicTreeMethods() ) {
383 System.out.println( "OK." );
387 System.out.println( "failed." );
390 System.out.print( "Tree methods: " );
391 if ( Test.testTreeMethods() ) {
392 System.out.println( "OK." );
396 System.out.println( "failed." );
399 System.out.print( "Postorder Iterator: " );
400 if ( Test.testPostOrderIterator() ) {
401 System.out.println( "OK." );
405 System.out.println( "failed." );
408 System.out.print( "Preorder Iterator: " );
409 if ( Test.testPreOrderIterator() ) {
410 System.out.println( "OK." );
414 System.out.println( "failed." );
417 System.out.print( "Levelorder Iterator: " );
418 if ( Test.testLevelOrderIterator() ) {
419 System.out.println( "OK." );
423 System.out.println( "failed." );
426 System.out.print( "Re-id methods: " );
427 if ( Test.testReIdMethods() ) {
428 System.out.println( "OK." );
432 System.out.println( "failed." );
435 System.out.print( "Methods on last external nodes: " );
436 if ( Test.testLastExternalNodeMethods() ) {
437 System.out.println( "OK." );
441 System.out.println( "failed." );
444 System.out.print( "Methods on external nodes: " );
445 if ( Test.testExternalNodeRelatedMethods() ) {
446 System.out.println( "OK." );
450 System.out.println( "failed." );
453 System.out.print( "Deletion of external nodes: " );
454 if ( Test.testDeletionOfExternalNodes() ) {
455 System.out.println( "OK." );
459 System.out.println( "failed." );
462 System.out.print( "Subtree deletion: " );
463 if ( Test.testSubtreeDeletion() ) {
464 System.out.println( "OK." );
468 System.out.println( "failed." );
471 System.out.print( "Phylogeny branch: " );
472 if ( Test.testPhylogenyBranch() ) {
473 System.out.println( "OK." );
477 System.out.println( "failed." );
480 System.out.print( "Rerooting: " );
481 if ( Test.testRerooting() ) {
482 System.out.println( "OK." );
486 System.out.println( "failed." );
489 System.out.print( "Mipoint rooting: " );
490 if ( Test.testMidpointrooting() ) {
491 System.out.println( "OK." );
495 System.out.println( "failed." );
498 System.out.print( "Node removal: " );
499 if ( Test.testNodeRemoval() ) {
500 System.out.println( "OK." );
504 System.out.println( "failed." );
507 System.out.print( "Support count: " );
508 if ( Test.testSupportCount() ) {
509 System.out.println( "OK." );
513 System.out.println( "failed." );
516 System.out.print( "Support transfer: " );
517 if ( Test.testSupportTransfer() ) {
518 System.out.println( "OK." );
522 System.out.println( "failed." );
525 System.out.print( "Finding of LCA: " );
526 if ( Test.testGetLCA() ) {
527 System.out.println( "OK." );
531 System.out.println( "failed." );
534 System.out.print( "Finding of LCA 2: " );
535 if ( Test.testGetLCA2() ) {
536 System.out.println( "OK." );
540 System.out.println( "failed." );
543 System.out.print( "Calculation of distance between nodes: " );
544 if ( Test.testGetDistance() ) {
545 System.out.println( "OK." );
549 System.out.println( "failed." );
552 System.out.print( "Descriptive statistics: " );
553 if ( Test.testDescriptiveStatistics() ) {
554 System.out.println( "OK." );
558 System.out.println( "failed." );
561 System.out.print( "Data objects and methods: " );
562 if ( Test.testDataObjects() ) {
563 System.out.println( "OK." );
567 System.out.println( "failed." );
570 System.out.print( "Properties map: " );
571 if ( Test.testPropertiesMap() ) {
572 System.out.println( "OK." );
576 System.out.println( "failed." );
579 System.out.print( "SDIse: " );
580 if ( Test.testSDIse() ) {
581 System.out.println( "OK." );
585 System.out.println( "failed." );
588 System.out.print( "SDIunrooted: " );
589 if ( Test.testSDIunrooted() ) {
590 System.out.println( "OK." );
594 System.out.println( "failed." );
597 System.out.print( "GSDI: " );
598 if ( TestGSDI.test() ) {
599 System.out.println( "OK." );
603 System.out.println( "failed." );
606 System.out.print( "RIO: " );
607 if ( TestRIO.test() ) {
608 System.out.println( "OK." );
612 System.out.println( "failed." );
615 System.out.print( "Phylogeny reconstruction:" );
616 System.out.println();
617 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
618 System.out.println( "OK." );
622 System.out.println( "failed." );
625 System.out.print( "Analysis of domain architectures: " );
626 System.out.println();
627 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
628 System.out.println( "OK." );
632 System.out.println( "failed." );
635 System.out.print( "GO: " );
636 System.out.println();
637 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
638 System.out.println( "OK." );
642 System.out.println( "failed." );
645 System.out.print( "Modeling tools: " );
646 if ( TestPccx.test() ) {
647 System.out.println( "OK." );
651 System.out.println( "failed." );
654 System.out.print( "Split Matrix strict: " );
655 if ( Test.testSplitStrict() ) {
656 System.out.println( "OK." );
660 System.out.println( "failed." );
663 System.out.print( "Split Matrix: " );
664 if ( Test.testSplit() ) {
665 System.out.println( "OK." );
669 System.out.println( "failed." );
672 System.out.print( "Confidence Assessor: " );
673 if ( Test.testConfidenceAssessor() ) {
674 System.out.println( "OK." );
678 System.out.println( "failed." );
681 System.out.print( "Basic table: " );
682 if ( Test.testBasicTable() ) {
683 System.out.println( "OK." );
687 System.out.println( "failed." );
690 System.out.print( "General table: " );
691 if ( Test.testGeneralTable() ) {
692 System.out.println( "OK." );
696 System.out.println( "failed." );
699 System.out.print( "Amino acid sequence: " );
700 if ( Test.testAminoAcidSequence() ) {
701 System.out.println( "OK." );
705 System.out.println( "failed." );
708 System.out.print( "General MSA parser: " );
709 if ( Test.testGeneralMsaParser() ) {
710 System.out.println( "OK." );
714 System.out.println( "failed." );
717 System.out.print( "Fasta parser for msa: " );
718 if ( Test.testFastaParser() ) {
719 System.out.println( "OK." );
723 System.out.println( "failed." );
726 System.out.print( "Creation of balanced phylogeny: " );
727 if ( Test.testCreateBalancedPhylogeny() ) {
728 System.out.println( "OK." );
732 System.out.println( "failed." );
735 System.out.print( "EMBL Entry Retrieval: " );
736 if ( Test.testEmblEntryRetrieval() ) {
737 System.out.println( "OK." );
741 System.out.println( "failed." );
744 System.out.print( "Uniprot Entry Retrieval: " );
745 if ( Test.testUniprotEntryRetrieval() ) {
746 System.out.println( "OK." );
750 System.out.println( "failed." );
753 System.out.print( "Uniprot Taxonomy Search: " );
754 if ( Test.testUniprotTaxonomySearch() ) {
755 System.out.println( "OK." );
759 System.out.println( "failed." );
764 final String os = ForesterUtil.OS_NAME.toLowerCase();
765 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
766 path = "/usr/local/bin/mafft";
768 else if ( os.indexOf( "win" ) >= 0 ) {
769 path = "C:\\Program Files\\mafft-win\\mafft.bat";
772 path = "/home/czmasek/bin/mafft";
774 if ( !MsaInferrer.isInstalled( path ) ) {
777 if ( !MsaInferrer.isInstalled( path ) ) {
778 path = "/usr/local/bin/mafft";
780 if ( MsaInferrer.isInstalled( path ) ) {
781 System.out.print( "MAFFT (external program): " );
782 if ( Test.testMafft( path ) ) {
783 System.out.println( "OK." );
787 System.out.println( "failed [will not count towards failed tests]" );
791 System.out.print( "Next nodes with collapsed: " );
792 if ( Test.testNextNodeWithCollapsing() ) {
793 System.out.println( "OK." );
797 System.out.println( "failed." );
800 System.out.print( "Simple MSA quality: " );
801 if ( Test.testMsaQualityMethod() ) {
802 System.out.println( "OK." );
806 System.out.println( "failed." );
809 System.out.println();
810 final Runtime rt = java.lang.Runtime.getRuntime();
811 final long free_memory = rt.freeMemory() / 1000000;
812 final long total_memory = rt.totalMemory() / 1000000;
813 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
814 + free_memory + "MB, total memory: " + total_memory + "MB)" );
815 System.out.println();
816 System.out.println( "Successful tests: " + succeeded );
817 System.out.println( "Failed tests: " + failed );
818 System.out.println();
820 System.out.println( "OK." );
823 System.out.println( "Not OK." );
827 private static boolean testExtractTaxonomyCodeFromNodeName() {
829 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
830 .equals( "MOUSE" ) ) {
833 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
837 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
840 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
841 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
842 .equals( "MOUSE" ) ) {
845 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445",
846 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
847 .equals( "MOUSE" ) ) {
850 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
851 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
852 .equals( "MOUSE" ) ) {
855 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
856 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
859 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
860 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
863 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
864 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
867 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445",
868 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
871 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
872 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
875 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
876 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
879 if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
880 TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
883 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
887 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
892 .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
893 .equals( "MOUSE" ) ) {
896 if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
897 .equals( "MOUSE" ) ) {
901 catch ( final Exception e ) {
902 e.printStackTrace( System.out );
908 private static boolean testBasicNodeMethods() {
910 if ( PhylogenyNode.getNodeCount() != 0 ) {
913 final PhylogenyNode n1 = new PhylogenyNode();
914 final PhylogenyNode n2 = PhylogenyNode
915 .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
916 final PhylogenyNode n3 = PhylogenyNode
917 .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
918 final PhylogenyNode n4 = PhylogenyNode
919 .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
920 if ( n1.isHasAssignedEvent() ) {
923 if ( PhylogenyNode.getNodeCount() != 4 ) {
926 if ( n3.getIndicator() != 0 ) {
929 if ( n3.getNumberOfExternalNodes() != 1 ) {
932 if ( !n3.isExternal() ) {
935 if ( !n3.isRoot() ) {
938 if ( !n4.getName().equals( "n4" ) ) {
942 catch ( final Exception e ) {
943 e.printStackTrace( System.out );
949 private static boolean testBasicPhyloXMLparsing() {
951 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
952 final PhyloXmlParser xml_parser = new PhyloXmlParser();
953 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
955 if ( xml_parser.getErrorCount() > 0 ) {
956 System.out.println( xml_parser.getErrorMessages().toString() );
959 if ( phylogenies_0.length != 4 ) {
962 final Phylogeny t1 = phylogenies_0[ 0 ];
963 final Phylogeny t2 = phylogenies_0[ 1 ];
964 final Phylogeny t3 = phylogenies_0[ 2 ];
965 final Phylogeny t4 = phylogenies_0[ 3 ];
966 if ( t1.getNumberOfExternalNodes() != 1 ) {
969 if ( !t1.isRooted() ) {
972 if ( t1.isRerootable() ) {
975 if ( !t1.getType().equals( "gene_tree" ) ) {
978 if ( t2.getNumberOfExternalNodes() != 2 ) {
981 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
984 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
987 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
990 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
993 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
996 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
999 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1000 .startsWith( "actgtgggggt" ) ) {
1003 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1004 .startsWith( "ctgtgatgcat" ) ) {
1007 if ( t3.getNumberOfExternalNodes() != 4 ) {
1010 if ( !t1.getName().equals( "t1" ) ) {
1013 if ( !t2.getName().equals( "t2" ) ) {
1016 if ( !t3.getName().equals( "t3" ) ) {
1019 if ( !t4.getName().equals( "t4" ) ) {
1022 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
1025 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
1028 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1031 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
1032 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1035 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1038 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1041 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
1044 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1045 .equals( "apoptosis" ) ) {
1048 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1049 .equals( "GO:0006915" ) ) {
1052 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1053 .equals( "UniProtKB" ) ) {
1056 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1057 .equals( "experimental" ) ) {
1060 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1061 .equals( "function" ) ) {
1064 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1065 .getValue() != 1 ) {
1068 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1069 .getType().equals( "ml" ) ) {
1072 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1073 .equals( "apoptosis" ) ) {
1076 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1077 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1080 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1081 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1084 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1085 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1088 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1089 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1092 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1093 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1096 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1097 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1100 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1101 .equals( "GO:0005829" ) ) {
1104 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1105 .equals( "intracellular organelle" ) ) {
1108 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1111 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1112 .equals( "UniProt link" ) ) ) {
1115 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1119 catch ( final Exception e ) {
1120 e.printStackTrace( System.out );
1126 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1128 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1129 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1130 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1131 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1134 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1136 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1138 if ( xml_parser.getErrorCount() > 0 ) {
1139 System.out.println( xml_parser.getErrorMessages().toString() );
1142 if ( phylogenies_0.length != 4 ) {
1145 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1146 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1147 if ( phylogenies_t1.length != 1 ) {
1150 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1151 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1154 if ( !t1_rt.isRooted() ) {
1157 if ( t1_rt.isRerootable() ) {
1160 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1163 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1164 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1165 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1166 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1169 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1172 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1175 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1178 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1179 .startsWith( "actgtgggggt" ) ) {
1182 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1183 .startsWith( "ctgtgatgcat" ) ) {
1186 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1187 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1188 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1189 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1190 if ( phylogenies_1.length != 1 ) {
1193 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1194 if ( !t3_rt.getName().equals( "t3" ) ) {
1197 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1200 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1203 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1206 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1209 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1210 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1213 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1216 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1219 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1220 .equals( "UniProtKB" ) ) {
1223 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1224 .equals( "apoptosis" ) ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
1228 .equals( "GO:0006915" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
1232 .equals( "UniProtKB" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
1236 .equals( "experimental" ) ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
1240 .equals( "function" ) ) {
1243 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1244 .getValue() != 1 ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
1248 .getType().equals( "ml" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1252 .equals( "apoptosis" ) ) {
1255 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1256 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1260 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1264 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1267 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1268 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1271 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1272 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1275 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
1276 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1279 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1280 .equals( "GO:0005829" ) ) {
1283 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
1284 .equals( "intracellular organelle" ) ) {
1287 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1290 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1291 .equals( "UniProt link" ) ) ) {
1294 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1297 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1300 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1301 .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." ) ) ) {
1304 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1307 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1310 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1313 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1316 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1317 .equals( "ncbi" ) ) {
1320 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1323 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1324 .getName().equals( "B" ) ) {
1327 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1328 .getFrom() != 21 ) {
1331 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1334 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1335 .getLength() != 24 ) {
1338 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1339 .getConfidence() != 2144 ) {
1342 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1343 .equals( "pfam" ) ) {
1346 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1349 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1352 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1355 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1358 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1359 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1362 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1365 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1368 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1371 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1374 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1377 if ( taxbb.getSynonyms().size() != 2 ) {
1380 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1383 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1386 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1389 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1392 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1395 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1396 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1400 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1403 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1406 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1409 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1412 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1415 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1418 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1422 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1425 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1426 .equalsIgnoreCase( "435" ) ) {
1429 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1432 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1433 .equalsIgnoreCase( "443.7" ) ) {
1436 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1439 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1442 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1443 .equalsIgnoreCase( "433" ) ) {
1447 catch ( final Exception e ) {
1448 e.printStackTrace( System.out );
1454 private static boolean testBasicPhyloXMLparsingValidating() {
1456 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1457 PhyloXmlParser xml_parser = null;
1459 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1461 catch ( final Exception e ) {
1462 // Do nothing -- means were not running from jar.
1464 if ( xml_parser == null ) {
1465 xml_parser = new PhyloXmlParser();
1466 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1467 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1470 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1473 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1475 if ( xml_parser.getErrorCount() > 0 ) {
1476 System.out.println( xml_parser.getErrorMessages().toString() );
1479 if ( phylogenies_0.length != 4 ) {
1482 final Phylogeny t1 = phylogenies_0[ 0 ];
1483 final Phylogeny t2 = phylogenies_0[ 1 ];
1484 final Phylogeny t3 = phylogenies_0[ 2 ];
1485 final Phylogeny t4 = phylogenies_0[ 3 ];
1486 if ( !t1.getName().equals( "t1" ) ) {
1489 if ( !t2.getName().equals( "t2" ) ) {
1492 if ( !t3.getName().equals( "t3" ) ) {
1495 if ( !t4.getName().equals( "t4" ) ) {
1498 if ( t1.getNumberOfExternalNodes() != 1 ) {
1501 if ( t2.getNumberOfExternalNodes() != 2 ) {
1504 if ( t3.getNumberOfExternalNodes() != 4 ) {
1507 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1508 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1509 if ( xml_parser.getErrorCount() > 0 ) {
1510 System.out.println( "errors:" );
1511 System.out.println( xml_parser.getErrorMessages().toString() );
1514 if ( phylogenies_1.length != 4 ) {
1517 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1519 if ( xml_parser.getErrorCount() > 0 ) {
1520 System.out.println( "errors:" );
1521 System.out.println( xml_parser.getErrorMessages().toString() );
1524 if ( phylogenies_2.length != 1 ) {
1527 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1530 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1532 if ( xml_parser.getErrorCount() > 0 ) {
1533 System.out.println( xml_parser.getErrorMessages().toString() );
1536 if ( phylogenies_3.length != 2 ) {
1539 final Phylogeny a = phylogenies_3[ 0 ];
1540 if ( !a.getName().equals( "tree 4" ) ) {
1543 if ( a.getNumberOfExternalNodes() != 3 ) {
1546 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1549 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1552 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1554 if ( xml_parser.getErrorCount() > 0 ) {
1555 System.out.println( xml_parser.getErrorMessages().toString() );
1558 if ( phylogenies_4.length != 1 ) {
1561 final Phylogeny s = phylogenies_4[ 0 ];
1562 if ( s.getNumberOfExternalNodes() != 6 ) {
1565 s.getNode( "first" );
1567 s.getNode( "\"<a'b&c'd\">\"" );
1568 s.getNode( "'''\"" );
1569 s.getNode( "\"\"\"" );
1570 s.getNode( "dick & doof" );
1572 catch ( final Exception e ) {
1573 e.printStackTrace( System.out );
1579 private static boolean testBasicTable() {
1581 final BasicTable<String> t0 = new BasicTable<String>();
1582 if ( t0.getNumberOfColumns() != 0 ) {
1585 if ( t0.getNumberOfRows() != 0 ) {
1588 t0.setValue( 3, 2, "23" );
1589 t0.setValue( 10, 1, "error" );
1590 t0.setValue( 10, 1, "110" );
1591 t0.setValue( 9, 1, "19" );
1592 t0.setValue( 1, 10, "101" );
1593 t0.setValue( 10, 10, "1010" );
1594 t0.setValue( 100, 10, "10100" );
1595 t0.setValue( 0, 0, "00" );
1596 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1599 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1602 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1605 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1608 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1611 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1614 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1617 if ( t0.getNumberOfColumns() != 101 ) {
1620 if ( t0.getNumberOfRows() != 11 ) {
1623 if ( t0.getValueAsString( 49, 4 ) != null ) {
1626 final String l = ForesterUtil.getLineSeparator();
1627 final StringBuffer source = new StringBuffer();
1628 source.append( "" + l );
1629 source.append( "# 1 1 1 1 1 1 1 1" + l );
1630 source.append( " 00 01 02 03" + l );
1631 source.append( " 10 11 12 13 " + l );
1632 source.append( "20 21 22 23 " + l );
1633 source.append( " 30 31 32 33" + l );
1634 source.append( "40 41 42 43" + l );
1635 source.append( " # 1 1 1 1 1 " + l );
1636 source.append( "50 51 52 53 54" + l );
1637 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1638 if ( t1.getNumberOfColumns() != 5 ) {
1641 if ( t1.getNumberOfRows() != 6 ) {
1644 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1647 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1650 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1653 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1656 final StringBuffer source1 = new StringBuffer();
1657 source1.append( "" + l );
1658 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1659 source1.append( " 00; 01 ;02;03" + l );
1660 source1.append( " 10; 11; 12; 13 " + l );
1661 source1.append( "20; 21; 22; 23 " + l );
1662 source1.append( " 30; 31; 32; 33" + l );
1663 source1.append( "40;41;42;43" + l );
1664 source1.append( " # 1 1 1 1 1 " + l );
1665 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1666 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1667 if ( t2.getNumberOfColumns() != 5 ) {
1670 if ( t2.getNumberOfRows() != 6 ) {
1673 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1676 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1679 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1682 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1685 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1688 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1691 final StringBuffer source2 = new StringBuffer();
1692 source2.append( "" + l );
1693 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1694 source2.append( " 00; 01 ;02;03" + l );
1695 source2.append( " 10; 11; 12; 13 " + l );
1696 source2.append( "20; 21; 22; 23 " + l );
1697 source2.append( " " + l );
1698 source2.append( " 30; 31; 32; 33" + l );
1699 source2.append( "40;41;42;43" + l );
1700 source2.append( " comment: 1 1 1 1 1 " + l );
1701 source2.append( ";;;50 ; 52; 53;;54 " + l );
1702 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1708 if ( tl.size() != 2 ) {
1711 final BasicTable<String> t3 = tl.get( 0 );
1712 final BasicTable<String> t4 = tl.get( 1 );
1713 if ( t3.getNumberOfColumns() != 4 ) {
1716 if ( t3.getNumberOfRows() != 3 ) {
1719 if ( t4.getNumberOfColumns() != 4 ) {
1722 if ( t4.getNumberOfRows() != 3 ) {
1725 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1728 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1732 catch ( final Exception e ) {
1733 e.printStackTrace( System.out );
1739 private static boolean testBasicTolXMLparsing() {
1741 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1742 final TolParser parser = new TolParser();
1743 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1744 if ( parser.getErrorCount() > 0 ) {
1745 System.out.println( parser.getErrorMessages().toString() );
1748 if ( phylogenies_0.length != 1 ) {
1751 final Phylogeny t1 = phylogenies_0[ 0 ];
1752 if ( t1.getNumberOfExternalNodes() != 5 ) {
1755 if ( !t1.isRooted() ) {
1758 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1761 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1764 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1767 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1770 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1771 if ( parser.getErrorCount() > 0 ) {
1772 System.out.println( parser.getErrorMessages().toString() );
1775 if ( phylogenies_1.length != 1 ) {
1778 final Phylogeny t2 = phylogenies_1[ 0 ];
1779 if ( t2.getNumberOfExternalNodes() != 664 ) {
1782 if ( !t2.isRooted() ) {
1785 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1788 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1791 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1794 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1797 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1800 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1801 .equals( "Aquifex" ) ) {
1804 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1805 if ( parser.getErrorCount() > 0 ) {
1806 System.out.println( parser.getErrorMessages().toString() );
1809 if ( phylogenies_2.length != 1 ) {
1812 final Phylogeny t3 = phylogenies_2[ 0 ];
1813 if ( t3.getNumberOfExternalNodes() != 184 ) {
1816 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1819 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1822 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1825 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1826 if ( parser.getErrorCount() > 0 ) {
1827 System.out.println( parser.getErrorMessages().toString() );
1830 if ( phylogenies_3.length != 1 ) {
1833 final Phylogeny t4 = phylogenies_3[ 0 ];
1834 if ( t4.getNumberOfExternalNodes() != 1 ) {
1837 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1840 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1843 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1846 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1847 if ( parser.getErrorCount() > 0 ) {
1848 System.out.println( parser.getErrorMessages().toString() );
1851 if ( phylogenies_4.length != 1 ) {
1854 final Phylogeny t5 = phylogenies_4[ 0 ];
1855 if ( t5.getNumberOfExternalNodes() != 13 ) {
1858 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1861 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1864 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1868 catch ( final Exception e ) {
1869 e.printStackTrace( System.out );
1875 private static boolean testBasicTreeMethods() {
1877 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1878 final Phylogeny t1 = factory.create();
1879 if ( !t1.isEmpty() ) {
1882 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1883 if ( t2.getNumberOfExternalNodes() != 4 ) {
1886 if ( t2.getHeight() != 8.5 ) {
1889 if ( !t2.isCompletelyBinary() ) {
1892 if ( t2.isEmpty() ) {
1895 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1896 if ( t3.getNumberOfExternalNodes() != 5 ) {
1899 if ( t3.getHeight() != 11 ) {
1902 if ( t3.isCompletelyBinary() ) {
1905 final PhylogenyNode n = t3.getNode( "ABC" );
1906 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 ];
1907 if ( t4.getNumberOfExternalNodes() != 9 ) {
1910 if ( t4.getHeight() != 11 ) {
1913 if ( t4.isCompletelyBinary() ) {
1916 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)" );
1917 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1918 if ( t5.getNumberOfExternalNodes() != 8 ) {
1921 if ( t5.getHeight() != 15 ) {
1924 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)" );
1925 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1926 if ( t6.getHeight() != 15 ) {
1929 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)" );
1930 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1931 if ( t7.getHeight() != 15 ) {
1934 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)" );
1935 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1936 if ( t8.getNumberOfExternalNodes() != 10 ) {
1939 if ( t8.getHeight() != 15 ) {
1942 final char[] a9 = new char[] { 'a' };
1943 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1944 if ( t9.getHeight() != 0 ) {
1947 final char[] a10 = new char[] { 'a', ':', '6' };
1948 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1949 if ( t10.getHeight() != 6 ) {
1953 catch ( final Exception e ) {
1954 e.printStackTrace( System.out );
1960 private static boolean testTreeMethods() {
1962 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1963 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
1964 PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
1965 if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
1966 System.out.println( t0.toNewHampshireX() );
1969 final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
1970 PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
1971 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
1974 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
1977 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
1981 catch ( final Exception e ) {
1982 e.printStackTrace( System.out );
1988 private static boolean testConfidenceAssessor() {
1990 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1991 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1992 final Phylogeny[] ev0 = factory
1993 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1995 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1996 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1999 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
2002 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2003 final Phylogeny[] ev1 = factory
2004 .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)));",
2006 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
2007 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2010 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2013 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2014 final Phylogeny[] ev_b = factory
2015 .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",
2017 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2018 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2021 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2025 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2026 final Phylogeny[] ev1x = factory
2027 .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)));",
2029 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2030 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2033 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2036 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2037 final Phylogeny[] ev_bx = factory
2038 .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",
2040 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2041 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2044 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2048 final Phylogeny[] t2 = factory
2049 .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);",
2051 final Phylogeny[] ev2 = factory
2052 .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);",
2054 for( final Phylogeny target : t2 ) {
2055 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2058 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2059 new NHXParser() )[ 0 ];
2060 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2061 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2062 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2065 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2068 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2072 catch ( final Exception e ) {
2073 e.printStackTrace();
2079 private static boolean testCopyOfNodeData() {
2081 final PhylogenyNode n1 = PhylogenyNode
2082 .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]" );
2083 final PhylogenyNode n2 = n1.copyNodeData();
2084 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2088 catch ( final Exception e ) {
2089 e.printStackTrace();
2095 private static boolean testDataObjects() {
2097 final Confidence s0 = new Confidence();
2098 final Confidence s1 = new Confidence();
2099 if ( !s0.isEqual( s1 ) ) {
2102 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2103 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2104 if ( s2.isEqual( s1 ) ) {
2107 if ( !s2.isEqual( s3 ) ) {
2110 final Confidence s4 = ( Confidence ) s3.copy();
2111 if ( !s4.isEqual( s3 ) ) {
2118 final Taxonomy t1 = new Taxonomy();
2119 final Taxonomy t2 = new Taxonomy();
2120 final Taxonomy t3 = new Taxonomy();
2121 final Taxonomy t4 = new Taxonomy();
2122 final Taxonomy t5 = new Taxonomy();
2123 t1.setIdentifier( new Identifier( "ecoli" ) );
2124 t1.setTaxonomyCode( "ECOLI" );
2125 t1.setScientificName( "E. coli" );
2126 t1.setCommonName( "coli" );
2127 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2128 if ( !t1.isEqual( t0 ) ) {
2131 t2.setIdentifier( new Identifier( "ecoli" ) );
2132 t2.setTaxonomyCode( "OTHER" );
2133 t2.setScientificName( "what" );
2134 t2.setCommonName( "something" );
2135 if ( !t1.isEqual( t2 ) ) {
2138 t2.setIdentifier( new Identifier( "nemve" ) );
2139 if ( t1.isEqual( t2 ) ) {
2142 t1.setIdentifier( null );
2143 t3.setTaxonomyCode( "ECOLI" );
2144 t3.setScientificName( "what" );
2145 t3.setCommonName( "something" );
2146 if ( !t1.isEqual( t3 ) ) {
2149 t1.setIdentifier( null );
2150 t1.setTaxonomyCode( "" );
2151 t4.setScientificName( "E. ColI" );
2152 t4.setCommonName( "something" );
2153 if ( !t1.isEqual( t4 ) ) {
2156 t4.setScientificName( "B. subtilis" );
2157 t4.setCommonName( "something" );
2158 if ( t1.isEqual( t4 ) ) {
2161 t1.setIdentifier( null );
2162 t1.setTaxonomyCode( "" );
2163 t1.setScientificName( "" );
2164 t5.setCommonName( "COLI" );
2165 if ( !t1.isEqual( t5 ) ) {
2168 t5.setCommonName( "vibrio" );
2169 if ( t1.isEqual( t5 ) ) {
2174 final Identifier id0 = new Identifier( "123", "pfam" );
2175 final Identifier id1 = ( Identifier ) id0.copy();
2176 if ( !id1.isEqual( id1 ) ) {
2179 if ( !id1.isEqual( id0 ) ) {
2182 if ( !id0.isEqual( id1 ) ) {
2189 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2190 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2191 if ( !pd1.isEqual( pd1 ) ) {
2194 if ( !pd1.isEqual( pd0 ) ) {
2199 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2200 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2201 if ( !pd3.isEqual( pd3 ) ) {
2204 if ( !pd2.isEqual( pd3 ) ) {
2207 if ( !pd0.isEqual( pd3 ) ) {
2212 // DomainArchitecture
2213 // ------------------
2214 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2215 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2216 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2217 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2218 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2219 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2224 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2225 if ( ds0.getNumberOfDomains() != 4 ) {
2228 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2229 if ( !ds0.isEqual( ds0 ) ) {
2232 if ( !ds0.isEqual( ds1 ) ) {
2235 if ( ds1.getNumberOfDomains() != 4 ) {
2238 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2243 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2244 if ( ds0.isEqual( ds2 ) ) {
2250 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2251 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2252 System.out.println( ds3.toNHX() );
2255 if ( ds3.getNumberOfDomains() != 3 ) {
2260 final Event e1 = new Event( Event.EventType.fusion );
2261 if ( e1.isDuplication() ) {
2264 if ( !e1.isFusion() ) {
2267 if ( !e1.asText().toString().equals( "fusion" ) ) {
2270 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2273 final Event e11 = new Event( Event.EventType.fusion );
2274 if ( !e11.isEqual( e1 ) ) {
2277 if ( !e11.toNHX().toString().equals( "" ) ) {
2280 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2281 if ( e2.isDuplication() ) {
2284 if ( !e2.isSpeciationOrDuplication() ) {
2287 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2290 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2293 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2296 if ( e11.isEqual( e2 ) ) {
2299 final Event e2c = ( Event ) e2.copy();
2300 if ( !e2c.isEqual( e2 ) ) {
2303 Event e3 = new Event( 1, 2, 3 );
2304 if ( e3.isDuplication() ) {
2307 if ( e3.isSpeciation() ) {
2310 if ( e3.isGeneLoss() ) {
2313 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2316 final Event e3c = ( Event ) e3.copy();
2317 final Event e3cc = ( Event ) e3c.copy();
2318 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2322 if ( !e3c.isEqual( e3cc ) ) {
2325 Event e4 = new Event( 1, 2, 3 );
2326 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2329 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2332 final Event e4c = ( Event ) e4.copy();
2334 final Event e4cc = ( Event ) e4c.copy();
2335 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2338 if ( !e4c.isEqual( e4cc ) ) {
2341 final Event e5 = new Event();
2342 if ( !e5.isUnassigned() ) {
2345 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2348 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2351 final Event e6 = new Event( 1, 0, 0 );
2352 if ( !e6.asText().toString().equals( "duplication" ) ) {
2355 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2358 final Event e7 = new Event( 0, 1, 0 );
2359 if ( !e7.asText().toString().equals( "speciation" ) ) {
2362 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2365 final Event e8 = new Event( 0, 0, 1 );
2366 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2369 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2373 catch ( final Exception e ) {
2374 e.printStackTrace( System.out );
2380 private static boolean testDeletionOfExternalNodes() {
2382 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2383 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2384 final PhylogenyWriter w = new PhylogenyWriter();
2385 if ( t0.isEmpty() ) {
2388 if ( t0.getNumberOfExternalNodes() != 1 ) {
2391 t0.deleteSubtree( t0.getNode( "A" ), false );
2392 if ( t0.getNumberOfExternalNodes() != 0 ) {
2395 if ( !t0.isEmpty() ) {
2398 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2399 if ( t1.getNumberOfExternalNodes() != 2 ) {
2402 t1.deleteSubtree( t1.getNode( "A" ), false );
2403 if ( t1.getNumberOfExternalNodes() != 1 ) {
2406 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2409 t1.deleteSubtree( t1.getNode( "B" ), false );
2410 if ( t1.getNumberOfExternalNodes() != 1 ) {
2413 t1.deleteSubtree( t1.getNode( "r" ), false );
2414 if ( !t1.isEmpty() ) {
2417 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2418 if ( t2.getNumberOfExternalNodes() != 3 ) {
2421 t2.deleteSubtree( t2.getNode( "B" ), false );
2422 if ( t2.getNumberOfExternalNodes() != 2 ) {
2425 t2.toNewHampshireX();
2426 PhylogenyNode n = t2.getNode( "A" );
2427 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2430 t2.deleteSubtree( t2.getNode( "A" ), false );
2431 if ( t2.getNumberOfExternalNodes() != 2 ) {
2434 t2.deleteSubtree( t2.getNode( "C" ), true );
2435 if ( t2.getNumberOfExternalNodes() != 1 ) {
2438 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2439 if ( t3.getNumberOfExternalNodes() != 4 ) {
2442 t3.deleteSubtree( t3.getNode( "B" ), true );
2443 if ( t3.getNumberOfExternalNodes() != 3 ) {
2446 n = t3.getNode( "A" );
2447 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2450 n = n.getNextExternalNode();
2451 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2454 t3.deleteSubtree( t3.getNode( "A" ), true );
2455 if ( t3.getNumberOfExternalNodes() != 2 ) {
2458 n = t3.getNode( "C" );
2459 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2462 t3.deleteSubtree( t3.getNode( "C" ), true );
2463 if ( t3.getNumberOfExternalNodes() != 1 ) {
2466 t3.deleteSubtree( t3.getNode( "D" ), true );
2467 if ( t3.getNumberOfExternalNodes() != 0 ) {
2470 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2471 if ( t4.getNumberOfExternalNodes() != 6 ) {
2474 t4.deleteSubtree( t4.getNode( "B2" ), true );
2475 if ( t4.getNumberOfExternalNodes() != 5 ) {
2478 String s = w.toNewHampshire( t4, false, true ).toString();
2479 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2482 t4.deleteSubtree( t4.getNode( "B11" ), true );
2483 if ( t4.getNumberOfExternalNodes() != 4 ) {
2486 t4.deleteSubtree( t4.getNode( "C" ), true );
2487 if ( t4.getNumberOfExternalNodes() != 3 ) {
2490 n = t4.getNode( "A" );
2491 n = n.getNextExternalNode();
2492 if ( !n.getName().equals( "B12" ) ) {
2495 n = n.getNextExternalNode();
2496 if ( !n.getName().equals( "D" ) ) {
2499 s = w.toNewHampshire( t4, false, true ).toString();
2500 if ( !s.equals( "((A,B12),D);" ) ) {
2503 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2504 t5.deleteSubtree( t5.getNode( "A" ), true );
2505 if ( t5.getNumberOfExternalNodes() != 5 ) {
2508 s = w.toNewHampshire( t5, false, true ).toString();
2509 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2512 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2513 t6.deleteSubtree( t6.getNode( "B11" ), true );
2514 if ( t6.getNumberOfExternalNodes() != 5 ) {
2517 s = w.toNewHampshire( t6, false, false ).toString();
2518 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2521 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2522 t7.deleteSubtree( t7.getNode( "B12" ), true );
2523 if ( t7.getNumberOfExternalNodes() != 5 ) {
2526 s = w.toNewHampshire( t7, false, true ).toString();
2527 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2530 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2531 t8.deleteSubtree( t8.getNode( "B2" ), true );
2532 if ( t8.getNumberOfExternalNodes() != 5 ) {
2535 s = w.toNewHampshire( t8, false, false ).toString();
2536 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2539 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2540 t9.deleteSubtree( t9.getNode( "C" ), true );
2541 if ( t9.getNumberOfExternalNodes() != 5 ) {
2544 s = w.toNewHampshire( t9, false, true ).toString();
2545 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2548 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2549 t10.deleteSubtree( t10.getNode( "D" ), true );
2550 if ( t10.getNumberOfExternalNodes() != 5 ) {
2553 s = w.toNewHampshire( t10, false, true ).toString();
2554 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2557 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2558 t11.deleteSubtree( t11.getNode( "A" ), true );
2559 if ( t11.getNumberOfExternalNodes() != 2 ) {
2562 s = w.toNewHampshire( t11, false, true ).toString();
2563 if ( !s.equals( "(B,C);" ) ) {
2566 t11.deleteSubtree( t11.getNode( "C" ), true );
2567 if ( t11.getNumberOfExternalNodes() != 1 ) {
2570 s = w.toNewHampshire( t11, false, false ).toString();
2571 if ( !s.equals( "B;" ) ) {
2574 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2575 t12.deleteSubtree( t12.getNode( "B2" ), true );
2576 if ( t12.getNumberOfExternalNodes() != 8 ) {
2579 s = w.toNewHampshire( t12, false, true ).toString();
2580 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2583 t12.deleteSubtree( t12.getNode( "B3" ), true );
2584 if ( t12.getNumberOfExternalNodes() != 7 ) {
2587 s = w.toNewHampshire( t12, false, true ).toString();
2588 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2591 t12.deleteSubtree( t12.getNode( "C3" ), true );
2592 if ( t12.getNumberOfExternalNodes() != 6 ) {
2595 s = w.toNewHampshire( t12, false, true ).toString();
2596 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2599 t12.deleteSubtree( t12.getNode( "A1" ), true );
2600 if ( t12.getNumberOfExternalNodes() != 5 ) {
2603 s = w.toNewHampshire( t12, false, true ).toString();
2604 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2607 t12.deleteSubtree( t12.getNode( "B1" ), true );
2608 if ( t12.getNumberOfExternalNodes() != 4 ) {
2611 s = w.toNewHampshire( t12, false, true ).toString();
2612 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2615 t12.deleteSubtree( t12.getNode( "A3" ), true );
2616 if ( t12.getNumberOfExternalNodes() != 3 ) {
2619 s = w.toNewHampshire( t12, false, true ).toString();
2620 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2623 t12.deleteSubtree( t12.getNode( "A2" ), true );
2624 if ( t12.getNumberOfExternalNodes() != 2 ) {
2627 s = w.toNewHampshire( t12, false, true ).toString();
2628 if ( !s.equals( "(C1,C2);" ) ) {
2631 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2632 t13.deleteSubtree( t13.getNode( "D" ), true );
2633 if ( t13.getNumberOfExternalNodes() != 4 ) {
2636 s = w.toNewHampshire( t13, false, true ).toString();
2637 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2640 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2641 t14.deleteSubtree( t14.getNode( "E" ), true );
2642 if ( t14.getNumberOfExternalNodes() != 5 ) {
2645 s = w.toNewHampshire( t14, false, true ).toString();
2646 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2649 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2650 t15.deleteSubtree( t15.getNode( "B2" ), true );
2651 if ( t15.getNumberOfExternalNodes() != 11 ) {
2654 t15.deleteSubtree( t15.getNode( "B1" ), true );
2655 if ( t15.getNumberOfExternalNodes() != 10 ) {
2658 t15.deleteSubtree( t15.getNode( "B3" ), true );
2659 if ( t15.getNumberOfExternalNodes() != 9 ) {
2662 t15.deleteSubtree( t15.getNode( "B4" ), true );
2663 if ( t15.getNumberOfExternalNodes() != 8 ) {
2666 t15.deleteSubtree( t15.getNode( "A1" ), true );
2667 if ( t15.getNumberOfExternalNodes() != 7 ) {
2670 t15.deleteSubtree( t15.getNode( "C4" ), true );
2671 if ( t15.getNumberOfExternalNodes() != 6 ) {
2675 catch ( final Exception e ) {
2676 e.printStackTrace( System.out );
2682 private static boolean testDescriptiveStatistics() {
2684 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2685 dss1.addValue( 82 );
2686 dss1.addValue( 78 );
2687 dss1.addValue( 70 );
2688 dss1.addValue( 58 );
2689 dss1.addValue( 42 );
2690 if ( dss1.getN() != 5 ) {
2693 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2696 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2699 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2702 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2705 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2708 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2711 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2714 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2717 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2720 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2723 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2726 dss1.addValue( 123 );
2727 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2730 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2733 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2736 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2737 dss2.addValue( -1.85 );
2738 dss2.addValue( 57.5 );
2739 dss2.addValue( 92.78 );
2740 dss2.addValue( 57.78 );
2741 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2744 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2747 final double[] a = dss2.getDataAsDoubleArray();
2748 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2751 dss2.addValue( -100 );
2752 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2755 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2758 final double[] ds = new double[ 14 ];
2773 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2774 if ( bins.length != 4 ) {
2777 if ( bins[ 0 ] != 2 ) {
2780 if ( bins[ 1 ] != 3 ) {
2783 if ( bins[ 2 ] != 4 ) {
2786 if ( bins[ 3 ] != 5 ) {
2789 final double[] ds1 = new double[ 9 ];
2799 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2800 if ( bins1.length != 4 ) {
2803 if ( bins1[ 0 ] != 2 ) {
2806 if ( bins1[ 1 ] != 3 ) {
2809 if ( bins1[ 2 ] != 0 ) {
2812 if ( bins1[ 3 ] != 4 ) {
2815 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2816 if ( bins1_1.length != 3 ) {
2819 if ( bins1_1[ 0 ] != 3 ) {
2822 if ( bins1_1[ 1 ] != 2 ) {
2825 if ( bins1_1[ 2 ] != 4 ) {
2828 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2829 if ( bins1_2.length != 3 ) {
2832 if ( bins1_2[ 0 ] != 2 ) {
2835 if ( bins1_2[ 1 ] != 2 ) {
2838 if ( bins1_2[ 2 ] != 2 ) {
2841 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2855 dss3.addValue( 10 );
2856 dss3.addValue( 10 );
2857 dss3.addValue( 10 );
2858 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2859 histo.toStringBuffer( 10, '=', 40, 5 );
2860 histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
2862 catch ( final Exception e ) {
2863 e.printStackTrace( System.out );
2869 private static boolean testDir( final String file ) {
2871 final File f = new File( file );
2872 if ( !f.exists() ) {
2875 if ( !f.isDirectory() ) {
2878 if ( !f.canRead() ) {
2882 catch ( final Exception e ) {
2888 private static boolean testExternalNodeRelatedMethods() {
2890 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2891 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2892 PhylogenyNode n = t1.getNode( "A" );
2893 n = n.getNextExternalNode();
2894 if ( !n.getName().equals( "B" ) ) {
2897 n = n.getNextExternalNode();
2898 if ( !n.getName().equals( "C" ) ) {
2901 n = n.getNextExternalNode();
2902 if ( !n.getName().equals( "D" ) ) {
2905 n = t1.getNode( "B" );
2906 while ( !n.isLastExternalNode() ) {
2907 n = n.getNextExternalNode();
2909 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2910 n = t2.getNode( "A" );
2911 n = n.getNextExternalNode();
2912 if ( !n.getName().equals( "B" ) ) {
2915 n = n.getNextExternalNode();
2916 if ( !n.getName().equals( "C" ) ) {
2919 n = n.getNextExternalNode();
2920 if ( !n.getName().equals( "D" ) ) {
2923 n = t2.getNode( "B" );
2924 while ( !n.isLastExternalNode() ) {
2925 n = n.getNextExternalNode();
2927 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2928 n = t3.getNode( "A" );
2929 n = n.getNextExternalNode();
2930 if ( !n.getName().equals( "B" ) ) {
2933 n = n.getNextExternalNode();
2934 if ( !n.getName().equals( "C" ) ) {
2937 n = n.getNextExternalNode();
2938 if ( !n.getName().equals( "D" ) ) {
2941 n = n.getNextExternalNode();
2942 if ( !n.getName().equals( "E" ) ) {
2945 n = n.getNextExternalNode();
2946 if ( !n.getName().equals( "F" ) ) {
2949 n = n.getNextExternalNode();
2950 if ( !n.getName().equals( "G" ) ) {
2953 n = n.getNextExternalNode();
2954 if ( !n.getName().equals( "H" ) ) {
2957 n = t3.getNode( "B" );
2958 while ( !n.isLastExternalNode() ) {
2959 n = n.getNextExternalNode();
2961 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2962 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2963 final PhylogenyNode node = iter.next();
2965 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2966 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2967 final PhylogenyNode node = iter.next();
2969 final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
2970 final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
2971 if ( !iter.next().getName().equals( "A" ) ) {
2974 if ( !iter.next().getName().equals( "B" ) ) {
2977 if ( !iter.next().getName().equals( "C" ) ) {
2980 if ( !iter.next().getName().equals( "D" ) ) {
2983 if ( !iter.next().getName().equals( "E" ) ) {
2986 if ( !iter.next().getName().equals( "F" ) ) {
2989 if ( iter.hasNext() ) {
2993 catch ( final Exception e ) {
2994 e.printStackTrace( System.out );
3000 private static boolean testGeneralTable() {
3002 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
3003 t0.setValue( 3, 2, "23" );
3004 t0.setValue( 10, 1, "error" );
3005 t0.setValue( 10, 1, "110" );
3006 t0.setValue( 9, 1, "19" );
3007 t0.setValue( 1, 10, "101" );
3008 t0.setValue( 10, 10, "1010" );
3009 t0.setValue( 100, 10, "10100" );
3010 t0.setValue( 0, 0, "00" );
3011 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
3014 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
3017 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
3020 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
3023 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
3026 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
3029 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3032 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3035 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3038 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3039 t1.setValue( "3", "2", "23" );
3040 t1.setValue( "10", "1", "error" );
3041 t1.setValue( "10", "1", "110" );
3042 t1.setValue( "9", "1", "19" );
3043 t1.setValue( "1", "10", "101" );
3044 t1.setValue( "10", "10", "1010" );
3045 t1.setValue( "100", "10", "10100" );
3046 t1.setValue( "0", "0", "00" );
3047 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3048 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3051 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3054 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3057 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3060 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3063 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3066 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3069 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3072 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3075 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3079 catch ( final Exception e ) {
3080 e.printStackTrace( System.out );
3086 private static boolean testGetDistance() {
3088 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3089 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",
3090 new NHXParser() )[ 0 ];
3091 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3094 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3097 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3100 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3103 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3106 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3109 if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3112 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3115 if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3118 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3121 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3124 if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3127 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3130 if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3133 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3136 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3139 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3142 if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3145 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3148 if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3151 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3154 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3157 if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3160 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3163 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3166 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3169 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3172 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3175 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3178 if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3181 if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3184 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",
3185 new NHXParser() )[ 0 ];
3186 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3189 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3192 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3195 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3198 if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3201 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3204 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3207 if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3210 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3213 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3216 if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3220 catch ( final Exception e ) {
3221 e.printStackTrace( System.out );
3227 private static boolean testGetLCA() {
3229 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3230 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3231 new NHXParser() )[ 0 ];
3232 final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3233 if ( !A.getName().equals( "A" ) ) {
3236 final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3237 if ( !gh.getName().equals( "gh" ) ) {
3240 final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3241 if ( !ab.getName().equals( "ab" ) ) {
3244 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3245 if ( !ab2.getName().equals( "ab" ) ) {
3248 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3249 if ( !gh2.getName().equals( "gh" ) ) {
3252 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3253 if ( !gh3.getName().equals( "gh" ) ) {
3256 final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3257 if ( !abc.getName().equals( "abc" ) ) {
3260 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3261 if ( !abc2.getName().equals( "abc" ) ) {
3264 final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3265 if ( !abcd.getName().equals( "abcd" ) ) {
3268 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3269 if ( !abcd2.getName().equals( "abcd" ) ) {
3272 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3273 if ( !abcdef.getName().equals( "abcdef" ) ) {
3276 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3277 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3280 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3281 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3284 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3285 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3288 final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3289 if ( !abcde.getName().equals( "abcde" ) ) {
3292 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3293 if ( !abcde2.getName().equals( "abcde" ) ) {
3296 final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3297 if ( !r.getName().equals( "abcdefgh" ) ) {
3300 final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3301 if ( !r2.getName().equals( "abcdefgh" ) ) {
3304 final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3305 if ( !r3.getName().equals( "abcdefgh" ) ) {
3308 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3309 if ( !abcde3.getName().equals( "abcde" ) ) {
3312 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3313 if ( !abcde4.getName().equals( "abcde" ) ) {
3316 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3317 if ( !ab3.getName().equals( "ab" ) ) {
3320 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3321 if ( !ab4.getName().equals( "ab" ) ) {
3324 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3325 final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3326 if ( !cd.getName().equals( "cd" ) ) {
3329 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3330 if ( !cd2.getName().equals( "cd" ) ) {
3333 final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3334 if ( !cde.getName().equals( "cde" ) ) {
3337 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3338 if ( !cde2.getName().equals( "cde" ) ) {
3341 final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3342 if ( !cdef.getName().equals( "cdef" ) ) {
3345 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3346 if ( !cdef2.getName().equals( "cdef" ) ) {
3349 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3350 if ( !cdef3.getName().equals( "cdef" ) ) {
3353 final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3354 if ( !rt.getName().equals( "r" ) ) {
3357 final Phylogeny p3 = factory
3358 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3359 new NHXParser() )[ 0 ];
3360 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3361 if ( !bc_3.getName().equals( "bc" ) ) {
3364 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3365 if ( !ac_3.getName().equals( "abc" ) ) {
3368 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3369 if ( !ad_3.getName().equals( "abcde" ) ) {
3372 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3373 if ( !af_3.getName().equals( "abcdef" ) ) {
3376 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3377 if ( !ag_3.getName().equals( "" ) ) {
3380 if ( !ag_3.isRoot() ) {
3383 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3384 if ( !al_3.getName().equals( "" ) ) {
3387 if ( !al_3.isRoot() ) {
3390 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3391 if ( !kl_3.getName().equals( "" ) ) {
3394 if ( !kl_3.isRoot() ) {
3397 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3398 if ( !fl_3.getName().equals( "" ) ) {
3401 if ( !fl_3.isRoot() ) {
3404 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3405 if ( !gk_3.getName().equals( "ghijk" ) ) {
3408 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3409 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3410 if ( !r_4.getName().equals( "r" ) ) {
3413 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3414 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3415 if ( !r_5.getName().equals( "root" ) ) {
3418 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3419 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3420 if ( !r_6.getName().equals( "rot" ) ) {
3423 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3424 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3425 if ( !r_7.getName().equals( "rott" ) ) {
3429 catch ( final Exception e ) {
3430 e.printStackTrace( System.out );
3436 private static boolean testGetLCA2() {
3438 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3439 final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
3440 PhylogenyMethods.preOrderReId( p_a );
3441 final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
3442 p_a.getNode( "a" ) );
3443 if ( !p_a_1.getName().equals( "a" ) ) {
3446 final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
3447 PhylogenyMethods.preOrderReId( p_b );
3448 final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
3449 p_b.getNode( "a" ) );
3450 if ( !p_b_1.getName().equals( "b" ) ) {
3453 final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
3454 p_b.getNode( "b" ) );
3455 if ( !p_b_2.getName().equals( "b" ) ) {
3458 final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
3459 PhylogenyMethods.preOrderReId( p_c );
3460 final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
3461 p_c.getNode( "a" ) );
3462 if ( !p_c_1.getName().equals( "b" ) ) {
3465 final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3466 p_c.getNode( "c" ) );
3467 if ( !p_c_2.getName().equals( "c" ) ) {
3468 System.out.println( p_c_2.getName() );
3472 final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
3473 p_c.getNode( "b" ) );
3474 if ( !p_c_3.getName().equals( "b" ) ) {
3477 final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
3478 p_c.getNode( "a" ) );
3479 if ( !p_c_4.getName().equals( "c" ) ) {
3482 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3483 new NHXParser() )[ 0 ];
3484 PhylogenyMethods.preOrderReId( p1 );
3485 final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3486 p1.getNode( "A" ) );
3487 if ( !A.getName().equals( "A" ) ) {
3490 final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
3491 p1.getNode( "gh" ) );
3492 if ( !gh.getName().equals( "gh" ) ) {
3495 final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3496 p1.getNode( "B" ) );
3497 if ( !ab.getName().equals( "ab" ) ) {
3500 final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3501 p1.getNode( "A" ) );
3502 if ( !ab2.getName().equals( "ab" ) ) {
3505 final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3506 p1.getNode( "G" ) );
3507 if ( !gh2.getName().equals( "gh" ) ) {
3510 final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
3511 p1.getNode( "H" ) );
3512 if ( !gh3.getName().equals( "gh" ) ) {
3515 final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
3516 p1.getNode( "A" ) );
3517 if ( !abc.getName().equals( "abc" ) ) {
3520 final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3521 p1.getNode( "C" ) );
3522 if ( !abc2.getName().equals( "abc" ) ) {
3525 final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3526 p1.getNode( "D" ) );
3527 if ( !abcd.getName().equals( "abcd" ) ) {
3530 final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
3531 p1.getNode( "A" ) );
3532 if ( !abcd2.getName().equals( "abcd" ) ) {
3535 final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3536 p1.getNode( "F" ) );
3537 if ( !abcdef.getName().equals( "abcdef" ) ) {
3540 final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3541 p1.getNode( "A" ) );
3542 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3545 final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3546 p1.getNode( "F" ) );
3547 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3550 final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
3551 p1.getNode( "ab" ) );
3552 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3555 final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3556 p1.getNode( "E" ) );
3557 if ( !abcde.getName().equals( "abcde" ) ) {
3560 final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3561 p1.getNode( "A" ) );
3562 if ( !abcde2.getName().equals( "abcde" ) ) {
3565 final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
3566 p1.getNode( "abcdefgh" ) );
3567 if ( !r.getName().equals( "abcdefgh" ) ) {
3570 final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
3571 p1.getNode( "H" ) );
3572 if ( !r2.getName().equals( "abcdefgh" ) ) {
3575 final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
3576 p1.getNode( "A" ) );
3577 if ( !r3.getName().equals( "abcdefgh" ) ) {
3580 final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
3581 p1.getNode( "abcde" ) );
3582 if ( !abcde3.getName().equals( "abcde" ) ) {
3585 final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
3586 p1.getNode( "E" ) );
3587 if ( !abcde4.getName().equals( "abcde" ) ) {
3590 final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
3591 p1.getNode( "B" ) );
3592 if ( !ab3.getName().equals( "ab" ) ) {
3595 final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
3596 p1.getNode( "ab" ) );
3597 if ( !ab4.getName().equals( "ab" ) ) {
3600 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3601 PhylogenyMethods.preOrderReId( p2 );
3602 final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3603 p2.getNode( "d" ) );
3604 if ( !cd.getName().equals( "cd" ) ) {
3607 final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3608 p2.getNode( "c" ) );
3609 if ( !cd2.getName().equals( "cd" ) ) {
3612 final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3613 p2.getNode( "e" ) );
3614 if ( !cde.getName().equals( "cde" ) ) {
3617 final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
3618 p2.getNode( "c" ) );
3619 if ( !cde2.getName().equals( "cde" ) ) {
3622 final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3623 p2.getNode( "f" ) );
3624 if ( !cdef.getName().equals( "cdef" ) ) {
3627 final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
3628 p2.getNode( "f" ) );
3629 if ( !cdef2.getName().equals( "cdef" ) ) {
3632 final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
3633 p2.getNode( "d" ) );
3634 if ( !cdef3.getName().equals( "cdef" ) ) {
3637 final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
3638 p2.getNode( "a" ) );
3639 if ( !rt.getName().equals( "r" ) ) {
3642 final Phylogeny p3 = factory
3643 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3644 new NHXParser() )[ 0 ];
3645 PhylogenyMethods.preOrderReId( p3 );
3646 final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
3647 p3.getNode( "c" ) );
3648 if ( !bc_3.getName().equals( "bc" ) ) {
3651 final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3652 p3.getNode( "c" ) );
3653 if ( !ac_3.getName().equals( "abc" ) ) {
3656 final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3657 p3.getNode( "d" ) );
3658 if ( !ad_3.getName().equals( "abcde" ) ) {
3661 final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3662 p3.getNode( "f" ) );
3663 if ( !af_3.getName().equals( "abcdef" ) ) {
3666 final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3667 p3.getNode( "g" ) );
3668 if ( !ag_3.getName().equals( "" ) ) {
3671 if ( !ag_3.isRoot() ) {
3674 final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
3675 p3.getNode( "l" ) );
3676 if ( !al_3.getName().equals( "" ) ) {
3679 if ( !al_3.isRoot() ) {
3682 final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
3683 p3.getNode( "l" ) );
3684 if ( !kl_3.getName().equals( "" ) ) {
3687 if ( !kl_3.isRoot() ) {
3690 final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
3691 p3.getNode( "l" ) );
3692 if ( !fl_3.getName().equals( "" ) ) {
3695 if ( !fl_3.isRoot() ) {
3698 final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
3699 p3.getNode( "k" ) );
3700 if ( !gk_3.getName().equals( "ghijk" ) ) {
3703 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3704 PhylogenyMethods.preOrderReId( p4 );
3705 final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
3706 p4.getNode( "c" ) );
3707 if ( !r_4.getName().equals( "r" ) ) {
3710 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3711 PhylogenyMethods.preOrderReId( p5 );
3712 final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
3713 p5.getNode( "c" ) );
3714 if ( !r_5.getName().equals( "root" ) ) {
3717 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3718 PhylogenyMethods.preOrderReId( p6 );
3719 final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
3720 p6.getNode( "a" ) );
3721 if ( !r_6.getName().equals( "rot" ) ) {
3724 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3725 PhylogenyMethods.preOrderReId( p7 );
3726 final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
3727 p7.getNode( "e" ) );
3728 if ( !r_7.getName().equals( "rott" ) ) {
3731 final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3732 p7.getNode( "a" ) );
3733 if ( !r_71.getName().equals( "rott" ) ) {
3736 final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3737 p7.getNode( "rott" ) );
3738 if ( !r_72.getName().equals( "rott" ) ) {
3741 final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3742 p7.getNode( "a" ) );
3743 if ( !r_73.getName().equals( "rott" ) ) {
3746 final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
3747 p7.getNode( "rott" ) );
3748 if ( !r_74.getName().equals( "rott" ) ) {
3751 final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
3752 p7.getNode( "e" ) );
3753 if ( !r_75.getName().equals( "e" ) ) {
3757 catch ( final Exception e ) {
3758 e.printStackTrace( System.out );
3764 private static boolean testHmmscanOutputParser() {
3765 final String test_dir = Test.PATH_TO_TEST_DATA;
3767 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3768 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3770 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3771 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3772 final List<Protein> proteins = parser2.parse();
3773 if ( parser2.getProteinsEncountered() != 4 ) {
3776 if ( proteins.size() != 4 ) {
3779 if ( parser2.getDomainsEncountered() != 69 ) {
3782 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3785 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3788 final Protein p1 = proteins.get( 0 );
3789 if ( p1.getNumberOfProteinDomains() != 15 ) {
3792 if ( p1.getLength() != 850 ) {
3795 final Protein p2 = proteins.get( 1 );
3796 if ( p2.getNumberOfProteinDomains() != 51 ) {
3799 if ( p2.getLength() != 1291 ) {
3802 final Protein p3 = proteins.get( 2 );
3803 if ( p3.getNumberOfProteinDomains() != 2 ) {
3806 final Protein p4 = proteins.get( 3 );
3807 if ( p4.getNumberOfProteinDomains() != 1 ) {
3810 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3813 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3816 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3819 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3822 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3825 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3828 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3831 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3834 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3838 catch ( final Exception e ) {
3839 e.printStackTrace( System.out );
3845 private static boolean testLastExternalNodeMethods() {
3847 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3848 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3849 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3850 final PhylogenyNode n1 = t0.getNode( "A" );
3851 if ( n1.isLastExternalNode() ) {
3854 final PhylogenyNode n2 = t0.getNode( "B" );
3855 if ( n2.isLastExternalNode() ) {
3858 final PhylogenyNode n3 = t0.getNode( "C" );
3859 if ( n3.isLastExternalNode() ) {
3862 final PhylogenyNode n4 = t0.getNode( "D" );
3863 if ( !n4.isLastExternalNode() ) {
3867 catch ( final Exception e ) {
3868 e.printStackTrace( System.out );
3874 private static boolean testLevelOrderIterator() {
3876 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3877 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3878 PhylogenyNodeIterator it0;
3879 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3882 for( it0.reset(); it0.hasNext(); ) {
3885 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3886 if ( !it.next().getName().equals( "r" ) ) {
3889 if ( !it.next().getName().equals( "ab" ) ) {
3892 if ( !it.next().getName().equals( "cd" ) ) {
3895 if ( !it.next().getName().equals( "A" ) ) {
3898 if ( !it.next().getName().equals( "B" ) ) {
3901 if ( !it.next().getName().equals( "C" ) ) {
3904 if ( !it.next().getName().equals( "D" ) ) {
3907 if ( it.hasNext() ) {
3910 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",
3911 new NHXParser() )[ 0 ];
3912 PhylogenyNodeIterator it2;
3913 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3916 for( it2.reset(); it2.hasNext(); ) {
3919 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3920 if ( !it3.next().getName().equals( "r" ) ) {
3923 if ( !it3.next().getName().equals( "abc" ) ) {
3926 if ( !it3.next().getName().equals( "defg" ) ) {
3929 if ( !it3.next().getName().equals( "A" ) ) {
3932 if ( !it3.next().getName().equals( "B" ) ) {
3935 if ( !it3.next().getName().equals( "C" ) ) {
3938 if ( !it3.next().getName().equals( "D" ) ) {
3941 if ( !it3.next().getName().equals( "E" ) ) {
3944 if ( !it3.next().getName().equals( "F" ) ) {
3947 if ( !it3.next().getName().equals( "G" ) ) {
3950 if ( !it3.next().getName().equals( "1" ) ) {
3953 if ( !it3.next().getName().equals( "2" ) ) {
3956 if ( !it3.next().getName().equals( "3" ) ) {
3959 if ( !it3.next().getName().equals( "4" ) ) {
3962 if ( !it3.next().getName().equals( "5" ) ) {
3965 if ( !it3.next().getName().equals( "6" ) ) {
3968 if ( !it3.next().getName().equals( "f1" ) ) {
3971 if ( !it3.next().getName().equals( "f2" ) ) {
3974 if ( !it3.next().getName().equals( "f3" ) ) {
3977 if ( !it3.next().getName().equals( "a" ) ) {
3980 if ( !it3.next().getName().equals( "b" ) ) {
3983 if ( !it3.next().getName().equals( "f21" ) ) {
3986 if ( !it3.next().getName().equals( "X" ) ) {
3989 if ( !it3.next().getName().equals( "Y" ) ) {
3992 if ( !it3.next().getName().equals( "Z" ) ) {
3995 if ( it3.hasNext() ) {
3998 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3999 PhylogenyNodeIterator it4;
4000 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
4003 for( it4.reset(); it4.hasNext(); ) {
4006 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
4007 if ( !it5.next().getName().equals( "r" ) ) {
4010 if ( !it5.next().getName().equals( "A" ) ) {
4013 if ( !it5.next().getName().equals( "B" ) ) {
4016 if ( !it5.next().getName().equals( "C" ) ) {
4019 if ( !it5.next().getName().equals( "D" ) ) {
4022 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
4023 PhylogenyNodeIterator it6;
4024 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
4027 for( it6.reset(); it6.hasNext(); ) {
4030 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
4031 if ( !it7.next().getName().equals( "A" ) ) {
4034 if ( it.hasNext() ) {
4038 catch ( final Exception e ) {
4039 e.printStackTrace( System.out );
4045 private static boolean testNodeRemoval() {
4047 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4048 final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
4049 PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
4050 if ( !t0.toNewHampshire().equals( "(a);" ) ) {
4053 final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
4054 PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
4055 if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
4058 final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
4059 PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
4060 if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
4064 catch ( final Exception e ) {
4065 e.printStackTrace( System.out );
4071 private static boolean testMidpointrooting() {
4073 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4074 final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
4075 PhylogenyMethods.midpointRoot( t0 );
4076 if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
4079 if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
4082 if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
4086 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",
4087 new NHXParser() )[ 0 ];
4088 if ( !t1.isRooted() ) {
4091 PhylogenyMethods.midpointRoot( t1 );
4092 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4095 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4098 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4101 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4104 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4107 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4110 t1.reRoot( t1.getNode( "A" ) );
4111 PhylogenyMethods.midpointRoot( t1 );
4112 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
4115 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
4118 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
4121 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
4124 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
4128 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
4132 catch ( final Exception e ) {
4133 e.printStackTrace( System.out );
4139 private static boolean testNexusCharactersParsing() {
4141 final NexusCharactersParser parser = new NexusCharactersParser();
4142 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
4144 String[] labels = parser.getCharStateLabels();
4145 if ( labels.length != 7 ) {
4148 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4151 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4154 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4157 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4160 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4163 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4166 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4169 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4171 labels = parser.getCharStateLabels();
4172 if ( labels.length != 7 ) {
4175 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4178 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4181 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4184 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4187 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4190 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4193 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4197 catch ( final Exception e ) {
4198 e.printStackTrace( System.out );
4204 private static boolean testNexusMatrixParsing() {
4206 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
4207 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
4209 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
4210 if ( m.getNumberOfCharacters() != 9 ) {
4213 if ( m.getNumberOfIdentifiers() != 5 ) {
4216 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
4219 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
4222 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
4225 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
4228 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
4231 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
4234 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
4237 // if ( labels.length != 7 ) {
4240 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4243 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4246 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4249 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4252 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4255 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4258 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4261 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
4263 // labels = parser.getCharStateLabels();
4264 // if ( labels.length != 7 ) {
4267 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
4270 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
4273 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
4276 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
4279 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
4282 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
4285 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
4289 catch ( final Exception e ) {
4290 e.printStackTrace( System.out );
4296 private static boolean testNexusTreeParsing() {
4298 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4299 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4300 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
4301 if ( phylogenies.length != 1 ) {
4304 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
4307 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4311 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
4312 if ( phylogenies.length != 1 ) {
4315 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4318 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
4322 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
4323 if ( phylogenies.length != 1 ) {
4326 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4329 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
4332 if ( phylogenies[ 0 ].isRooted() ) {
4336 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
4337 if ( phylogenies.length != 18 ) {
4340 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
4343 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
4346 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
4349 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
4352 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4355 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
4358 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
4361 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
4364 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
4367 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
4370 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
4373 if ( phylogenies[ 8 ].isRooted() ) {
4376 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
4379 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
4382 if ( !phylogenies[ 9 ].isRooted() ) {
4385 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
4388 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
4391 if ( !phylogenies[ 10 ].isRooted() ) {
4394 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
4397 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
4400 if ( phylogenies[ 11 ].isRooted() ) {
4403 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4406 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4409 if ( !phylogenies[ 12 ].isRooted() ) {
4412 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4415 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4418 if ( !phylogenies[ 13 ].isRooted() ) {
4421 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4424 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4427 if ( !phylogenies[ 14 ].isRooted() ) {
4430 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4433 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4436 if ( phylogenies[ 15 ].isRooted() ) {
4439 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4442 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4445 if ( !phylogenies[ 16 ].isRooted() ) {
4448 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4451 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4454 if ( phylogenies[ 17 ].isRooted() ) {
4457 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4461 catch ( final Exception e ) {
4462 e.printStackTrace( System.out );
4468 private static boolean testNexusTreeParsingIterating() {
4470 final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
4471 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
4472 if ( !p.hasNext() ) {
4475 Phylogeny phy = p.next();
4476 if ( phy == null ) {
4479 if ( phy.getNumberOfExternalNodes() != 25 ) {
4482 if ( !phy.getName().equals( "" ) ) {
4485 if ( p.hasNext() ) {
4489 if ( phy != null ) {
4494 if ( !p.hasNext() ) {
4498 if ( phy == null ) {
4501 if ( phy.getNumberOfExternalNodes() != 25 ) {
4504 if ( !phy.getName().equals( "" ) ) {
4507 if ( p.hasNext() ) {
4511 if ( phy != null ) {
4515 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
4516 if ( !p.hasNext() ) {
4520 if ( phy == null ) {
4523 if ( phy.getNumberOfExternalNodes() != 10 ) {
4526 if ( !phy.getName().equals( "name" ) ) {
4529 if ( p.hasNext() ) {
4533 if ( phy != null ) {
4538 if ( !p.hasNext() ) {
4542 if ( phy == null ) {
4545 if ( phy.getNumberOfExternalNodes() != 10 ) {
4548 if ( !phy.getName().equals( "name" ) ) {
4551 if ( p.hasNext() ) {
4555 if ( phy != null ) {
4559 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
4560 if ( !p.hasNext() ) {
4564 if ( phy == null ) {
4567 if ( phy.getNumberOfExternalNodes() != 3 ) {
4570 if ( !phy.getName().equals( "" ) ) {
4573 if ( phy.isRooted() ) {
4576 if ( p.hasNext() ) {
4580 if ( phy != null ) {
4585 if ( !p.hasNext() ) {
4589 if ( phy == null ) {
4592 if ( phy.getNumberOfExternalNodes() != 3 ) {
4595 if ( !phy.getName().equals( "" ) ) {
4598 if ( p.hasNext() ) {
4602 if ( phy != null ) {
4606 p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
4607 // if ( phylogenies.length != 18 ) {
4611 if ( !p.hasNext() ) {
4615 if ( phy == null ) {
4618 if ( phy.getNumberOfExternalNodes() != 10 ) {
4621 if ( !phy.getName().equals( "tree 0" ) ) {
4625 if ( !p.hasNext() ) {
4629 if ( phy == null ) {
4632 if ( phy.getNumberOfExternalNodes() != 10 ) {
4635 if ( !phy.getName().equals( "tree 1" ) ) {
4639 if ( !p.hasNext() ) {
4643 if ( phy == null ) {
4646 if ( phy.getNumberOfExternalNodes() != 3 ) {
4649 if ( !phy.getName().equals( "" ) ) {
4652 if ( phy.isRooted() ) {
4656 if ( !p.hasNext() ) {
4660 if ( phy == null ) {
4663 if ( phy.getNumberOfExternalNodes() != 4 ) {
4666 if ( !phy.getName().equals( "" ) ) {
4669 if ( !phy.isRooted() ) {
4673 if ( !p.hasNext() ) {
4677 if ( phy == null ) {
4680 if ( phy.getNumberOfExternalNodes() != 5 ) {
4681 System.out.println( phy.getNumberOfExternalNodes() );
4684 if ( !phy.getName().equals( "" ) ) {
4687 if ( !phy.isRooted() ) {
4691 if ( !p.hasNext() ) {
4695 if ( phy == null ) {
4698 if ( phy.getNumberOfExternalNodes() != 3 ) {
4701 if ( !phy.getName().equals( "" ) ) {
4704 if ( phy.isRooted() ) {
4708 if ( !p.hasNext() ) {
4712 if ( phy == null ) {
4715 if ( phy.getNumberOfExternalNodes() != 2 ) {
4718 if ( !phy.getName().equals( "" ) ) {
4721 if ( !phy.isRooted() ) {
4725 if ( !p.hasNext() ) {
4729 if ( phy.getNumberOfExternalNodes() != 3 ) {
4732 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4735 if ( !phy.isRooted() ) {
4739 if ( !p.hasNext() ) {
4743 if ( phy.getNumberOfExternalNodes() != 3 ) {
4746 if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
4749 if ( !phy.getName().equals( "tree 8" ) ) {
4753 if ( !p.hasNext() ) {
4757 if ( phy.getNumberOfExternalNodes() != 3 ) {
4760 if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
4763 if ( !phy.getName().equals( "tree 9" ) ) {
4767 if ( !p.hasNext() ) {
4771 if ( phy.getNumberOfExternalNodes() != 3 ) {
4774 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4777 if ( !phy.getName().equals( "tree 10" ) ) {
4780 if ( !phy.isRooted() ) {
4784 if ( !p.hasNext() ) {
4788 if ( phy.getNumberOfExternalNodes() != 3 ) {
4791 if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
4794 if ( !phy.getName().equals( "tree 11" ) ) {
4797 if ( phy.isRooted() ) {
4801 if ( !p.hasNext() ) {
4805 if ( phy.getNumberOfExternalNodes() != 3 ) {
4808 if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
4811 if ( !phy.getName().equals( "tree 12" ) ) {
4814 if ( !phy.isRooted() ) {
4818 if ( !p.hasNext() ) {
4822 if ( phy.getNumberOfExternalNodes() != 3 ) {
4825 if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
4828 if ( !phy.getName().equals( "tree 13" ) ) {
4831 if ( !phy.isRooted() ) {
4835 if ( !p.hasNext() ) {
4839 if ( phy.getNumberOfExternalNodes() != 10 ) {
4840 System.out.println( phy.getNumberOfExternalNodes() );
4845 .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;" ) ) {
4846 System.out.println( phy.toNewHampshire() );
4849 if ( !phy.getName().equals( "tree 14" ) ) {
4852 if ( !phy.isRooted() ) {
4856 if ( !p.hasNext() ) {
4860 if ( phy.getNumberOfExternalNodes() != 10 ) {
4861 System.out.println( phy.getNumberOfExternalNodes() );
4866 .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;" ) ) {
4867 System.out.println( phy.toNewHampshire() );
4870 if ( !phy.getName().equals( "tree 15" ) ) {
4873 if ( phy.isRooted() ) {
4877 if ( !p.hasNext() ) {
4881 if ( phy.getNumberOfExternalNodes() != 10 ) {
4882 System.out.println( phy.getNumberOfExternalNodes() );
4887 .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;" ) ) {
4888 System.out.println( phy.toNewHampshire() );
4891 if ( !phy.getName().equals( "tree 16" ) ) {
4894 if ( !phy.isRooted() ) {
4898 if ( !p.hasNext() ) {
4902 if ( phy.getNumberOfExternalNodes() != 10 ) {
4903 System.out.println( phy.getNumberOfExternalNodes() );
4908 .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;" ) ) {
4909 System.out.println( phy.toNewHampshire() );
4912 if ( !phy.getName().equals( "tree 17" ) ) {
4915 if ( phy.isRooted() ) {
4919 if ( p.hasNext() ) {
4923 if ( phy != null ) {
4928 if ( !p.hasNext() ) {
4932 if ( phy == null ) {
4935 if ( phy.getNumberOfExternalNodes() != 10 ) {
4938 if ( !phy.getName().equals( "tree 0" ) ) {
4942 if ( !p.hasNext() ) {
4946 if ( phy == null ) {
4949 if ( phy.getNumberOfExternalNodes() != 10 ) {
4952 if ( !phy.getName().equals( "tree 1" ) ) {
4956 if ( !p.hasNext() ) {
4960 if ( phy == null ) {
4963 if ( phy.getNumberOfExternalNodes() != 3 ) {
4966 if ( !phy.getName().equals( "" ) ) {
4969 if ( phy.isRooted() ) {
4973 if ( !p.hasNext() ) {
4977 if ( phy == null ) {
4980 if ( phy.getNumberOfExternalNodes() != 4 ) {
4983 if ( !phy.getName().equals( "" ) ) {
4986 if ( !phy.isRooted() ) {
4990 if ( !p.hasNext() ) {
4994 if ( phy == null ) {
4997 if ( phy.getNumberOfExternalNodes() != 5 ) {
4998 System.out.println( phy.getNumberOfExternalNodes() );
5001 if ( !phy.getName().equals( "" ) ) {
5004 if ( !phy.isRooted() ) {
5008 if ( !p.hasNext() ) {
5012 if ( phy == null ) {
5015 if ( phy.getNumberOfExternalNodes() != 3 ) {
5018 if ( !phy.getName().equals( "" ) ) {
5021 if ( phy.isRooted() ) {
5025 catch ( final Exception e ) {
5026 e.printStackTrace( System.out );
5032 private static boolean testNexusTreeParsingTranslating() {
5034 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5035 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
5036 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
5037 if ( phylogenies.length != 1 ) {
5040 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5043 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5046 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5049 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5052 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5053 .equals( "Aranaeus" ) ) {
5057 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
5058 if ( phylogenies.length != 3 ) {
5061 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5064 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5067 if ( phylogenies[ 0 ].isRooted() ) {
5070 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5073 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5076 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5077 .equals( "Aranaeus" ) ) {
5080 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
5083 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
5086 if ( phylogenies[ 1 ].isRooted() ) {
5089 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5092 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5095 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5096 .equals( "Aranaeus" ) ) {
5099 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
5102 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
5105 if ( !phylogenies[ 2 ].isRooted() ) {
5108 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5111 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5114 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5115 .equals( "Aranaeus" ) ) {
5119 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
5120 if ( phylogenies.length != 3 ) {
5123 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
5126 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
5129 if ( phylogenies[ 0 ].isRooted() ) {
5132 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5135 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5138 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5139 .equals( "Aranaeus" ) ) {
5142 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
5145 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
5148 if ( phylogenies[ 1 ].isRooted() ) {
5151 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5154 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5157 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5158 .equals( "Aranaeus" ) ) {
5161 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
5164 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
5167 if ( !phylogenies[ 2 ].isRooted() ) {
5170 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
5173 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
5176 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
5177 .equals( "Aranaeus" ) ) {
5181 catch ( final Exception e ) {
5182 e.printStackTrace( System.out );
5188 private static boolean testNHParsing() {
5190 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5191 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
5192 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
5195 final NHXParser nhxp = new NHXParser();
5196 nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
5197 nhxp.setReplaceUnderscores( true );
5198 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
5199 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
5202 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
5205 final Phylogeny p1b = factory
5206 .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 ",
5207 new NHXParser() )[ 0 ];
5208 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
5211 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
5214 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
5215 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
5216 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
5217 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
5218 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
5219 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
5220 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
5221 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
5222 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
5223 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
5224 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
5225 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
5226 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
5228 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
5231 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
5234 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
5237 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
5240 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
5241 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
5242 final String p16_S = "((A,B),C)";
5243 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
5244 if ( p16.length != 1 ) {
5247 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
5250 final String p17_S = "(C,(A,B))";
5251 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
5252 if ( p17.length != 1 ) {
5255 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
5258 final String p18_S = "((A,B),(C,D))";
5259 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
5260 if ( p18.length != 1 ) {
5263 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
5266 final String p19_S = "(((A,B),C),D)";
5267 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
5268 if ( p19.length != 1 ) {
5271 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
5274 final String p20_S = "(A,(B,(C,D)))";
5275 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
5276 if ( p20.length != 1 ) {
5279 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
5282 final String p21_S = "(A,(B,(C,(D,E))))";
5283 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
5284 if ( p21.length != 1 ) {
5287 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
5290 final String p22_S = "((((A,B),C),D),E)";
5291 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
5292 if ( p22.length != 1 ) {
5295 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
5298 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5299 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
5300 if ( p23.length != 1 ) {
5301 System.out.println( "xl=" + p23.length );
5305 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
5308 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5309 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
5310 if ( p24.length != 1 ) {
5313 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
5316 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5317 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5318 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
5319 if ( p241.length != 2 ) {
5322 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
5325 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
5328 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
5329 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
5330 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
5331 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
5332 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
5333 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
5334 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
5335 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
5336 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
5337 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
5340 final String p26_S = "(A,B)ab";
5341 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
5342 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
5345 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5346 final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
5347 if ( p27s.length != 1 ) {
5348 System.out.println( "xxl=" + p27s.length );
5352 if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
5353 System.out.println( p27s[ 0 ].toNewHampshireX() );
5357 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
5359 if ( p27.length != 1 ) {
5360 System.out.println( "yl=" + p27.length );
5364 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
5365 System.out.println( p27[ 0 ].toNewHampshireX() );
5369 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5370 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5371 final String p28_S3 = "(A,B)ab";
5372 final String p28_S4 = "((((A,B),C),D),;E;)";
5373 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
5375 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
5378 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
5381 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
5384 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
5387 if ( p28.length != 4 ) {
5390 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";
5391 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
5392 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
5395 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";
5396 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
5397 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
5400 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
5401 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
5402 if ( ( p32.length != 0 ) ) {
5405 final String p33_S = "A";
5406 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
5407 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
5410 final String p34_S = "B;";
5411 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
5412 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
5415 final String p35_S = "B:0.2";
5416 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
5417 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
5420 final String p36_S = "(A)";
5421 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
5422 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
5425 final String p37_S = "((A))";
5426 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
5427 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
5430 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
5431 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
5432 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
5435 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
5436 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
5437 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
5440 final String p40_S = "(A,B,C)";
5441 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
5442 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
5445 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
5446 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
5447 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
5450 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
5451 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
5452 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
5455 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)";
5456 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
5457 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
5460 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)))";
5461 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
5462 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
5465 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
5466 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
5467 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
5470 final String p46_S = "";
5471 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
5472 if ( p46.length != 0 ) {
5475 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
5476 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5479 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5480 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5483 final Phylogeny p49 = factory
5484 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
5485 new NHXParser() )[ 0 ];
5486 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
5489 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5490 if ( p50.getNode( "A" ) == null ) {
5493 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
5494 .equals( "((A,B)ab:2.0[88],C);" ) ) {
5497 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
5500 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
5501 .equals( "((A,B)88:2.0,C);" ) ) {
5504 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5505 if ( p51.getNode( "A(A" ) == null ) {
5508 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
5509 if ( p52.getNode( "A(A" ) == null ) {
5512 final Phylogeny p53 = factory
5513 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
5514 new NHXParser() )[ 0 ];
5515 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
5519 final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
5520 if ( p54.getNode( "A" ) == null ) {
5523 if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
5524 .equals( "((A,B)[88],C);" ) ) {
5528 catch ( final Exception e ) {
5529 e.printStackTrace( System.out );
5535 private static boolean testNHParsingIter() {
5537 final String p0_str = "(A,B);";
5538 final NHXParser p = new NHXParser();
5539 p.setSource( p0_str );
5540 if ( !p.hasNext() ) {
5543 final Phylogeny p0 = p.next();
5544 if ( !p0.toNewHampshire().equals( p0_str ) ) {
5545 System.out.println( p0.toNewHampshire() );
5548 if ( p.hasNext() ) {
5551 if ( p.next() != null ) {
5555 final String p00_str = "(A,B)root;";
5556 p.setSource( p00_str );
5557 final Phylogeny p00 = p.next();
5558 if ( !p00.toNewHampshire().equals( p00_str ) ) {
5559 System.out.println( p00.toNewHampshire() );
5563 final String p000_str = "A;";
5564 p.setSource( p000_str );
5565 final Phylogeny p000 = p.next();
5566 if ( !p000.toNewHampshire().equals( p000_str ) ) {
5567 System.out.println( p000.toNewHampshire() );
5571 final String p0000_str = "A";
5572 p.setSource( p0000_str );
5573 final Phylogeny p0000 = p.next();
5574 if ( !p0000.toNewHampshire().equals( "A;" ) ) {
5575 System.out.println( p0000.toNewHampshire() );
5579 p.setSource( "(A)" );
5580 final Phylogeny p00000 = p.next();
5581 if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
5582 System.out.println( p00000.toNewHampshire() );
5586 final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
5587 p.setSource( p1_str );
5588 if ( !p.hasNext() ) {
5591 final Phylogeny p1_0 = p.next();
5592 if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
5593 System.out.println( p1_0.toNewHampshire() );
5596 if ( !p.hasNext() ) {
5599 final Phylogeny p1_1 = p.next();
5600 if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
5601 System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
5604 if ( !p.hasNext() ) {
5607 final Phylogeny p1_2 = p.next();
5608 if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
5609 System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
5612 if ( !p.hasNext() ) {
5615 final Phylogeny p1_3 = p.next();
5616 if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
5617 System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
5620 if ( p.hasNext() ) {
5623 if ( p.next() != null ) {
5627 final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
5628 p.setSource( p2_str );
5629 if ( !p.hasNext() ) {
5632 Phylogeny p2_0 = p.next();
5633 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5634 System.out.println( p2_0.toNewHampshire() );
5637 if ( !p.hasNext() ) {
5640 Phylogeny p2_1 = p.next();
5641 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5642 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5645 if ( !p.hasNext() ) {
5648 Phylogeny p2_2 = p.next();
5649 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5650 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5653 if ( !p.hasNext() ) {
5656 Phylogeny p2_3 = p.next();
5657 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5658 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5661 if ( !p.hasNext() ) {
5664 Phylogeny p2_4 = p.next();
5665 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5666 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5669 if ( p.hasNext() ) {
5672 if ( p.next() != null ) {
5677 if ( !p.hasNext() ) {
5681 if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
5682 System.out.println( p2_0.toNewHampshire() );
5685 if ( !p.hasNext() ) {
5689 if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
5690 System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
5693 if ( !p.hasNext() ) {
5697 if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
5698 System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
5701 if ( !p.hasNext() ) {
5705 if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
5706 System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
5709 if ( !p.hasNext() ) {
5713 if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
5714 System.out.println( "(X) != " + p2_4.toNewHampshire() );
5717 if ( p.hasNext() ) {
5720 if ( p.next() != null ) {
5724 final String p3_str = "((A,B),C)abc";
5725 p.setSource( p3_str );
5726 if ( !p.hasNext() ) {
5729 final Phylogeny p3_0 = p.next();
5730 if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
5733 if ( p.hasNext() ) {
5736 if ( p.next() != null ) {
5740 final String p4_str = "((A,B)ab,C)abc";
5741 p.setSource( p4_str );
5742 if ( !p.hasNext() ) {
5745 final Phylogeny p4_0 = p.next();
5746 if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
5749 if ( p.hasNext() ) {
5752 if ( p.next() != null ) {
5756 final String p5_str = "(((A,B)ab,C)abc,D)abcd";
5757 p.setSource( p5_str );
5758 if ( !p.hasNext() ) {
5761 final Phylogeny p5_0 = p.next();
5762 if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
5765 if ( p.hasNext() ) {
5768 if ( p.next() != null ) {
5772 final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
5773 p.setSource( p6_str );
5774 if ( !p.hasNext() ) {
5777 Phylogeny p6_0 = p.next();
5778 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5781 if ( p.hasNext() ) {
5784 if ( p.next() != null ) {
5788 if ( !p.hasNext() ) {
5792 if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
5795 if ( p.hasNext() ) {
5798 if ( p.next() != null ) {
5802 final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
5803 p.setSource( p7_str );
5804 if ( !p.hasNext() ) {
5807 Phylogeny p7_0 = p.next();
5808 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5811 if ( p.hasNext() ) {
5814 if ( p.next() != null ) {
5818 if ( !p.hasNext() ) {
5822 if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5825 if ( p.hasNext() ) {
5828 if ( p.next() != null ) {
5832 final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
5833 p.setSource( p8_str );
5834 if ( !p.hasNext() ) {
5837 Phylogeny p8_0 = p.next();
5838 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5841 if ( !p.hasNext() ) {
5844 if ( !p.hasNext() ) {
5847 Phylogeny p8_1 = p.next();
5848 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5851 if ( p.hasNext() ) {
5854 if ( p.next() != null ) {
5858 if ( !p.hasNext() ) {
5862 if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
5865 if ( !p.hasNext() ) {
5869 if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
5872 if ( p.hasNext() ) {
5875 if ( p.next() != null ) {
5881 if ( p.hasNext() ) {
5885 p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
5886 if ( !p.hasNext() ) {
5889 Phylogeny p_27 = p.next();
5890 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5891 System.out.println( p_27.toNewHampshireX() );
5895 if ( p.hasNext() ) {
5898 if ( p.next() != null ) {
5902 if ( !p.hasNext() ) {
5906 if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
5907 System.out.println( p_27.toNewHampshireX() );
5911 if ( p.hasNext() ) {
5914 if ( p.next() != null ) {
5918 catch ( final Exception e ) {
5919 e.printStackTrace( System.out );
5925 private static boolean testNHXconversion() {
5927 final PhylogenyNode n1 = new PhylogenyNode();
5928 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
5929 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
5930 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
5931 final PhylogenyNode n5 = PhylogenyNode
5932 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
5933 final PhylogenyNode n6 = PhylogenyNode
5934 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
5935 if ( !n1.toNewHampshireX().equals( "" ) ) {
5938 if ( !n2.toNewHampshireX().equals( "" ) ) {
5941 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
5944 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
5947 if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
5950 if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
5951 System.out.println( n6.toNewHampshireX() );
5955 catch ( final Exception e ) {
5956 e.printStackTrace( System.out );
5962 private static boolean testTaxonomyExtraction() {
5964 final PhylogenyNode n0 = PhylogenyNode
5965 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
5966 if ( n0.getNodeData().isHasTaxonomy() ) {
5969 final PhylogenyNode n1 = PhylogenyNode
5970 .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
5971 if ( n1.getNodeData().isHasTaxonomy() ) {
5972 System.out.println( n1.toString() );
5975 final PhylogenyNode n2 = PhylogenyNode
5976 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
5977 if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5978 System.out.println( n2.toString() );
5981 final PhylogenyNode n2x = PhylogenyNode
5982 .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
5983 if ( n2x.getNodeData().isHasTaxonomy() ) {
5986 final PhylogenyNode n3 = PhylogenyNode
5987 .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
5988 if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
5989 System.out.println( n3.toString() );
5992 final PhylogenyNode n4 = PhylogenyNode
5993 .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
5994 if ( n4.getNodeData().isHasTaxonomy() ) {
5995 System.out.println( n4.toString() );
5998 final PhylogenyNode n5 = PhylogenyNode
5999 .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6000 if ( n5.getNodeData().isHasTaxonomy() ) {
6001 System.out.println( n5.toString() );
6004 final PhylogenyNode n6 = PhylogenyNode
6005 .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6006 if ( n6.getNodeData().isHasTaxonomy() ) {
6007 System.out.println( n6.toString() );
6010 final PhylogenyNode n7 = PhylogenyNode
6011 .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6012 if ( n7.getNodeData().isHasTaxonomy() ) {
6013 System.out.println( n7.toString() );
6016 final PhylogenyNode n8 = PhylogenyNode
6017 .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6018 if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
6019 System.out.println( n8.toString() );
6022 final PhylogenyNode n9 = PhylogenyNode
6023 .createInstanceFromNhxString( "blag_12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6024 if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
6025 System.out.println( n9.toString() );
6028 final PhylogenyNode n10x = PhylogenyNode
6029 .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6030 if ( n10x.getNodeData().isHasTaxonomy() ) {
6031 System.out.println( n10x.toString() );
6034 final PhylogenyNode n10xx = PhylogenyNode
6035 .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6036 if ( n10xx.getNodeData().isHasTaxonomy() ) {
6037 System.out.println( n10xx.toString() );
6040 final PhylogenyNode n10 = PhylogenyNode
6041 .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6042 if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
6043 System.out.println( n10.toString() );
6046 final PhylogenyNode n11 = PhylogenyNode
6047 .createInstanceFromNhxString( "blag_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6048 if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
6049 System.out.println( n11.toString() );
6052 final PhylogenyNode n12 = PhylogenyNode
6053 .createInstanceFromNhxString( "blag_Mus_musculus_musculus",
6054 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6055 if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
6056 System.out.println( n12.toString() );
6059 final PhylogenyNode n13 = PhylogenyNode
6060 .createInstanceFromNhxString( "blag_Mus_musculus1",
6061 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6062 if ( n13.getNodeData().isHasTaxonomy() ) {
6063 System.out.println( n13.toString() );
6066 final PhylogenyNode n14 = PhylogenyNode
6067 .createInstanceFromNhxString( "blag_Mus_musculus_11",
6068 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6069 if ( n14.getNodeData().isHasTaxonomy() ) {
6070 System.out.println( n14.toString() );
6073 final PhylogenyNode n15 = PhylogenyNode
6074 .createInstanceFromNhxString( "blag_Mus_musculus_v11",
6075 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6076 if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
6077 System.out.println( n15.toString() );
6080 final PhylogenyNode n16 = PhylogenyNode
6081 .createInstanceFromNhxString( "blag_Mus_musculus_/11",
6082 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6083 if ( n16.getNodeData().isHasTaxonomy() ) {
6084 System.out.println( n16.toString() );
6087 final PhylogenyNode n17 = PhylogenyNode
6088 .createInstanceFromNhxString( "blag_Mus_musculus_v",
6089 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6090 if ( n17.getNodeData().isHasTaxonomy() ) {
6091 System.out.println( n17.toString() );
6095 catch ( final Exception e ) {
6096 e.printStackTrace( System.out );
6102 private static boolean testNHXNodeParsing() {
6104 final PhylogenyNode n1 = new PhylogenyNode();
6105 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
6106 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
6107 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
6108 final PhylogenyNode n5 = PhylogenyNode
6109 .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]" );
6110 if ( !n3.getName().equals( "n3" ) ) {
6113 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6116 if ( n3.isDuplication() ) {
6119 if ( n3.isHasAssignedEvent() ) {
6122 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
6125 if ( !n4.getName().equals( "n4" ) ) {
6128 if ( n4.getDistanceToParent() != 0.01 ) {
6131 if ( !n5.getName().equals( "n5" ) ) {
6134 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
6137 if ( n5.getDistanceToParent() != 0.1 ) {
6140 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
6143 if ( !n5.isDuplication() ) {
6146 if ( !n5.isHasAssignedEvent() ) {
6149 final PhylogenyNode n8 = PhylogenyNode
6150 .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6151 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
6154 if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
6157 final PhylogenyNode n9 = PhylogenyNode
6158 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
6159 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6160 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
6163 if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
6166 final PhylogenyNode n10 = PhylogenyNode
6167 .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6168 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
6171 final PhylogenyNode n20 = PhylogenyNode
6172 .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6173 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
6176 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
6179 final PhylogenyNode n20x = PhylogenyNode
6180 .createInstanceFromNhxString( "n20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6181 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
6184 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
6187 final PhylogenyNode n20xx = PhylogenyNode
6188 .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6189 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
6192 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
6195 final PhylogenyNode n20xxx = PhylogenyNode
6196 .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6197 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
6200 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
6203 final PhylogenyNode n20xxxx = PhylogenyNode
6204 .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6205 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
6208 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
6211 final PhylogenyNode n21 = PhylogenyNode
6212 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6213 if ( !n21.getName().equals( "n21_PIG" ) ) {
6216 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
6219 final PhylogenyNode n21x = PhylogenyNode
6220 .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6221 if ( !n21x.getName().equals( "n21_PIG" ) ) {
6224 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
6227 final PhylogenyNode n22 = PhylogenyNode
6228 .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6229 if ( !n22.getName().equals( "n22/PIG" ) ) {
6232 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
6235 final PhylogenyNode n23 = PhylogenyNode
6236 .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6237 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
6240 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
6243 final PhylogenyNode a = PhylogenyNode
6244 .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6245 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
6248 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
6251 final PhylogenyNode b = PhylogenyNode
6252 .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6253 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
6256 if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
6259 final PhylogenyNode c = PhylogenyNode
6260 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
6261 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6262 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
6265 if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
6268 final PhylogenyNode c1 = PhylogenyNode
6269 .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
6270 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6271 if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
6274 if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
6277 final PhylogenyNode c2 = PhylogenyNode
6278 .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
6279 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6280 if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
6283 if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
6286 final PhylogenyNode d = PhylogenyNode
6287 .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6288 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
6291 if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
6294 final PhylogenyNode e = PhylogenyNode
6295 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6296 if ( !e.getName().equals( "n10_RAT1" ) ) {
6299 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
6302 final PhylogenyNode e2 = PhylogenyNode
6303 .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6304 if ( !e2.getName().equals( "n10_RAT1" ) ) {
6307 if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
6310 final PhylogenyNode e3 = PhylogenyNode
6311 .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6312 if ( !e3.getName().equals( "n10_RAT~" ) ) {
6315 if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
6318 final PhylogenyNode n11 = PhylogenyNode
6319 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
6320 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6321 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
6324 if ( n11.getDistanceToParent() != 0.4 ) {
6327 if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
6330 final PhylogenyNode n12 = PhylogenyNode
6331 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
6332 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6333 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
6336 if ( n12.getDistanceToParent() != 0.4 ) {
6339 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
6342 final PhylogenyNode m = PhylogenyNode
6343 .createInstanceFromNhxString( "n10_MOUSEa", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6344 if ( !m.getName().equals( "n10_MOUSEa" ) ) {
6347 if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
6350 final PhylogenyNode o = PhylogenyNode
6351 .createInstanceFromNhxString( "n10_MOUSE_", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6352 if ( !o.getName().equals( "n10_MOUSE_" ) ) {
6355 if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
6358 if ( n1.getName().compareTo( "" ) != 0 ) {
6361 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
6364 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6367 if ( n2.getName().compareTo( "" ) != 0 ) {
6370 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
6373 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
6376 final PhylogenyNode n00 = PhylogenyNode
6377 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
6378 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
6381 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
6384 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
6385 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
6388 final PhylogenyNode n13 = PhylogenyNode
6389 .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
6390 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
6393 if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
6396 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
6399 if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6402 final PhylogenyNode n14 = PhylogenyNode
6403 .createInstanceFromNhxString( "blah_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6404 if ( !n14.getName().equals( "blah_9QX45/1-2" ) ) {
6407 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
6410 final PhylogenyNode n15 = PhylogenyNode
6411 .createInstanceFromNhxString( "something_wicked[123]",
6412 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6413 if ( !n15.getName().equals( "something_wicked" ) ) {
6416 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
6419 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
6422 final PhylogenyNode n16 = PhylogenyNode
6423 .createInstanceFromNhxString( "something_wicked2[9]",
6424 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6425 if ( !n16.getName().equals( "something_wicked2" ) ) {
6428 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
6431 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
6434 final PhylogenyNode n17 = PhylogenyNode
6435 .createInstanceFromNhxString( "something_wicked3[a]",
6436 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6437 if ( !n17.getName().equals( "something_wicked3" ) ) {
6440 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
6443 final PhylogenyNode n18 = PhylogenyNode
6444 .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
6445 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
6448 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
6451 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
6454 final PhylogenyNode n19 = PhylogenyNode
6455 .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6456 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
6459 if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6462 final PhylogenyNode n30 = PhylogenyNode
6463 .createInstanceFromNhxString( "blah_1234567-roejojoej",
6464 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6465 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
6468 if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
6471 final PhylogenyNode n31 = PhylogenyNode
6472 .createInstanceFromNhxString( "blah_12345678-roejojoej",
6473 NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6474 if ( n31.getNodeData().isHasTaxonomy() ) {
6477 final PhylogenyNode n32 = PhylogenyNode
6478 .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
6479 if ( n32.getNodeData().isHasTaxonomy() ) {
6483 catch ( final Exception e ) {
6484 e.printStackTrace( System.out );
6490 private static boolean testNHXParsing() {
6492 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6493 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
6494 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
6497 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]";
6498 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
6499 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6502 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]";
6503 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
6504 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
6507 final Phylogeny[] p3 = factory
6508 .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]",
6510 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6513 final Phylogeny[] p4 = factory
6514 .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(]",
6516 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6519 final Phylogeny[] p5 = factory
6520 .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(((]",
6522 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
6525 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)";
6526 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)";
6527 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
6528 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
6531 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)))";
6532 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)))";
6533 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
6534 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
6537 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]) ))[,,, ])))))))";
6538 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
6539 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
6540 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
6543 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
6544 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
6547 final Phylogeny p10 = factory
6548 .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]",
6549 new NHXParser() )[ 0 ];
6550 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
6554 catch ( final Exception e ) {
6555 e.printStackTrace( System.out );
6561 private static boolean testNHXParsingQuotes() {
6563 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6564 final NHXParser p = new NHXParser();
6565 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
6566 if ( phylogenies_0.length != 5 ) {
6569 final Phylogeny phy = phylogenies_0[ 4 ];
6570 if ( phy.getNumberOfExternalNodes() != 7 ) {
6573 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
6576 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
6579 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
6580 .getScientificName().equals( "hsapiens" ) ) {
6583 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
6586 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
6589 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
6592 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
6595 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
6598 final NHXParser p1p = new NHXParser();
6599 p1p.setIgnoreQuotes( true );
6600 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
6601 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
6604 final NHXParser p2p = new NHXParser();
6605 p1p.setIgnoreQuotes( false );
6606 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
6607 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
6610 final NHXParser p3p = new NHXParser();
6611 p3p.setIgnoreQuotes( false );
6612 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
6613 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
6616 final NHXParser p4p = new NHXParser();
6617 p4p.setIgnoreQuotes( false );
6618 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
6619 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
6622 final Phylogeny p10 = factory
6623 .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]",
6624 new NHXParser() )[ 0 ];
6625 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]";
6626 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
6629 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
6630 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
6634 final Phylogeny p12 = factory
6635 .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]",
6636 new NHXParser() )[ 0 ];
6637 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]";
6638 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
6641 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
6642 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
6645 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;";
6646 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
6649 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
6650 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
6654 catch ( final Exception e ) {
6655 e.printStackTrace( System.out );
6661 private static boolean testNHXParsingMB() {
6663 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6664 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
6665 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6666 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6667 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6668 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6669 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6670 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6671 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6672 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
6673 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
6676 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
6679 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
6680 0.1100000000000000e+00 ) ) {
6683 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
6686 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
6689 final Phylogeny p2 = factory
6690 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
6691 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6692 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
6693 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
6694 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
6695 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
6696 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
6697 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
6698 + "7.369400000000000e-02}])",
6699 new NHXParser() )[ 0 ];
6700 if ( p2.getNode( "1" ) == null ) {
6703 if ( p2.getNode( "2" ) == null ) {
6707 catch ( final Exception e ) {
6708 e.printStackTrace( System.out );
6715 private static boolean testPhylogenyBranch() {
6717 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
6718 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
6719 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
6720 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
6721 if ( !a1b1.equals( a1b1 ) ) {
6724 if ( !a1b1.equals( b1a1 ) ) {
6727 if ( !b1a1.equals( a1b1 ) ) {
6730 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
6731 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
6732 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
6733 if ( a1_b1.equals( b1_a1 ) ) {
6736 if ( a1_b1.equals( a1_b1_ ) ) {
6739 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
6740 if ( !a1_b1.equals( b1_a1_ ) ) {
6743 if ( a1_b1_.equals( b1_a1_ ) ) {
6746 if ( !a1_b1_.equals( b1_a1 ) ) {
6750 catch ( final Exception e ) {
6751 e.printStackTrace( System.out );
6757 private static boolean testPhyloXMLparsingOfDistributionElement() {
6759 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6760 PhyloXmlParser xml_parser = null;
6762 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
6764 catch ( final Exception e ) {
6765 // Do nothing -- means were not running from jar.
6767 if ( xml_parser == null ) {
6768 xml_parser = new PhyloXmlParser();
6769 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
6770 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
6773 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
6776 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
6778 if ( xml_parser.getErrorCount() > 0 ) {
6779 System.out.println( xml_parser.getErrorMessages().toString() );
6782 if ( phylogenies_0.length != 1 ) {
6785 final Phylogeny t1 = phylogenies_0[ 0 ];
6786 PhylogenyNode n = null;
6787 Distribution d = null;
6788 n = t1.getNode( "root node" );
6789 if ( !n.getNodeData().isHasDistribution() ) {
6792 if ( n.getNodeData().getDistributions().size() != 1 ) {
6795 d = n.getNodeData().getDistribution();
6796 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6799 if ( d.getPoints().size() != 1 ) {
6802 if ( d.getPolygons() != null ) {
6805 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6808 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6811 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6814 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6817 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6820 n = t1.getNode( "node a" );
6821 if ( !n.getNodeData().isHasDistribution() ) {
6824 if ( n.getNodeData().getDistributions().size() != 2 ) {
6827 d = n.getNodeData().getDistribution( 1 );
6828 if ( !d.getDesc().equals( "San Diego" ) ) {
6831 if ( d.getPoints().size() != 1 ) {
6834 if ( d.getPolygons() != null ) {
6837 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6840 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6843 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6846 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6849 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6852 n = t1.getNode( "node bb" );
6853 if ( !n.getNodeData().isHasDistribution() ) {
6856 if ( n.getNodeData().getDistributions().size() != 1 ) {
6859 d = n.getNodeData().getDistribution( 0 );
6860 if ( d.getPoints().size() != 3 ) {
6863 if ( d.getPolygons().size() != 2 ) {
6866 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
6869 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
6872 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
6875 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
6878 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
6881 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
6884 Polygon p = d.getPolygons().get( 0 );
6885 if ( p.getPoints().size() != 3 ) {
6888 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
6891 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
6894 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6897 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
6900 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
6903 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
6906 p = d.getPolygons().get( 1 );
6907 if ( p.getPoints().size() != 3 ) {
6910 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
6913 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
6916 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
6920 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
6921 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
6922 if ( rt.length != 1 ) {
6925 final Phylogeny t1_rt = rt[ 0 ];
6926 n = t1_rt.getNode( "root node" );
6927 if ( !n.getNodeData().isHasDistribution() ) {
6930 if ( n.getNodeData().getDistributions().size() != 1 ) {
6933 d = n.getNodeData().getDistribution();
6934 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
6937 if ( d.getPoints().size() != 1 ) {
6940 if ( d.getPolygons() != null ) {
6943 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
6946 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6949 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6952 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
6955 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
6958 n = t1_rt.getNode( "node a" );
6959 if ( !n.getNodeData().isHasDistribution() ) {
6962 if ( n.getNodeData().getDistributions().size() != 2 ) {
6965 d = n.getNodeData().getDistribution( 1 );
6966 if ( !d.getDesc().equals( "San Diego" ) ) {
6969 if ( d.getPoints().size() != 1 ) {
6972 if ( d.getPolygons() != null ) {
6975 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
6978 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
6981 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
6984 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
6987 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
6990 n = t1_rt.getNode( "node bb" );
6991 if ( !n.getNodeData().isHasDistribution() ) {
6994 if ( n.getNodeData().getDistributions().size() != 1 ) {
6997 d = n.getNodeData().getDistribution( 0 );
6998 if ( d.getPoints().size() != 3 ) {
7001 if ( d.getPolygons().size() != 2 ) {
7004 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
7007 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
7010 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
7013 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
7016 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
7019 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
7022 p = d.getPolygons().get( 0 );
7023 if ( p.getPoints().size() != 3 ) {
7026 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
7029 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
7032 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
7035 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
7038 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
7041 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
7044 p = d.getPolygons().get( 1 );
7045 if ( p.getPoints().size() != 3 ) {
7048 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
7051 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
7054 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
7058 catch ( final Exception e ) {
7059 e.printStackTrace( System.out );
7065 private static boolean testPostOrderIterator() {
7067 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7068 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
7069 PhylogenyNodeIterator it0;
7070 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
7073 for( it0.reset(); it0.hasNext(); ) {
7076 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
7077 final PhylogenyNodeIterator it = t1.iteratorPostorder();
7078 if ( !it.next().getName().equals( "A" ) ) {
7081 if ( !it.next().getName().equals( "B" ) ) {
7084 if ( !it.next().getName().equals( "ab" ) ) {
7087 if ( !it.next().getName().equals( "C" ) ) {
7090 if ( !it.next().getName().equals( "D" ) ) {
7093 if ( !it.next().getName().equals( "cd" ) ) {
7096 if ( !it.next().getName().equals( "abcd" ) ) {
7099 if ( !it.next().getName().equals( "E" ) ) {
7102 if ( !it.next().getName().equals( "F" ) ) {
7105 if ( !it.next().getName().equals( "ef" ) ) {
7108 if ( !it.next().getName().equals( "G" ) ) {
7111 if ( !it.next().getName().equals( "H" ) ) {
7114 if ( !it.next().getName().equals( "gh" ) ) {
7117 if ( !it.next().getName().equals( "efgh" ) ) {
7120 if ( !it.next().getName().equals( "r" ) ) {
7123 if ( it.hasNext() ) {
7127 catch ( final Exception e ) {
7128 e.printStackTrace( System.out );
7134 private static boolean testPreOrderIterator() {
7136 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7137 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
7138 PhylogenyNodeIterator it0;
7139 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
7142 for( it0.reset(); it0.hasNext(); ) {
7145 PhylogenyNodeIterator it = t0.iteratorPreorder();
7146 if ( !it.next().getName().equals( "r" ) ) {
7149 if ( !it.next().getName().equals( "ab" ) ) {
7152 if ( !it.next().getName().equals( "A" ) ) {
7155 if ( !it.next().getName().equals( "B" ) ) {
7158 if ( !it.next().getName().equals( "cd" ) ) {
7161 if ( !it.next().getName().equals( "C" ) ) {
7164 if ( !it.next().getName().equals( "D" ) ) {
7167 if ( it.hasNext() ) {
7170 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
7171 it = t1.iteratorPreorder();
7172 if ( !it.next().getName().equals( "r" ) ) {
7175 if ( !it.next().getName().equals( "abcd" ) ) {
7178 if ( !it.next().getName().equals( "ab" ) ) {
7181 if ( !it.next().getName().equals( "A" ) ) {
7184 if ( !it.next().getName().equals( "B" ) ) {
7187 if ( !it.next().getName().equals( "cd" ) ) {
7190 if ( !it.next().getName().equals( "C" ) ) {
7193 if ( !it.next().getName().equals( "D" ) ) {
7196 if ( !it.next().getName().equals( "efgh" ) ) {
7199 if ( !it.next().getName().equals( "ef" ) ) {
7202 if ( !it.next().getName().equals( "E" ) ) {
7205 if ( !it.next().getName().equals( "F" ) ) {
7208 if ( !it.next().getName().equals( "gh" ) ) {
7211 if ( !it.next().getName().equals( "G" ) ) {
7214 if ( !it.next().getName().equals( "H" ) ) {
7217 if ( it.hasNext() ) {
7221 catch ( final Exception e ) {
7222 e.printStackTrace( System.out );
7228 private static boolean testPropertiesMap() {
7230 final PropertiesMap pm = new PropertiesMap();
7231 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
7232 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
7233 final Property p2 = new Property( "something:else",
7235 "improbable:research",
7238 pm.addProperty( p0 );
7239 pm.addProperty( p1 );
7240 pm.addProperty( p2 );
7241 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
7244 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
7247 if ( pm.getProperties().size() != 3 ) {
7250 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
7253 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
7256 if ( pm.getProperties().size() != 3 ) {
7259 pm.removeProperty( "dimensions:diameter" );
7260 if ( pm.getProperties().size() != 2 ) {
7263 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
7266 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
7270 catch ( final Exception e ) {
7271 e.printStackTrace( System.out );
7277 private static boolean testReIdMethods() {
7279 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7280 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
7281 final long count = PhylogenyNode.getNodeCount();
7283 if ( p.getNode( "r" ).getId() != count ) {
7286 if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
7289 if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
7292 if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
7295 if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
7298 if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
7301 if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
7304 if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
7307 if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
7310 if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
7313 if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
7316 if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
7319 if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
7322 if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
7325 if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
7329 catch ( final Exception e ) {
7330 e.printStackTrace( System.out );
7336 private static boolean testRerooting() {
7338 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7339 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",
7340 new NHXParser() )[ 0 ];
7341 if ( !t1.isRooted() ) {
7344 t1.reRoot( t1.getNode( "D" ) );
7345 t1.reRoot( t1.getNode( "CD" ) );
7346 t1.reRoot( t1.getNode( "A" ) );
7347 t1.reRoot( t1.getNode( "B" ) );
7348 t1.reRoot( t1.getNode( "AB" ) );
7349 t1.reRoot( t1.getNode( "D" ) );
7350 t1.reRoot( t1.getNode( "C" ) );
7351 t1.reRoot( t1.getNode( "CD" ) );
7352 t1.reRoot( t1.getNode( "A" ) );
7353 t1.reRoot( t1.getNode( "B" ) );
7354 t1.reRoot( t1.getNode( "AB" ) );
7355 t1.reRoot( t1.getNode( "D" ) );
7356 t1.reRoot( t1.getNode( "D" ) );
7357 t1.reRoot( t1.getNode( "C" ) );
7358 t1.reRoot( t1.getNode( "A" ) );
7359 t1.reRoot( t1.getNode( "B" ) );
7360 t1.reRoot( t1.getNode( "AB" ) );
7361 t1.reRoot( t1.getNode( "C" ) );
7362 t1.reRoot( t1.getNode( "D" ) );
7363 t1.reRoot( t1.getNode( "CD" ) );
7364 t1.reRoot( t1.getNode( "D" ) );
7365 t1.reRoot( t1.getNode( "A" ) );
7366 t1.reRoot( t1.getNode( "B" ) );
7367 t1.reRoot( t1.getNode( "AB" ) );
7368 t1.reRoot( t1.getNode( "C" ) );
7369 t1.reRoot( t1.getNode( "D" ) );
7370 t1.reRoot( t1.getNode( "CD" ) );
7371 t1.reRoot( t1.getNode( "D" ) );
7372 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
7375 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
7378 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
7381 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
7384 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
7387 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
7390 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",
7391 new NHXParser() )[ 0 ];
7392 t2.reRoot( t2.getNode( "A" ) );
7393 t2.reRoot( t2.getNode( "D" ) );
7394 t2.reRoot( t2.getNode( "ABC" ) );
7395 t2.reRoot( t2.getNode( "A" ) );
7396 t2.reRoot( t2.getNode( "B" ) );
7397 t2.reRoot( t2.getNode( "D" ) );
7398 t2.reRoot( t2.getNode( "C" ) );
7399 t2.reRoot( t2.getNode( "ABC" ) );
7400 t2.reRoot( t2.getNode( "A" ) );
7401 t2.reRoot( t2.getNode( "B" ) );
7402 t2.reRoot( t2.getNode( "AB" ) );
7403 t2.reRoot( t2.getNode( "AB" ) );
7404 t2.reRoot( t2.getNode( "D" ) );
7405 t2.reRoot( t2.getNode( "C" ) );
7406 t2.reRoot( t2.getNode( "B" ) );
7407 t2.reRoot( t2.getNode( "AB" ) );
7408 t2.reRoot( t2.getNode( "D" ) );
7409 t2.reRoot( t2.getNode( "D" ) );
7410 t2.reRoot( t2.getNode( "ABC" ) );
7411 t2.reRoot( t2.getNode( "A" ) );
7412 t2.reRoot( t2.getNode( "B" ) );
7413 t2.reRoot( t2.getNode( "AB" ) );
7414 t2.reRoot( t2.getNode( "D" ) );
7415 t2.reRoot( t2.getNode( "C" ) );
7416 t2.reRoot( t2.getNode( "ABC" ) );
7417 t2.reRoot( t2.getNode( "A" ) );
7418 t2.reRoot( t2.getNode( "B" ) );
7419 t2.reRoot( t2.getNode( "AB" ) );
7420 t2.reRoot( t2.getNode( "D" ) );
7421 t2.reRoot( t2.getNode( "D" ) );
7422 t2.reRoot( t2.getNode( "C" ) );
7423 t2.reRoot( t2.getNode( "A" ) );
7424 t2.reRoot( t2.getNode( "B" ) );
7425 t2.reRoot( t2.getNode( "AB" ) );
7426 t2.reRoot( t2.getNode( "C" ) );
7427 t2.reRoot( t2.getNode( "D" ) );
7428 t2.reRoot( t2.getNode( "ABC" ) );
7429 t2.reRoot( t2.getNode( "D" ) );
7430 t2.reRoot( t2.getNode( "A" ) );
7431 t2.reRoot( t2.getNode( "B" ) );
7432 t2.reRoot( t2.getNode( "AB" ) );
7433 t2.reRoot( t2.getNode( "C" ) );
7434 t2.reRoot( t2.getNode( "D" ) );
7435 t2.reRoot( t2.getNode( "ABC" ) );
7436 t2.reRoot( t2.getNode( "D" ) );
7437 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7440 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7443 t2.reRoot( t2.getNode( "ABC" ) );
7444 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7447 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7450 t2.reRoot( t2.getNode( "AB" ) );
7451 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7454 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7457 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7460 t2.reRoot( t2.getNode( "AB" ) );
7461 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7464 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7467 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7470 t2.reRoot( t2.getNode( "D" ) );
7471 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7474 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7477 t2.reRoot( t2.getNode( "ABC" ) );
7478 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
7481 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
7484 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
7485 new NHXParser() )[ 0 ];
7486 t3.reRoot( t3.getNode( "B" ) );
7487 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7490 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7493 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7496 t3.reRoot( t3.getNode( "B" ) );
7497 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7500 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7503 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7506 t3.reRoot( t3.getRoot() );
7507 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7510 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
7513 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
7517 catch ( final Exception e ) {
7518 e.printStackTrace( System.out );
7524 private static boolean testSDIse() {
7526 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7527 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
7528 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
7529 gene1.setRooted( true );
7530 species1.setRooted( true );
7531 final SDI sdi = new SDI( gene1, species1 );
7532 if ( !gene1.getRoot().isDuplication() ) {
7535 final Phylogeny species2 = 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 gene2 = factory
7539 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7540 new NHXParser() )[ 0 ];
7541 species2.setRooted( true );
7542 gene2.setRooted( true );
7543 final SDI sdi2 = new SDI( gene2, species2 );
7544 if ( sdi2.getDuplicationsSum() != 0 ) {
7547 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
7550 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
7553 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
7556 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
7559 if ( !gene2.getNode( "r" ).isSpeciation() ) {
7562 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
7565 final Phylogeny species3 = factory
7566 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7567 new NHXParser() )[ 0 ];
7568 final Phylogeny gene3 = factory
7569 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7570 new NHXParser() )[ 0 ];
7571 species3.setRooted( true );
7572 gene3.setRooted( true );
7573 final SDI sdi3 = new SDI( gene3, species3 );
7574 if ( sdi3.getDuplicationsSum() != 1 ) {
7577 if ( !gene3.getNode( "aa" ).isDuplication() ) {
7580 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
7583 final Phylogeny species4 = factory
7584 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7585 new NHXParser() )[ 0 ];
7586 final Phylogeny gene4 = factory
7587 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7588 new NHXParser() )[ 0 ];
7589 species4.setRooted( true );
7590 gene4.setRooted( true );
7591 final SDI sdi4 = new SDI( gene4, species4 );
7592 if ( sdi4.getDuplicationsSum() != 1 ) {
7595 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
7598 if ( !gene4.getNode( "abc" ).isDuplication() ) {
7601 if ( gene4.getNode( "abcd" ).isDuplication() ) {
7604 if ( species4.getNumberOfExternalNodes() != 6 ) {
7607 if ( gene4.getNumberOfExternalNodes() != 6 ) {
7610 final Phylogeny species5 = factory
7611 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7612 new NHXParser() )[ 0 ];
7613 final Phylogeny gene5 = factory
7614 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
7615 new NHXParser() )[ 0 ];
7616 species5.setRooted( true );
7617 gene5.setRooted( true );
7618 final SDI sdi5 = new SDI( gene5, species5 );
7619 if ( sdi5.getDuplicationsSum() != 2 ) {
7622 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
7625 if ( !gene5.getNode( "adc" ).isDuplication() ) {
7628 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
7631 if ( species5.getNumberOfExternalNodes() != 6 ) {
7634 if ( gene5.getNumberOfExternalNodes() != 6 ) {
7637 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
7638 // Conjecture for Comparing Molecular Phylogenies"
7639 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
7640 final Phylogeny species6 = factory
7641 .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,"
7642 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7643 new NHXParser() )[ 0 ];
7644 final Phylogeny gene6 = factory
7645 .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,"
7646 + "((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,"
7647 + "(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;",
7648 new NHXParser() )[ 0 ];
7649 species6.setRooted( true );
7650 gene6.setRooted( true );
7651 final SDI sdi6 = new SDI( gene6, species6 );
7652 if ( sdi6.getDuplicationsSum() != 3 ) {
7655 if ( !gene6.getNode( "r" ).isDuplication() ) {
7658 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
7661 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
7664 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
7667 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
7670 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
7673 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
7676 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
7679 sdi6.computeMappingCostL();
7680 if ( sdi6.computeMappingCostL() != 17 ) {
7683 if ( species6.getNumberOfExternalNodes() != 9 ) {
7686 if ( gene6.getNumberOfExternalNodes() != 9 ) {
7689 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
7690 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
7691 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
7692 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
7693 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
7694 species7.setRooted( true );
7695 final Phylogeny gene7_1 = Test
7696 .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])" );
7697 gene7_1.setRooted( true );
7698 final SDI sdi7 = new SDI( gene7_1, species7 );
7699 if ( sdi7.getDuplicationsSum() != 0 ) {
7702 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
7705 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
7708 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
7711 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
7714 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
7717 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
7720 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
7723 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
7726 final Phylogeny gene7_2 = Test
7727 .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])" );
7728 gene7_2.setRooted( true );
7729 final SDI sdi7_2 = new SDI( gene7_2, species7 );
7730 if ( sdi7_2.getDuplicationsSum() != 1 ) {
7733 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
7736 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
7739 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
7742 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
7745 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
7748 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
7751 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
7754 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
7757 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
7761 catch ( final Exception e ) {
7767 private static boolean testSDIunrooted() {
7769 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7770 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
7771 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
7772 final Iterator<PhylogenyBranch> iter = l.iterator();
7773 PhylogenyBranch br = iter.next();
7774 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
7777 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
7781 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7784 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7788 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
7791 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
7795 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7798 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7802 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7805 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7809 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
7812 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
7816 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7819 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7823 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7826 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7830 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7833 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7837 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
7840 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
7844 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7847 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7851 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
7854 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
7858 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
7861 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
7865 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
7868 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
7872 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
7875 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
7878 if ( iter.hasNext() ) {
7881 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
7882 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
7883 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
7885 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7888 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7892 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7895 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7899 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7902 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7905 if ( iter1.hasNext() ) {
7908 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
7909 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
7910 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
7912 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
7915 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
7919 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
7922 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
7926 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
7929 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
7932 if ( iter2.hasNext() ) {
7935 final Phylogeny species0 = factory
7936 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
7937 new NHXParser() )[ 0 ];
7938 final Phylogeny gene1 = factory
7939 .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])",
7940 new NHXParser() )[ 0 ];
7941 species0.setRooted( true );
7942 gene1.setRooted( true );
7943 final SDIR sdi_unrooted = new SDIR();
7944 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
7945 if ( sdi_unrooted.getCount() != 1 ) {
7948 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
7951 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
7954 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
7957 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7960 final Phylogeny gene2 = factory
7961 .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])",
7962 new NHXParser() )[ 0 ];
7963 gene2.setRooted( true );
7964 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
7965 if ( sdi_unrooted.getCount() != 1 ) {
7968 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
7971 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
7974 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
7977 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
7980 final Phylogeny species6 = factory
7981 .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,"
7982 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
7983 new NHXParser() )[ 0 ];
7984 final Phylogeny gene6 = factory
7985 .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],"
7986 + "(((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],"
7987 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
7988 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
7989 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
7990 new NHXParser() )[ 0 ];
7991 species6.setRooted( true );
7992 gene6.setRooted( true );
7993 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
7994 if ( sdi_unrooted.getCount() != 1 ) {
7997 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
8000 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
8003 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
8006 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
8009 if ( !p6[ 0 ].getRoot().isDuplication() ) {
8012 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
8015 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
8018 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
8021 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8024 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
8027 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
8030 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8034 final Phylogeny species7 = factory
8035 .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,"
8036 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
8037 new NHXParser() )[ 0 ];
8038 final Phylogeny gene7 = factory
8039 .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],"
8040 + "(((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],"
8041 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
8042 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
8043 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
8044 new NHXParser() )[ 0 ];
8045 species7.setRooted( true );
8046 gene7.setRooted( true );
8047 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
8048 if ( sdi_unrooted.getCount() != 1 ) {
8051 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
8054 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
8057 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
8060 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
8063 if ( !p7[ 0 ].getRoot().isDuplication() ) {
8066 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
8069 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
8072 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
8075 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8078 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
8081 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
8084 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8088 final Phylogeny species8 = factory
8089 .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,"
8090 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
8091 new NHXParser() )[ 0 ];
8092 final Phylogeny gene8 = factory
8093 .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],"
8094 + "(((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],"
8095 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
8096 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
8097 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
8098 new NHXParser() )[ 0 ];
8099 species8.setRooted( true );
8100 gene8.setRooted( true );
8101 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
8102 if ( sdi_unrooted.getCount() != 1 ) {
8105 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
8108 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
8111 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
8114 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
8117 if ( !p8[ 0 ].getRoot().isDuplication() ) {
8120 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
8123 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
8126 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
8129 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
8132 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
8135 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
8138 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
8143 catch ( final Exception e ) {
8144 e.printStackTrace( System.out );
8150 private static boolean testSplit() {
8152 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8153 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
8154 //Archaeopteryx.createApplication( p0 );
8155 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
8156 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8157 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8158 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8159 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8160 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8161 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8162 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8163 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8164 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8165 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
8166 // System.out.println( s0.toString() );
8168 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
8169 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8170 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8171 if ( s0.match( query_nodes ) ) {
8174 query_nodes = new HashSet<PhylogenyNode>();
8175 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8176 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8177 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8178 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8179 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8180 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8181 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
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( "B" ) );
8189 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8190 if ( !s0.match( query_nodes ) ) {
8194 query_nodes = new HashSet<PhylogenyNode>();
8195 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8196 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8197 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8198 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8199 if ( !s0.match( query_nodes ) ) {
8203 query_nodes = new HashSet<PhylogenyNode>();
8204 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8205 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8206 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8207 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8208 if ( !s0.match( query_nodes ) ) {
8212 query_nodes = new HashSet<PhylogenyNode>();
8213 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8214 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8215 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8216 if ( !s0.match( query_nodes ) ) {
8220 query_nodes = new HashSet<PhylogenyNode>();
8221 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8222 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8223 if ( !s0.match( query_nodes ) ) {
8227 query_nodes = new HashSet<PhylogenyNode>();
8228 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8229 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8230 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8231 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8232 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8233 if ( !s0.match( query_nodes ) ) {
8237 query_nodes = new HashSet<PhylogenyNode>();
8238 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8239 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8240 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8241 if ( !s0.match( query_nodes ) ) {
8245 query_nodes = new HashSet<PhylogenyNode>();
8246 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8247 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8248 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8249 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8250 if ( !s0.match( query_nodes ) ) {
8254 query_nodes = new HashSet<PhylogenyNode>();
8255 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8256 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8257 if ( s0.match( query_nodes ) ) {
8261 query_nodes = new HashSet<PhylogenyNode>();
8262 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8263 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8264 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8265 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8266 if ( s0.match( query_nodes ) ) {
8270 query_nodes = new HashSet<PhylogenyNode>();
8271 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8272 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8273 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8274 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8275 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8276 if ( s0.match( query_nodes ) ) {
8280 query_nodes = new HashSet<PhylogenyNode>();
8281 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8282 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8283 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8284 if ( s0.match( query_nodes ) ) {
8288 query_nodes = new HashSet<PhylogenyNode>();
8289 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8290 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8291 if ( s0.match( query_nodes ) ) {
8295 query_nodes = new HashSet<PhylogenyNode>();
8296 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8297 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8298 if ( s0.match( query_nodes ) ) {
8302 query_nodes = new HashSet<PhylogenyNode>();
8303 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8304 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8305 if ( s0.match( query_nodes ) ) {
8309 query_nodes = new HashSet<PhylogenyNode>();
8310 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8311 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8312 if ( s0.match( query_nodes ) ) {
8316 query_nodes = new HashSet<PhylogenyNode>();
8317 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8318 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8319 if ( s0.match( query_nodes ) ) {
8323 query_nodes = new HashSet<PhylogenyNode>();
8324 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8325 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8326 if ( s0.match( query_nodes ) ) {
8330 query_nodes = new HashSet<PhylogenyNode>();
8331 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8332 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8333 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8334 if ( s0.match( query_nodes ) ) {
8338 query_nodes = new HashSet<PhylogenyNode>();
8339 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8340 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8341 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8342 if ( s0.match( query_nodes ) ) {
8346 query_nodes = new HashSet<PhylogenyNode>();
8347 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8348 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8349 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8350 if ( s0.match( query_nodes ) ) {
8354 query_nodes = new HashSet<PhylogenyNode>();
8355 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8356 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8357 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8358 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8359 if ( s0.match( query_nodes ) ) {
8363 // query_nodes = new HashSet<PhylogenyNode>();
8364 // query_nodes.add( new PhylogenyNode( "X" ) );
8365 // query_nodes.add( new PhylogenyNode( "Y" ) );
8366 // query_nodes.add( new PhylogenyNode( "A" ) );
8367 // query_nodes.add( new PhylogenyNode( "B" ) );
8368 // query_nodes.add( new PhylogenyNode( "C" ) );
8369 // query_nodes.add( new PhylogenyNode( "D" ) );
8370 // query_nodes.add( new PhylogenyNode( "E" ) );
8371 // query_nodes.add( new PhylogenyNode( "F" ) );
8372 // query_nodes.add( new PhylogenyNode( "G" ) );
8373 // if ( !s0.match( query_nodes ) ) {
8376 // query_nodes = new HashSet<PhylogenyNode>();
8377 // query_nodes.add( new PhylogenyNode( "X" ) );
8378 // query_nodes.add( new PhylogenyNode( "Y" ) );
8379 // query_nodes.add( new PhylogenyNode( "A" ) );
8380 // query_nodes.add( new PhylogenyNode( "B" ) );
8381 // query_nodes.add( new PhylogenyNode( "C" ) );
8382 // if ( !s0.match( query_nodes ) ) {
8386 // query_nodes = new HashSet<PhylogenyNode>();
8387 // query_nodes.add( new PhylogenyNode( "X" ) );
8388 // query_nodes.add( new PhylogenyNode( "Y" ) );
8389 // query_nodes.add( new PhylogenyNode( "D" ) );
8390 // query_nodes.add( new PhylogenyNode( "E" ) );
8391 // query_nodes.add( new PhylogenyNode( "F" ) );
8392 // query_nodes.add( new PhylogenyNode( "G" ) );
8393 // if ( !s0.match( query_nodes ) ) {
8397 // query_nodes = new HashSet<PhylogenyNode>();
8398 // query_nodes.add( new PhylogenyNode( "X" ) );
8399 // query_nodes.add( new PhylogenyNode( "Y" ) );
8400 // query_nodes.add( new PhylogenyNode( "A" ) );
8401 // query_nodes.add( new PhylogenyNode( "B" ) );
8402 // query_nodes.add( new PhylogenyNode( "C" ) );
8403 // query_nodes.add( new PhylogenyNode( "D" ) );
8404 // if ( !s0.match( query_nodes ) ) {
8408 // query_nodes = new HashSet<PhylogenyNode>();
8409 // query_nodes.add( new PhylogenyNode( "X" ) );
8410 // query_nodes.add( new PhylogenyNode( "Y" ) );
8411 // query_nodes.add( new PhylogenyNode( "E" ) );
8412 // query_nodes.add( new PhylogenyNode( "F" ) );
8413 // query_nodes.add( new PhylogenyNode( "G" ) );
8414 // if ( !s0.match( query_nodes ) ) {
8418 // query_nodes = new HashSet<PhylogenyNode>();
8419 // query_nodes.add( new PhylogenyNode( "X" ) );
8420 // query_nodes.add( new PhylogenyNode( "Y" ) );
8421 // query_nodes.add( new PhylogenyNode( "F" ) );
8422 // query_nodes.add( new PhylogenyNode( "G" ) );
8423 // if ( !s0.match( query_nodes ) ) {
8427 query_nodes = new HashSet<PhylogenyNode>();
8428 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8429 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8430 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8431 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8432 if ( s0.match( query_nodes ) ) {
8436 query_nodes = new HashSet<PhylogenyNode>();
8437 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8438 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8439 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8440 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8441 if ( s0.match( query_nodes ) ) {
8444 ///////////////////////////
8446 query_nodes = new HashSet<PhylogenyNode>();
8447 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8448 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8449 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8450 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8451 if ( s0.match( query_nodes ) ) {
8455 query_nodes = new HashSet<PhylogenyNode>();
8456 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8457 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8458 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8459 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8460 if ( s0.match( query_nodes ) ) {
8464 query_nodes = new HashSet<PhylogenyNode>();
8465 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8466 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8467 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8468 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8469 if ( s0.match( query_nodes ) ) {
8473 query_nodes = new HashSet<PhylogenyNode>();
8474 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8475 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8476 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8477 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8478 if ( s0.match( query_nodes ) ) {
8482 query_nodes = new HashSet<PhylogenyNode>();
8483 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8484 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8485 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8486 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8487 if ( s0.match( query_nodes ) ) {
8491 query_nodes = new HashSet<PhylogenyNode>();
8492 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8493 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8494 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8495 if ( s0.match( query_nodes ) ) {
8499 query_nodes = new HashSet<PhylogenyNode>();
8500 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8501 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8502 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8503 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8504 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8505 if ( s0.match( query_nodes ) ) {
8509 query_nodes = new HashSet<PhylogenyNode>();
8510 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8511 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8512 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8513 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8514 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8515 if ( s0.match( query_nodes ) ) {
8519 query_nodes = new HashSet<PhylogenyNode>();
8520 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8523 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8524 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8525 if ( s0.match( query_nodes ) ) {
8529 query_nodes = new HashSet<PhylogenyNode>();
8530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
8531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
8532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8533 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8534 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8535 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8536 if ( s0.match( query_nodes ) ) {
8540 catch ( final Exception e ) {
8541 e.printStackTrace();
8547 private static boolean testSplitStrict() {
8549 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8550 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
8551 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
8552 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8553 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8554 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8555 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8556 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8557 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8558 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8559 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
8560 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
8561 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8562 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8563 if ( s0.match( query_nodes ) ) {
8566 query_nodes = new HashSet<PhylogenyNode>();
8567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8568 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8569 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8570 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8571 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8572 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8573 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
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( "B" ) );
8581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8582 if ( !s0.match( query_nodes ) ) {
8586 query_nodes = new HashSet<PhylogenyNode>();
8587 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8588 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8589 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8591 if ( !s0.match( query_nodes ) ) {
8595 query_nodes = new HashSet<PhylogenyNode>();
8596 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8600 if ( !s0.match( query_nodes ) ) {
8604 query_nodes = new HashSet<PhylogenyNode>();
8605 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8606 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8608 if ( !s0.match( query_nodes ) ) {
8612 query_nodes = new HashSet<PhylogenyNode>();
8613 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8615 if ( !s0.match( query_nodes ) ) {
8619 query_nodes = new HashSet<PhylogenyNode>();
8620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8621 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8622 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8625 if ( !s0.match( query_nodes ) ) {
8629 query_nodes = new HashSet<PhylogenyNode>();
8630 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8631 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8632 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8633 if ( !s0.match( query_nodes ) ) {
8637 query_nodes = new HashSet<PhylogenyNode>();
8638 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8639 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8640 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8642 if ( !s0.match( query_nodes ) ) {
8646 query_nodes = new HashSet<PhylogenyNode>();
8647 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8649 if ( s0.match( query_nodes ) ) {
8653 query_nodes = new HashSet<PhylogenyNode>();
8654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8657 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8658 if ( s0.match( query_nodes ) ) {
8662 query_nodes = new HashSet<PhylogenyNode>();
8663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8664 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8665 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8666 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8667 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8668 if ( s0.match( query_nodes ) ) {
8672 query_nodes = new HashSet<PhylogenyNode>();
8673 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8674 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8675 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8676 if ( s0.match( query_nodes ) ) {
8680 query_nodes = new HashSet<PhylogenyNode>();
8681 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8682 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8683 if ( s0.match( query_nodes ) ) {
8687 query_nodes = new HashSet<PhylogenyNode>();
8688 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8689 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8690 if ( s0.match( query_nodes ) ) {
8694 query_nodes = new HashSet<PhylogenyNode>();
8695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
8697 if ( s0.match( query_nodes ) ) {
8701 query_nodes = new HashSet<PhylogenyNode>();
8702 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8704 if ( s0.match( query_nodes ) ) {
8708 query_nodes = new HashSet<PhylogenyNode>();
8709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8711 if ( s0.match( query_nodes ) ) {
8715 query_nodes = new HashSet<PhylogenyNode>();
8716 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8717 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8718 if ( s0.match( query_nodes ) ) {
8722 query_nodes = new HashSet<PhylogenyNode>();
8723 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8724 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
8725 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8726 if ( s0.match( query_nodes ) ) {
8730 query_nodes = new HashSet<PhylogenyNode>();
8731 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8732 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
8733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8734 if ( s0.match( query_nodes ) ) {
8738 query_nodes = new HashSet<PhylogenyNode>();
8739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8741 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8742 if ( s0.match( query_nodes ) ) {
8746 query_nodes = new HashSet<PhylogenyNode>();
8747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
8748 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
8749 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
8750 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
8751 if ( s0.match( query_nodes ) ) {
8755 catch ( final Exception e ) {
8756 e.printStackTrace();
8762 private static boolean testSubtreeDeletion() {
8764 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8765 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8766 t1.deleteSubtree( t1.getNode( "A" ), false );
8767 if ( t1.getNumberOfExternalNodes() != 5 ) {
8770 t1.toNewHampshireX();
8771 t1.deleteSubtree( t1.getNode( "E" ), false );
8772 if ( t1.getNumberOfExternalNodes() != 4 ) {
8775 t1.toNewHampshireX();
8776 t1.deleteSubtree( t1.getNode( "F" ), false );
8777 if ( t1.getNumberOfExternalNodes() != 3 ) {
8780 t1.toNewHampshireX();
8781 t1.deleteSubtree( t1.getNode( "D" ), false );
8782 t1.toNewHampshireX();
8783 if ( t1.getNumberOfExternalNodes() != 3 ) {
8786 t1.deleteSubtree( t1.getNode( "def" ), false );
8787 t1.toNewHampshireX();
8788 if ( t1.getNumberOfExternalNodes() != 2 ) {
8791 t1.deleteSubtree( t1.getNode( "B" ), false );
8792 t1.toNewHampshireX();
8793 if ( t1.getNumberOfExternalNodes() != 1 ) {
8796 t1.deleteSubtree( t1.getNode( "C" ), false );
8797 t1.toNewHampshireX();
8798 if ( t1.getNumberOfExternalNodes() != 1 ) {
8801 t1.deleteSubtree( t1.getNode( "abc" ), false );
8802 t1.toNewHampshireX();
8803 if ( t1.getNumberOfExternalNodes() != 1 ) {
8806 t1.deleteSubtree( t1.getNode( "r" ), false );
8807 if ( t1.getNumberOfExternalNodes() != 0 ) {
8810 if ( !t1.isEmpty() ) {
8813 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
8814 t2.deleteSubtree( t2.getNode( "A" ), false );
8815 t2.toNewHampshireX();
8816 if ( t2.getNumberOfExternalNodes() != 5 ) {
8819 t2.deleteSubtree( t2.getNode( "abc" ), false );
8820 t2.toNewHampshireX();
8821 if ( t2.getNumberOfExternalNodes() != 3 ) {
8824 t2.deleteSubtree( t2.getNode( "def" ), false );
8825 t2.toNewHampshireX();
8826 if ( t2.getNumberOfExternalNodes() != 1 ) {
8830 catch ( final Exception e ) {
8831 e.printStackTrace( System.out );
8837 private static boolean testSupportCount() {
8839 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8840 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
8841 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
8842 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
8843 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
8844 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
8845 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
8847 SupportCount.count( t0_1, phylogenies_1, true, false );
8848 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
8849 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
8850 + "(((((A,B),C),D),E),((F,G),X))"
8851 + "(((((A,Y),B),C),D),((F,G),E))"
8852 + "(((((A,B),C),D),E),(F,G))"
8853 + "(((((A,B),C),D),E),(F,G))"
8854 + "(((((A,B),C),D),E),(F,G))"
8855 + "(((((A,B),C),D),E),(F,G),Z)"
8856 + "(((((A,B),C),D),E),(F,G))"
8857 + "((((((A,B),C),D),E),F),G)"
8858 + "(((((X,Y),F,G),E),((A,B),C)),D)",
8860 SupportCount.count( t0_2, phylogenies_2, true, false );
8861 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
8862 while ( it.hasNext() ) {
8863 final PhylogenyNode n = it.next();
8864 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
8868 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
8869 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
8870 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
8871 SupportCount.count( t0_3, phylogenies_3, true, false );
8872 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
8873 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
8876 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
8879 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
8882 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
8885 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
8888 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
8891 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
8894 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
8897 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
8900 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
8903 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8904 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
8905 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
8906 SupportCount.count( t0_4, phylogenies_4, true, false );
8907 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
8908 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
8911 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
8914 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
8917 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
8920 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
8923 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
8926 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
8929 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
8932 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
8935 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
8938 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8939 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8940 double d = SupportCount.compare( b1, a, true, true, true );
8941 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
8944 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8945 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8946 d = SupportCount.compare( b2, a, true, true, true );
8947 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
8950 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
8951 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
8952 d = SupportCount.compare( b3, a, true, true, true );
8953 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
8956 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
8957 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
8958 d = SupportCount.compare( b4, a, true, true, false );
8959 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
8963 catch ( final Exception e ) {
8964 e.printStackTrace( System.out );
8970 private static boolean testSupportTransfer() {
8972 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8973 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)",
8974 new NHXParser() )[ 0 ];
8975 final Phylogeny p2 = factory
8976 .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 ];
8977 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
8980 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
8983 support_transfer.moveBranchLengthsToBootstrap( p1 );
8984 support_transfer.transferSupportValues( p1, p2 );
8985 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
8988 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
8991 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
8994 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
8997 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
9000 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
9003 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
9006 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
9010 catch ( final Exception e ) {
9011 e.printStackTrace( System.out );
9017 private static boolean testUniprotTaxonomySearch() {
9019 List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
9021 if ( results.size() != 1 ) {
9024 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
9027 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
9030 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
9033 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9036 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9040 results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
9041 if ( results.size() != 1 ) {
9044 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
9047 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
9050 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
9053 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9056 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9060 results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
9061 if ( results.size() != 1 ) {
9064 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
9067 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
9070 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
9073 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9076 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9080 results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
9081 if ( results.size() != 1 ) {
9084 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
9087 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
9090 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
9093 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
9096 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
9099 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
9102 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
9105 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
9106 .equals( "Nematostella vectensis" ) ) {
9107 System.out.println( results.get( 0 ).getLineage() );
9111 catch ( final IOException e ) {
9112 System.out.println();
9113 System.out.println( "the following might be due to absence internet connection:" );
9114 e.printStackTrace( System.out );
9117 catch ( final Exception e ) {
9123 private static boolean testEmblEntryRetrieval() {
9124 //The format for GenBank Accession numbers are:
9125 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
9126 //Protein: 3 letters + 5 numerals
9127 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
9128 if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
9131 if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
9134 if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
9137 if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
9140 if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
9143 if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
9146 if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
9149 if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
9152 if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
9155 if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
9158 if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
9161 if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
9164 if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
9170 private static boolean testUniprotEntryRetrieval() {
9171 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
9174 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
9177 if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
9180 if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
9183 if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
9186 if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
9189 if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
9192 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
9195 if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
9198 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
9201 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
9204 if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
9207 if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
9211 final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
9212 if ( !entry.getAccession().equals( "P12345" ) ) {
9215 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
9218 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
9221 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
9224 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
9228 catch ( final IOException e ) {
9229 System.out.println();
9230 System.out.println( "the following might be due to absence internet connection:" );
9231 e.printStackTrace( System.out );
9234 catch ( final Exception e ) {
9240 private static boolean testWabiTxSearch() {
9243 result = TxSearch.searchSimple( "nematostella" );
9244 result = TxSearch.getTxId( "nematostella" );
9245 if ( !result.equals( "45350" ) ) {
9248 result = TxSearch.getTxName( "45350" );
9249 if ( !result.equals( "Nematostella" ) ) {
9252 result = TxSearch.getTxId( "nematostella vectensis" );
9253 if ( !result.equals( "45351" ) ) {
9256 result = TxSearch.getTxName( "45351" );
9257 if ( !result.equals( "Nematostella vectensis" ) ) {
9260 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
9261 if ( !result.equals( "536089" ) ) {
9264 result = TxSearch.getTxName( "536089" );
9265 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
9268 final List<String> queries = new ArrayList<String>();
9269 queries.add( "Campylobacter coli" );
9270 queries.add( "Escherichia coli" );
9271 queries.add( "Arabidopsis" );
9272 queries.add( "Trichoplax" );
9273 queries.add( "Samanea saman" );
9274 queries.add( "Kluyveromyces marxianus" );
9275 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
9276 queries.add( "Bornavirus parrot/PDD/2008" );
9277 final List<RANKS> ranks = new ArrayList<RANKS>();
9278 ranks.add( RANKS.SUPERKINGDOM );
9279 ranks.add( RANKS.KINGDOM );
9280 ranks.add( RANKS.FAMILY );
9281 ranks.add( RANKS.GENUS );
9282 ranks.add( RANKS.TRIBE );
9283 result = TxSearch.searchLineage( queries, ranks );
9284 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
9285 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
9287 catch ( final Exception e ) {
9288 System.out.println();
9289 System.out.println( "the following might be due to absence internet connection:" );
9290 e.printStackTrace( System.out );
9296 private static boolean testAminoAcidSequence() {
9298 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
9299 if ( aa1.getLength() != 13 ) {
9302 if ( aa1.getResidueAt( 0 ) != 'A' ) {
9305 if ( aa1.getResidueAt( 2 ) != 'K' ) {
9308 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
9311 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
9312 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
9315 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
9316 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
9319 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
9320 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
9324 catch ( final Exception e ) {
9325 e.printStackTrace();
9331 private static boolean testCreateBalancedPhylogeny() {
9333 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
9334 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
9337 if ( p0.getNumberOfExternalNodes() != 15625 ) {
9340 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
9341 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
9344 if ( p1.getNumberOfExternalNodes() != 100 ) {
9348 catch ( final Exception e ) {
9349 e.printStackTrace();
9355 private static boolean testFastaParser() {
9357 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
9360 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
9363 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
9364 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
9367 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
9370 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
9373 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
9376 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
9379 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
9383 catch ( final Exception e ) {
9384 e.printStackTrace();
9390 private static boolean testGeneralMsaParser() {
9392 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
9393 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
9394 final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
9395 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
9396 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
9397 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
9398 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
9399 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
9400 if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9403 if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9406 if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9409 if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9412 if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9415 if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9418 if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9421 if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9424 if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
9427 if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
9430 if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
9433 if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
9436 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
9437 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
9440 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
9443 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
9446 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
9447 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
9450 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
9453 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
9456 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
9457 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
9460 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
9463 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
9467 catch ( final Exception e ) {
9468 e.printStackTrace();
9474 private static boolean testMafft( final String path ) {
9476 final List<String> opts = new ArrayList<String>();
9477 opts.add( "--maxiterate" );
9479 opts.add( "--localpair" );
9480 opts.add( "--quiet" );
9482 final MsaInferrer mafft = Mafft.createInstance( path );
9483 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
9484 if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
9487 if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
9491 catch ( final Exception e ) {
9492 e.printStackTrace( System.out );
9498 private static boolean testNextNodeWithCollapsing() {
9500 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
9502 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
9503 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9504 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
9505 t0.getNode( "cd" ).setCollapse( true );
9506 t0.getNode( "cde" ).setCollapse( true );
9507 n = t0.getFirstExternalNode();
9508 while ( n != null ) {
9510 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9512 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9515 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9518 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
9521 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
9524 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
9527 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
9531 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9532 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
9533 t1.getNode( "ab" ).setCollapse( true );
9534 t1.getNode( "cd" ).setCollapse( true );
9535 t1.getNode( "cde" ).setCollapse( true );
9536 n = t1.getNode( "ab" );
9537 ext = new ArrayList<PhylogenyNode>();
9538 while ( n != null ) {
9540 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9542 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9545 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9548 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
9551 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
9554 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
9560 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9561 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
9562 t2.getNode( "ab" ).setCollapse( true );
9563 t2.getNode( "cd" ).setCollapse( true );
9564 t2.getNode( "cde" ).setCollapse( true );
9565 t2.getNode( "c" ).setCollapse( true );
9566 t2.getNode( "d" ).setCollapse( true );
9567 t2.getNode( "e" ).setCollapse( true );
9568 t2.getNode( "gh" ).setCollapse( true );
9569 n = t2.getNode( "ab" );
9570 ext = new ArrayList<PhylogenyNode>();
9571 while ( n != null ) {
9573 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9575 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9578 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9581 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
9584 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
9590 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9591 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
9592 t3.getNode( "ab" ).setCollapse( true );
9593 t3.getNode( "cd" ).setCollapse( true );
9594 t3.getNode( "cde" ).setCollapse( true );
9595 t3.getNode( "c" ).setCollapse( true );
9596 t3.getNode( "d" ).setCollapse( true );
9597 t3.getNode( "e" ).setCollapse( true );
9598 t3.getNode( "gh" ).setCollapse( true );
9599 t3.getNode( "fgh" ).setCollapse( true );
9600 n = t3.getNode( "ab" );
9601 ext = new ArrayList<PhylogenyNode>();
9602 while ( n != null ) {
9604 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9606 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9609 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
9612 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
9618 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9619 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
9620 t4.getNode( "ab" ).setCollapse( true );
9621 t4.getNode( "cd" ).setCollapse( true );
9622 t4.getNode( "cde" ).setCollapse( true );
9623 t4.getNode( "c" ).setCollapse( true );
9624 t4.getNode( "d" ).setCollapse( true );
9625 t4.getNode( "e" ).setCollapse( true );
9626 t4.getNode( "gh" ).setCollapse( true );
9627 t4.getNode( "fgh" ).setCollapse( true );
9628 t4.getNode( "abcdefgh" ).setCollapse( true );
9629 n = t4.getNode( "abcdefgh" );
9630 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
9635 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9636 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
9638 n = t5.getFirstExternalNode();
9639 while ( n != null ) {
9641 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9643 if ( ext.size() != 8 ) {
9646 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9649 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9652 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9655 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9658 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9661 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9664 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
9667 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
9672 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9673 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
9675 t6.getNode( "ab" ).setCollapse( true );
9676 n = t6.getNode( "ab" );
9677 while ( n != null ) {
9679 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9681 if ( ext.size() != 7 ) {
9684 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9687 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9690 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9693 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9696 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9699 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9702 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9707 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9708 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
9710 t7.getNode( "cd" ).setCollapse( true );
9711 n = t7.getNode( "a" );
9712 while ( n != null ) {
9714 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9716 if ( ext.size() != 7 ) {
9719 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9722 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9725 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9728 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9731 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9734 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9737 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9742 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
9743 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
9745 t8.getNode( "cd" ).setCollapse( true );
9746 t8.getNode( "c" ).setCollapse( true );
9747 t8.getNode( "d" ).setCollapse( true );
9748 n = t8.getNode( "a" );
9749 while ( n != null ) {
9751 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9753 if ( ext.size() != 7 ) {
9756 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9759 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9762 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
9763 System.out.println( "2 fail" );
9766 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9769 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
9772 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
9775 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
9780 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9781 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
9783 t9.getNode( "gh" ).setCollapse( true );
9784 n = t9.getNode( "a" );
9785 while ( n != null ) {
9787 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9789 if ( ext.size() != 7 ) {
9792 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9795 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9798 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9801 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9804 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9807 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9810 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9815 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9816 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
9818 t10.getNode( "gh" ).setCollapse( true );
9819 t10.getNode( "g" ).setCollapse( true );
9820 t10.getNode( "h" ).setCollapse( true );
9821 n = t10.getNode( "a" );
9822 while ( n != null ) {
9824 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9826 if ( ext.size() != 7 ) {
9829 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9832 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9835 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9838 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9841 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9844 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
9847 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
9852 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9853 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
9855 t11.getNode( "gh" ).setCollapse( true );
9856 t11.getNode( "fgh" ).setCollapse( true );
9857 n = t11.getNode( "a" );
9858 while ( n != null ) {
9860 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9862 if ( ext.size() != 6 ) {
9865 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9868 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9871 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9874 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9877 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9880 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9885 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9886 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
9888 t12.getNode( "gh" ).setCollapse( true );
9889 t12.getNode( "fgh" ).setCollapse( true );
9890 t12.getNode( "g" ).setCollapse( true );
9891 t12.getNode( "h" ).setCollapse( true );
9892 t12.getNode( "f" ).setCollapse( true );
9893 n = t12.getNode( "a" );
9894 while ( n != null ) {
9896 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9898 if ( ext.size() != 6 ) {
9901 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
9904 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
9907 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
9910 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
9913 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
9916 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
9921 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
9922 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
9924 t13.getNode( "ab" ).setCollapse( true );
9925 t13.getNode( "b" ).setCollapse( true );
9926 t13.getNode( "fgh" ).setCollapse( true );
9927 t13.getNode( "gh" ).setCollapse( true );
9928 n = t13.getNode( "ab" );
9929 while ( n != null ) {
9931 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9933 if ( ext.size() != 5 ) {
9936 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9939 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9942 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9945 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9948 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9953 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
9954 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
9956 t14.getNode( "ab" ).setCollapse( true );
9957 t14.getNode( "a" ).setCollapse( true );
9958 t14.getNode( "fgh" ).setCollapse( true );
9959 t14.getNode( "gh" ).setCollapse( true );
9960 n = t14.getNode( "ab" );
9961 while ( n != null ) {
9963 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9965 if ( ext.size() != 5 ) {
9968 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
9971 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
9974 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
9977 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
9980 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
9985 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" );
9986 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
9988 t15.getNode( "ab" ).setCollapse( true );
9989 t15.getNode( "a" ).setCollapse( true );
9990 t15.getNode( "fgh" ).setCollapse( true );
9991 t15.getNode( "gh" ).setCollapse( true );
9992 n = t15.getNode( "ab" );
9993 while ( n != null ) {
9995 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
9997 if ( ext.size() != 6 ) {
10000 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
10003 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
10006 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
10009 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
10012 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
10015 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
10020 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" );
10021 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
10023 t16.getNode( "ab" ).setCollapse( true );
10024 t16.getNode( "a" ).setCollapse( true );
10025 t16.getNode( "fgh" ).setCollapse( true );
10026 t16.getNode( "gh" ).setCollapse( true );
10027 t16.getNode( "cd" ).setCollapse( true );
10028 t16.getNode( "cde" ).setCollapse( true );
10029 t16.getNode( "d" ).setCollapse( true );
10030 t16.getNode( "x" ).setCollapse( true );
10031 n = t16.getNode( "ab" );
10032 while ( n != null ) {
10034 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
10036 if ( ext.size() != 4 ) {
10039 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
10042 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
10045 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
10048 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
10052 catch ( final Exception e ) {
10053 e.printStackTrace( System.out );
10059 private static boolean testMsaQualityMethod() {
10061 final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
10062 final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
10063 final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
10064 final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
10065 final List<Sequence> l = new ArrayList<Sequence>();
10070 final Msa msa = BasicMsa.createInstance( l );
10071 if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
10074 if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
10077 if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
10080 if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
10084 catch ( final Exception e ) {
10085 e.printStackTrace( System.out );
10091 private static boolean testSequenceIdParsing() {
10093 Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
10094 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10095 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10096 if ( id != null ) {
10097 System.out.println( "value =" + id.getValue() );
10098 System.out.println( "provider=" + id.getProvider() );
10103 id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
10104 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10105 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10106 if ( id != null ) {
10107 System.out.println( "value =" + id.getValue() );
10108 System.out.println( "provider=" + id.getProvider() );
10113 id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
10114 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10115 || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
10116 if ( id != null ) {
10117 System.out.println( "value =" + id.getValue() );
10118 System.out.println( "provider=" + id.getProvider() );
10123 id = SequenceIdParser.parse( "gb_AAA96518_1" );
10124 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10125 || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
10126 if ( id != null ) {
10127 System.out.println( "value =" + id.getValue() );
10128 System.out.println( "provider=" + id.getProvider() );
10133 id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
10134 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10135 || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
10136 if ( id != null ) {
10137 System.out.println( "value =" + id.getValue() );
10138 System.out.println( "provider=" + id.getProvider() );
10143 id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
10144 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10145 || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
10146 if ( id != null ) {
10147 System.out.println( "value =" + id.getValue() );
10148 System.out.println( "provider=" + id.getProvider() );
10153 id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
10154 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10155 || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
10156 if ( id != null ) {
10157 System.out.println( "value =" + id.getValue() );
10158 System.out.println( "provider=" + id.getProvider() );
10163 id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
10164 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10165 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
10166 if ( id != null ) {
10167 System.out.println( "value =" + id.getValue() );
10168 System.out.println( "provider=" + id.getProvider() );
10173 id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
10174 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10175 || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
10176 if ( id != null ) {
10177 System.out.println( "value =" + id.getValue() );
10178 System.out.println( "provider=" + id.getProvider() );
10183 id = SequenceIdParser.parse( "P4A123" );
10184 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10185 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
10186 if ( id != null ) {
10187 System.out.println( "value =" + id.getValue() );
10188 System.out.println( "provider=" + id.getProvider() );
10193 id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
10194 if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
10195 || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
10196 if ( id != null ) {
10197 System.out.println( "value =" + id.getValue() );
10198 System.out.println( "provider=" + id.getProvider() );
10203 id = SequenceIdParser.parse( "XP_12345" );
10204 if ( id != null ) {
10205 System.out.println( "value =" + id.getValue() );
10206 System.out.println( "provider=" + id.getProvider() );
10209 // lcl_91970_unknown_
10211 catch ( final Exception e ) {
10212 e.printStackTrace( System.out );