2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.Mafft;
58 import org.forester.msa.Msa;
59 import org.forester.msa.MsaInferrer;
60 import org.forester.pccx.TestPccx;
61 import org.forester.phylogeny.Phylogeny;
62 import org.forester.phylogeny.PhylogenyBranch;
63 import org.forester.phylogeny.PhylogenyMethods;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
66 import org.forester.phylogeny.data.BinaryCharacters;
67 import org.forester.phylogeny.data.BranchWidth;
68 import org.forester.phylogeny.data.Confidence;
69 import org.forester.phylogeny.data.Distribution;
70 import org.forester.phylogeny.data.DomainArchitecture;
71 import org.forester.phylogeny.data.Event;
72 import org.forester.phylogeny.data.Identifier;
73 import org.forester.phylogeny.data.PhylogenyData;
74 import org.forester.phylogeny.data.PhylogenyDataUtil;
75 import org.forester.phylogeny.data.Polygon;
76 import org.forester.phylogeny.data.PropertiesMap;
77 import org.forester.phylogeny.data.Property;
78 import org.forester.phylogeny.data.Property.AppliesTo;
79 import org.forester.phylogeny.data.ProteinDomain;
80 import org.forester.phylogeny.data.Taxonomy;
81 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
82 import org.forester.phylogeny.factories.PhylogenyFactory;
83 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
84 import org.forester.sdi.SDI;
85 import org.forester.sdi.SDIR;
86 import org.forester.sdi.SDIse;
87 import org.forester.sdi.TaxonomyAssigner;
88 import org.forester.sdi.TestGSDI;
89 import org.forester.sequence.BasicSequence;
90 import org.forester.sequence.Sequence;
91 import org.forester.surfacing.Protein;
92 import org.forester.surfacing.TestSurfacing;
93 import org.forester.tools.ConfidenceAssessor;
94 import org.forester.tools.SupportCount;
95 import org.forester.tools.TreeSplitMatrix;
96 import org.forester.util.AsciiHistogram;
97 import org.forester.util.BasicDescriptiveStatistics;
98 import org.forester.util.BasicTable;
99 import org.forester.util.BasicTableParser;
100 import org.forester.util.DescriptiveStatistics;
101 import org.forester.util.ForesterConstants;
102 import org.forester.util.ForesterUtil;
103 import org.forester.util.GeneralTable;
104 import org.forester.ws.uniprot.DatabaseTools;
105 import org.forester.ws.uniprot.SequenceDatabaseEntry;
106 import org.forester.ws.uniprot.UniProtTaxonomy;
107 import org.forester.ws.uniprot.UniProtWsTools;
108 import org.forester.ws.wabi.TxSearch;
109 import org.forester.ws.wabi.TxSearch.RANKS;
110 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
111 import org.forester.ws.wabi.TxSearch.TAX_RANK;
113 @SuppressWarnings( "unused")
114 public final class Test {
116 private final static double ZERO_DIFF = 1.0E-9;
117 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
118 + ForesterUtil.getFileSeparator() + "test_data"
119 + ForesterUtil.getFileSeparator();
120 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
121 + ForesterUtil.getFileSeparator() + "resources"
122 + ForesterUtil.getFileSeparator();
123 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
124 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
125 + ForesterConstants.PHYLO_XML_VERSION + "/"
126 + ForesterConstants.PHYLO_XML_XSD;
127 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
128 + ForesterConstants.PHYLO_XML_VERSION + "/"
129 + ForesterConstants.PHYLO_XML_XSD;
131 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
132 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
136 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
137 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
138 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
141 public static boolean isEqual( final double a, final double b ) {
142 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
145 public static void main( final String[] args ) {
146 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
147 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
149 Locale.setDefault( Locale.US );
150 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
153 System.out.print( "[Test if directory with files for testing exists/is readable: " );
154 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
155 System.out.println( "OK.]" );
158 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
159 System.out.println( "Testing aborted." );
162 System.out.print( "[Test if resources directory exists/is readable: " );
163 if ( testDir( PATH_TO_RESOURCES ) ) {
164 System.out.println( "OK.]" );
167 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
168 System.out.println( "Testing aborted." );
171 final long start_time = new Date().getTime();
172 System.out.print( "Hmmscan output parser: " );
173 if ( testHmmscanOutputParser() ) {
174 System.out.println( "OK." );
178 System.out.println( "failed." );
181 System.out.print( "Basic node methods: " );
182 if ( Test.testBasicNodeMethods() ) {
183 System.out.println( "OK." );
187 System.out.println( "failed." );
190 System.out.print( "Basic node construction and parsing of NHX (node level): " );
191 if ( Test.testNHXNodeParsing() ) {
192 System.out.println( "OK." );
196 System.out.println( "failed." );
199 System.out.print( "NH parsing: " );
200 if ( Test.testNHParsing() ) {
201 System.out.println( "OK." );
205 System.out.println( "failed." );
208 System.out.print( "Conversion to NHX (node level): " );
209 if ( Test.testNHXconversion() ) {
210 System.out.println( "OK." );
214 System.out.println( "failed." );
217 System.out.print( "NHX parsing: " );
218 if ( Test.testNHXParsing() ) {
219 System.out.println( "OK." );
223 System.out.println( "failed." );
226 System.out.print( "NHX parsing with quotes: " );
227 if ( Test.testNHXParsingQuotes() ) {
228 System.out.println( "OK." );
232 System.out.println( "failed." );
235 System.out.print( "NHX parsing (MrBayes): " );
236 if ( Test.testNHXParsingMB() ) {
237 System.out.println( "OK." );
241 System.out.println( "failed." );
244 System.out.print( "Nexus characters parsing: " );
245 if ( Test.testNexusCharactersParsing() ) {
246 System.out.println( "OK." );
250 System.out.println( "failed." );
253 System.out.print( "Nexus tree parsing: " );
254 if ( Test.testNexusTreeParsing() ) {
255 System.out.println( "OK." );
259 System.out.println( "failed." );
262 System.out.print( "Nexus tree parsing (translating): " );
263 if ( Test.testNexusTreeParsingTranslating() ) {
264 System.out.println( "OK." );
268 System.out.println( "failed." );
271 System.out.print( "Nexus matrix parsing: " );
272 if ( Test.testNexusMatrixParsing() ) {
273 System.out.println( "OK." );
277 System.out.println( "failed." );
280 System.out.print( "Basic phyloXML parsing: " );
281 if ( Test.testBasicPhyloXMLparsing() ) {
282 System.out.println( "OK." );
286 System.out.println( "failed." );
289 System.out.print( "Basic phyloXML parsing (validating against schema): " );
290 if ( testBasicPhyloXMLparsingValidating() ) {
291 System.out.println( "OK." );
295 System.out.println( "failed." );
298 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
299 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
300 System.out.println( "OK." );
304 System.out.println( "failed." );
307 System.out.print( "phyloXML Distribution Element: " );
308 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
309 System.out.println( "OK." );
313 System.out.println( "failed." );
316 System.out.print( "Tol XML parsing: " );
317 if ( Test.testBasicTolXMLparsing() ) {
318 System.out.println( "OK." );
322 System.out.println( "failed." );
325 System.out.print( "Copying of node data: " );
326 if ( Test.testCopyOfNodeData() ) {
327 System.out.println( "OK." );
331 System.out.println( "failed." );
334 System.out.print( "Basic tree methods: " );
335 if ( Test.testBasicTreeMethods() ) {
336 System.out.println( "OK." );
340 System.out.println( "failed." );
343 System.out.print( "Postorder Iterator: " );
344 if ( Test.testPostOrderIterator() ) {
345 System.out.println( "OK." );
349 System.out.println( "failed." );
352 System.out.print( "Preorder Iterator: " );
353 if ( Test.testPreOrderIterator() ) {
354 System.out.println( "OK." );
358 System.out.println( "failed." );
361 System.out.print( "Levelorder Iterator: " );
362 if ( Test.testLevelOrderIterator() ) {
363 System.out.println( "OK." );
367 System.out.println( "failed." );
370 System.out.print( "Re-id methods: " );
371 if ( Test.testReIdMethods() ) {
372 System.out.println( "OK." );
376 System.out.println( "failed." );
379 System.out.print( "Methods on last external nodes: " );
380 if ( Test.testLastExternalNodeMethods() ) {
381 System.out.println( "OK." );
385 System.out.println( "failed." );
388 System.out.print( "Methods on external nodes: " );
389 if ( Test.testExternalNodeRelatedMethods() ) {
390 System.out.println( "OK." );
394 System.out.println( "failed." );
397 System.out.print( "Deletion of external nodes: " );
398 if ( Test.testDeletionOfExternalNodes() ) {
399 System.out.println( "OK." );
403 System.out.println( "failed." );
406 System.out.print( "Subtree deletion: " );
407 if ( Test.testSubtreeDeletion() ) {
408 System.out.println( "OK." );
412 System.out.println( "failed." );
415 System.out.print( "Phylogeny branch: " );
416 if ( Test.testPhylogenyBranch() ) {
417 System.out.println( "OK." );
421 System.out.println( "failed." );
424 System.out.print( "Rerooting: " );
425 if ( Test.testRerooting() ) {
426 System.out.println( "OK." );
430 System.out.println( "failed." );
433 System.out.print( "Mipoint rooting: " );
434 if ( Test.testMidpointrooting() ) {
435 System.out.println( "OK." );
439 System.out.println( "failed." );
442 System.out.print( "Support count: " );
443 if ( Test.testSupportCount() ) {
444 System.out.println( "OK." );
448 System.out.println( "failed." );
451 System.out.print( "Support transfer: " );
452 if ( Test.testSupportTransfer() ) {
453 System.out.println( "OK." );
457 System.out.println( "failed." );
460 System.out.print( "Finding of LCA: " );
461 if ( Test.testGetLCA() ) {
462 System.out.println( "OK." );
466 System.out.println( "failed." );
469 System.out.print( "Calculation of distance between nodes: " );
470 if ( Test.testGetDistance() ) {
471 System.out.println( "OK." );
475 System.out.println( "failed." );
478 System.out.print( "SDIse: " );
479 if ( Test.testSDIse() ) {
480 System.out.println( "OK." );
484 System.out.println( "failed." );
487 System.out.print( "Taxonomy assigner: " );
488 if ( Test.testTaxonomyAssigner() ) {
489 System.out.println( "OK." );
493 System.out.println( "failed." );
496 System.out.print( "SDIunrooted: " );
497 if ( Test.testSDIunrooted() ) {
498 System.out.println( "OK." );
502 System.out.println( "failed." );
505 System.out.print( "GSDI: " );
506 if ( TestGSDI.test() ) {
507 System.out.println( "OK." );
511 System.out.println( "failed." );
514 System.out.print( "Descriptive statistics: " );
515 if ( Test.testDescriptiveStatistics() ) {
516 System.out.println( "OK." );
520 System.out.println( "failed." );
523 System.out.print( "Data objects and methods: " );
524 if ( Test.testDataObjects() ) {
525 System.out.println( "OK." );
529 System.out.println( "failed." );
532 System.out.print( "Properties map: " );
533 if ( Test.testPropertiesMap() ) {
534 System.out.println( "OK." );
538 System.out.println( "failed." );
541 System.out.print( "Phylogeny reconstruction:" );
542 System.out.println();
543 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
544 System.out.println( "OK." );
548 System.out.println( "failed." );
551 System.out.print( "Analysis of domain architectures: " );
552 System.out.println();
553 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
554 System.out.println( "OK." );
558 System.out.println( "failed." );
561 System.out.print( "GO: " );
562 System.out.println();
563 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
564 System.out.println( "OK." );
568 System.out.println( "failed." );
571 System.out.print( "Modeling tools: " );
572 if ( TestPccx.test() ) {
573 System.out.println( "OK." );
577 System.out.println( "failed." );
580 System.out.print( "Split Matrix strict: " );
581 if ( Test.testSplitStrict() ) {
582 System.out.println( "OK." );
586 System.out.println( "failed." );
589 System.out.print( "Split Matrix: " );
590 if ( Test.testSplit() ) {
591 System.out.println( "OK." );
595 System.out.println( "failed." );
598 System.out.print( "Confidence Assessor: " );
599 if ( Test.testConfidenceAssessor() ) {
600 System.out.println( "OK." );
604 System.out.println( "failed." );
607 System.out.print( "Basic table: " );
608 if ( Test.testBasicTable() ) {
609 System.out.println( "OK." );
613 System.out.println( "failed." );
616 System.out.print( "General table: " );
617 if ( Test.testGeneralTable() ) {
618 System.out.println( "OK." );
622 System.out.println( "failed." );
625 System.out.print( "Amino acid sequence: " );
626 if ( Test.testAminoAcidSequence() ) {
627 System.out.println( "OK." );
631 System.out.println( "failed." );
634 System.out.print( "General MSA parser: " );
635 if ( Test.testGeneralMsaParser() ) {
636 System.out.println( "OK." );
640 System.out.println( "failed." );
643 System.out.print( "Fasta parser for msa: " );
644 if ( Test.testFastaParser() ) {
645 System.out.println( "OK." );
649 System.out.println( "failed." );
652 System.out.print( "Creation of balanced phylogeny: " );
653 if ( Test.testCreateBalancedPhylogeny() ) {
654 System.out.println( "OK." );
658 System.out.println( "failed." );
661 System.out.print( "EMBL Entry Retrieval: " );
662 if ( Test.testEmblEntryRetrieval() ) {
663 System.out.println( "OK." );
667 System.out.println( "failed." );
670 System.out.print( "Uniprot Entry Retrieval: " );
671 if ( Test.testUniprotEntryRetrieval() ) {
672 System.out.println( "OK." );
676 System.out.println( "failed." );
679 System.out.print( "Uniprot Taxonomy Search: " );
680 if ( Test.testUniprotTaxonomySearch() ) {
681 System.out.println( "OK." );
685 System.out.println( "failed." );
688 if ( Mafft.isInstalled() ) {
689 System.out.print( "MAFFT (external program): " );
690 if ( Test.testMafft() ) {
691 System.out.println( "OK." );
695 System.out.println( "failed [will not count towards failed tests]" );
698 System.out.print( "Next nodes with collapsed: " );
699 if ( Test.testNextNodeWithCollapsing() ) {
700 System.out.println( "OK." );
704 System.out.println( "failed." );
707 // System.out.print( "WABI TxSearch: " );
708 // if ( Test.testWabiTxSearch() ) {
709 // System.out.println( "OK." );
714 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
716 System.out.println();
717 final Runtime rt = java.lang.Runtime.getRuntime();
718 final long free_memory = rt.freeMemory() / 1000000;
719 final long total_memory = rt.totalMemory() / 1000000;
720 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
721 + free_memory + "MB, total memory: " + total_memory + "MB)" );
722 System.out.println();
723 System.out.println( "Successful tests: " + succeeded );
724 System.out.println( "Failed tests: " + failed );
725 System.out.println();
727 System.out.println( "OK." );
730 System.out.println( "Not OK." );
732 // System.out.println();
733 // Development.setTime( true );
735 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
736 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
737 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
738 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
739 // "multifurcations_ex_1.nhx";
740 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
741 // final Phylogeny t1 = factory.create( new File( domains ), new
742 // NHXParser() )[ 0 ];
743 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
745 // catch ( final Exception e ) {
746 // e.printStackTrace();
748 // t1.getRoot().preorderPrint();
749 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
753 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
754 // + "\\AtNBSpos.nhx" ) );
756 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
757 // new NHXParser() );
758 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
759 // + "\\AtNBSpos.nhx" ) );
761 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
762 // new NHXParser() );
765 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
766 // + "\\big_tree.nhx" ) );
767 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
768 // + "\\big_tree.nhx" ) );
770 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
771 // new NHXParser() );
773 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
774 // new NHXParser() );
776 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
777 // + "\\big_tree.nhx" ) );
778 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
779 // + "\\big_tree.nhx" ) );
782 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
783 // new NHXParser() );
785 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
786 // new NHXParser() );
788 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
789 // + "\\AtNBSpos.nhx" ) );
791 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
792 // new NHXParser() );
795 // catch ( IOException e ) {
796 // // TODO Auto-generated catch block
797 // e.printStackTrace();
801 private static boolean testBasicNodeMethods() {
803 if ( PhylogenyNode.getNodeCount() != 0 ) {
806 final PhylogenyNode n1 = new PhylogenyNode();
807 final PhylogenyNode n2 = PhylogenyNode
808 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
809 final PhylogenyNode n3 = PhylogenyNode
810 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
811 final PhylogenyNode n4 = PhylogenyNode
812 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
813 if ( n1.isHasAssignedEvent() ) {
816 if ( PhylogenyNode.getNodeCount() != 4 ) {
819 if ( n3.getIndicator() != 0 ) {
822 if ( n3.getNumberOfExternalNodes() != 1 ) {
825 if ( !n3.isExternal() ) {
828 if ( !n3.isRoot() ) {
831 if ( !n4.getName().equals( "n4" ) ) {
835 catch ( final Exception e ) {
836 e.printStackTrace( System.out );
842 private static boolean testBasicPhyloXMLparsing() {
844 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
845 final PhyloXmlParser xml_parser = new PhyloXmlParser();
846 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
848 if ( xml_parser.getErrorCount() > 0 ) {
849 System.out.println( xml_parser.getErrorMessages().toString() );
852 if ( phylogenies_0.length != 4 ) {
855 final Phylogeny t1 = phylogenies_0[ 0 ];
856 final Phylogeny t2 = phylogenies_0[ 1 ];
857 final Phylogeny t3 = phylogenies_0[ 2 ];
858 final Phylogeny t4 = phylogenies_0[ 3 ];
859 if ( t1.getNumberOfExternalNodes() != 1 ) {
862 if ( !t1.isRooted() ) {
865 if ( t1.isRerootable() ) {
868 if ( !t1.getType().equals( "gene_tree" ) ) {
871 if ( t2.getNumberOfExternalNodes() != 2 ) {
874 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
877 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
880 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
883 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
886 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
889 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
892 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
893 .startsWith( "actgtgggggt" ) ) {
896 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
897 .startsWith( "ctgtgatgcat" ) ) {
900 if ( t3.getNumberOfExternalNodes() != 4 ) {
903 if ( !t1.getName().equals( "t1" ) ) {
906 if ( !t2.getName().equals( "t2" ) ) {
909 if ( !t3.getName().equals( "t3" ) ) {
912 if ( !t4.getName().equals( "t4" ) ) {
915 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
918 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
921 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
924 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
925 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
928 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
931 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
934 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
937 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
938 .equals( "apoptosis" ) ) {
941 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
942 .equals( "GO:0006915" ) ) {
945 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
946 .equals( "UniProtKB" ) ) {
949 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
950 .equals( "experimental" ) ) {
953 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
954 .equals( "function" ) ) {
957 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
961 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
962 .getType().equals( "ml" ) ) {
965 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
966 .equals( "apoptosis" ) ) {
969 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
970 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
973 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
974 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
977 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
978 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
981 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
982 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
985 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
986 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
989 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
990 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
993 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
994 .equals( "GO:0005829" ) ) {
997 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
998 .equals( "intracellular organelle" ) ) {
1001 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1004 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1005 .equals( "UniProt link" ) ) ) {
1008 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1011 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1014 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1017 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1020 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1023 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1026 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1029 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1032 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1035 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1038 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1039 // .equals( "B" ) ) {
1042 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1045 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1048 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1051 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1052 // .getConfidence() != 2144 ) {
1055 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1056 // .equals( "pfam" ) ) {
1059 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1062 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1065 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1068 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1071 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1072 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1076 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1079 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1082 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1085 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1088 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1091 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1094 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1097 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1099 // if ( xml_parser.getErrorCount() > 0 ) {
1100 // System.out.println( xml_parser.getErrorMessages().toString() );
1103 // if ( phylogenies_1.length != 2 ) {
1106 // final Phylogeny a = phylogenies_1[ 0 ];
1107 // if ( !a.getName().equals( "tree 4" ) ) {
1110 // if ( a.getNumberOfExternalNodes() != 3 ) {
1113 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1116 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1120 catch ( final Exception e ) {
1121 e.printStackTrace( System.out );
1127 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1129 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1130 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1131 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1132 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1135 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1137 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1139 if ( xml_parser.getErrorCount() > 0 ) {
1140 System.out.println( xml_parser.getErrorMessages().toString() );
1143 if ( phylogenies_0.length != 4 ) {
1146 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1147 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1148 if ( phylogenies_t1.length != 1 ) {
1151 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1152 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1155 if ( !t1_rt.isRooted() ) {
1158 if ( t1_rt.isRerootable() ) {
1161 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1164 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1165 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1166 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1167 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1170 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1173 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1176 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1179 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1180 .startsWith( "actgtgggggt" ) ) {
1183 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1184 .startsWith( "ctgtgatgcat" ) ) {
1187 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1188 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1189 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1190 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1191 if ( phylogenies_1.length != 1 ) {
1194 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1195 if ( !t3_rt.getName().equals( "t3" ) ) {
1198 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1201 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1204 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1207 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1210 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1211 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1214 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1217 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1220 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1221 .equals( "UniProtKB" ) ) {
1224 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1225 .equals( "apoptosis" ) ) {
1228 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1229 .equals( "GO:0006915" ) ) {
1232 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1233 .equals( "UniProtKB" ) ) {
1236 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1237 .equals( "experimental" ) ) {
1240 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1241 .equals( "function" ) ) {
1244 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1245 .getValue() != 1 ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1249 .getType().equals( "ml" ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1253 .equals( "apoptosis" ) ) {
1256 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1257 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1260 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1261 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1264 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1265 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1268 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1269 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1272 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1273 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1276 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1277 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1280 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1281 .equals( "GO:0005829" ) ) {
1284 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1285 .equals( "intracellular organelle" ) ) {
1288 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1291 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1292 .equals( "UniProt link" ) ) ) {
1295 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1298 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1301 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1302 .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." ) ) ) {
1305 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1308 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1311 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1314 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1317 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1318 .equals( "ncbi" ) ) {
1321 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1324 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1325 .getName().equals( "B" ) ) {
1328 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1329 .getFrom() != 21 ) {
1332 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1335 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1336 .getLength() != 24 ) {
1339 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1340 .getConfidence() != 2144 ) {
1343 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1344 .equals( "pfam" ) ) {
1347 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1350 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1353 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1356 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1359 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1360 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1363 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1366 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1369 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1372 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1375 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1378 if ( taxbb.getSynonyms().size() != 2 ) {
1381 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1384 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1387 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1390 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1393 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1396 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1397 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1401 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1404 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1407 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1410 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1413 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1416 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1419 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1423 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1426 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1427 .equalsIgnoreCase( "435" ) ) {
1430 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1433 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1434 .equalsIgnoreCase( "443.7" ) ) {
1437 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1440 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1443 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1444 .equalsIgnoreCase( "433" ) ) {
1448 catch ( final Exception e ) {
1449 e.printStackTrace( System.out );
1455 private static boolean testBasicPhyloXMLparsingValidating() {
1457 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1458 PhyloXmlParser xml_parser = null;
1460 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1462 catch ( final Exception e ) {
1463 // Do nothing -- means were not running from jar.
1465 if ( xml_parser == null ) {
1466 xml_parser = new PhyloXmlParser();
1467 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1468 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1471 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1474 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1476 if ( xml_parser.getErrorCount() > 0 ) {
1477 System.out.println( xml_parser.getErrorMessages().toString() );
1480 if ( phylogenies_0.length != 4 ) {
1483 final Phylogeny t1 = phylogenies_0[ 0 ];
1484 final Phylogeny t2 = phylogenies_0[ 1 ];
1485 final Phylogeny t3 = phylogenies_0[ 2 ];
1486 final Phylogeny t4 = phylogenies_0[ 3 ];
1487 if ( !t1.getName().equals( "t1" ) ) {
1490 if ( !t2.getName().equals( "t2" ) ) {
1493 if ( !t3.getName().equals( "t3" ) ) {
1496 if ( !t4.getName().equals( "t4" ) ) {
1499 if ( t1.getNumberOfExternalNodes() != 1 ) {
1502 if ( t2.getNumberOfExternalNodes() != 2 ) {
1505 if ( t3.getNumberOfExternalNodes() != 4 ) {
1508 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1509 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1510 if ( xml_parser.getErrorCount() > 0 ) {
1511 System.out.println( "errors:" );
1512 System.out.println( xml_parser.getErrorMessages().toString() );
1515 if ( phylogenies_1.length != 4 ) {
1518 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1520 if ( xml_parser.getErrorCount() > 0 ) {
1521 System.out.println( "errors:" );
1522 System.out.println( xml_parser.getErrorMessages().toString() );
1525 if ( phylogenies_2.length != 1 ) {
1528 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1531 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1533 if ( xml_parser.getErrorCount() > 0 ) {
1534 System.out.println( xml_parser.getErrorMessages().toString() );
1537 if ( phylogenies_3.length != 2 ) {
1540 final Phylogeny a = phylogenies_3[ 0 ];
1541 if ( !a.getName().equals( "tree 4" ) ) {
1544 if ( a.getNumberOfExternalNodes() != 3 ) {
1547 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1550 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1553 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1555 if ( xml_parser.getErrorCount() > 0 ) {
1556 System.out.println( xml_parser.getErrorMessages().toString() );
1559 if ( phylogenies_4.length != 1 ) {
1562 final Phylogeny s = phylogenies_4[ 0 ];
1563 if ( s.getNumberOfExternalNodes() != 6 ) {
1566 s.getNode( "first" );
1568 s.getNode( "\"<a'b&c'd\">\"" );
1569 s.getNode( "'''\"" );
1570 s.getNode( "\"\"\"" );
1571 s.getNode( "dick & doof" );
1573 catch ( final Exception e ) {
1574 e.printStackTrace( System.out );
1580 private static boolean testBasicTable() {
1582 final BasicTable<String> t0 = new BasicTable<String>();
1583 if ( t0.getNumberOfColumns() != 0 ) {
1586 if ( t0.getNumberOfRows() != 0 ) {
1589 t0.setValue( 3, 2, "23" );
1590 t0.setValue( 10, 1, "error" );
1591 t0.setValue( 10, 1, "110" );
1592 t0.setValue( 9, 1, "19" );
1593 t0.setValue( 1, 10, "101" );
1594 t0.setValue( 10, 10, "1010" );
1595 t0.setValue( 100, 10, "10100" );
1596 t0.setValue( 0, 0, "00" );
1597 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1600 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1603 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1606 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1609 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1612 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1615 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1618 if ( t0.getNumberOfColumns() != 101 ) {
1621 if ( t0.getNumberOfRows() != 11 ) {
1624 if ( t0.getValueAsString( 49, 4 ) != null ) {
1627 final String l = ForesterUtil.getLineSeparator();
1628 final StringBuffer source = new StringBuffer();
1629 source.append( "" + l );
1630 source.append( "# 1 1 1 1 1 1 1 1" + l );
1631 source.append( " 00 01 02 03" + l );
1632 source.append( " 10 11 12 13 " + l );
1633 source.append( "20 21 22 23 " + l );
1634 source.append( " 30 31 32 33" + l );
1635 source.append( "40 41 42 43" + l );
1636 source.append( " # 1 1 1 1 1 " + l );
1637 source.append( "50 51 52 53 54" + l );
1638 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1639 if ( t1.getNumberOfColumns() != 5 ) {
1642 if ( t1.getNumberOfRows() != 6 ) {
1645 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1648 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1651 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1654 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1657 final StringBuffer source1 = new StringBuffer();
1658 source1.append( "" + l );
1659 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1660 source1.append( " 00; 01 ;02;03" + l );
1661 source1.append( " 10; 11; 12; 13 " + l );
1662 source1.append( "20; 21; 22; 23 " + l );
1663 source1.append( " 30; 31; 32; 33" + l );
1664 source1.append( "40;41;42;43" + l );
1665 source1.append( " # 1 1 1 1 1 " + l );
1666 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1667 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1668 if ( t2.getNumberOfColumns() != 5 ) {
1671 if ( t2.getNumberOfRows() != 6 ) {
1674 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1677 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1680 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1683 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1686 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1689 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1692 final StringBuffer source2 = new StringBuffer();
1693 source2.append( "" + l );
1694 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1695 source2.append( " 00; 01 ;02;03" + l );
1696 source2.append( " 10; 11; 12; 13 " + l );
1697 source2.append( "20; 21; 22; 23 " + l );
1698 source2.append( " " + l );
1699 source2.append( " 30; 31; 32; 33" + l );
1700 source2.append( "40;41;42;43" + l );
1701 source2.append( " comment: 1 1 1 1 1 " + l );
1702 source2.append( ";;;50 ; 52; 53;;54 " + l );
1703 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 PhylogenyNodeIterator it;
1907 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1910 for( it.reset(); it.hasNext(); ) {
1913 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1914 if ( !it2.next().getName().equals( "A" ) ) {
1917 if ( !it2.next().getName().equals( "B" ) ) {
1920 if ( !it2.next().getName().equals( "C" ) ) {
1923 if ( it2.hasNext() ) {
1926 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 ];
1927 if ( t4.getNumberOfExternalNodes() != 9 ) {
1930 if ( t4.getHeight() != 11 ) {
1933 if ( t4.isCompletelyBinary() ) {
1936 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)" );
1937 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1938 if ( t5.getNumberOfExternalNodes() != 8 ) {
1941 if ( t5.getHeight() != 15 ) {
1944 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)" );
1945 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1946 if ( t6.getHeight() != 15 ) {
1949 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)" );
1950 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1951 if ( t7.getHeight() != 15 ) {
1954 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)" );
1955 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1956 if ( t8.getNumberOfExternalNodes() != 10 ) {
1959 if ( t8.getHeight() != 15 ) {
1962 final char[] a9 = new char[] {};
1963 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1964 if ( t9.getHeight() != 0 ) {
1967 final char[] a10 = new char[] { 'a', ':', '6' };
1968 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1969 if ( t10.getHeight() != 6 ) {
1973 catch ( final Exception e ) {
1974 e.printStackTrace( System.out );
1980 private static boolean testConfidenceAssessor() {
1982 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1983 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1984 final Phylogeny[] ev0 = factory
1985 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1987 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1988 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1991 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1994 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1995 final Phylogeny[] ev1 = factory
1996 .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)));",
1998 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1999 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2002 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2005 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2006 final Phylogeny[] ev_b = factory
2007 .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",
2009 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2010 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2011 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2014 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2018 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2019 final Phylogeny[] ev1x = factory
2020 .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)));",
2022 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2023 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2026 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2029 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2030 final Phylogeny[] ev_bx = factory
2031 .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",
2033 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2034 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2037 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2041 final Phylogeny[] t2 = factory
2042 .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);",
2044 final Phylogeny[] ev2 = factory
2045 .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);",
2047 for( final Phylogeny target : t2 ) {
2048 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2051 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2052 new NHXParser() )[ 0 ];
2053 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2054 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2055 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2058 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2061 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2065 catch ( final Exception e ) {
2066 e.printStackTrace();
2072 private static boolean testCopyOfNodeData() {
2074 final PhylogenyNode n1 = PhylogenyNode
2075 .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]" );
2076 final PhylogenyNode n2 = n1.copyNodeData();
2077 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2081 catch ( final Exception e ) {
2082 e.printStackTrace();
2088 private static boolean testDataObjects() {
2090 final Confidence s0 = new Confidence();
2091 final Confidence s1 = new Confidence();
2092 if ( !s0.isEqual( s1 ) ) {
2095 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2096 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2097 if ( s2.isEqual( s1 ) ) {
2100 if ( !s2.isEqual( s3 ) ) {
2103 final Confidence s4 = ( Confidence ) s3.copy();
2104 if ( !s4.isEqual( s3 ) ) {
2111 final Taxonomy t1 = new Taxonomy();
2112 final Taxonomy t2 = new Taxonomy();
2113 final Taxonomy t3 = new Taxonomy();
2114 final Taxonomy t4 = new Taxonomy();
2115 final Taxonomy t5 = new Taxonomy();
2116 t1.setIdentifier( new Identifier( "ecoli" ) );
2117 t1.setTaxonomyCode( "ECOLI" );
2118 t1.setScientificName( "E. coli" );
2119 t1.setCommonName( "coli" );
2120 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2121 if ( !t1.isEqual( t0 ) ) {
2124 t2.setIdentifier( new Identifier( "ecoli" ) );
2125 t2.setTaxonomyCode( "other" );
2126 t2.setScientificName( "what" );
2127 t2.setCommonName( "something" );
2128 if ( !t1.isEqual( t2 ) ) {
2131 t2.setIdentifier( new Identifier( "nemve" ) );
2132 if ( t1.isEqual( t2 ) ) {
2135 t1.setIdentifier( null );
2136 t3.setTaxonomyCode( "ECOLI" );
2137 t3.setScientificName( "what" );
2138 t3.setCommonName( "something" );
2139 if ( !t1.isEqual( t3 ) ) {
2142 t1.setIdentifier( null );
2143 t1.setTaxonomyCode( "" );
2144 t4.setScientificName( "E. ColI" );
2145 t4.setCommonName( "something" );
2146 if ( !t1.isEqual( t4 ) ) {
2149 t4.setScientificName( "B. subtilis" );
2150 t4.setCommonName( "something" );
2151 if ( t1.isEqual( t4 ) ) {
2154 t1.setIdentifier( null );
2155 t1.setTaxonomyCode( "" );
2156 t1.setScientificName( "" );
2157 t5.setCommonName( "COLI" );
2158 if ( !t1.isEqual( t5 ) ) {
2161 t5.setCommonName( "vibrio" );
2162 if ( t1.isEqual( t5 ) ) {
2167 final Identifier id0 = new Identifier( "123", "pfam" );
2168 final Identifier id1 = ( Identifier ) id0.copy();
2169 if ( !id1.isEqual( id1 ) ) {
2172 if ( !id1.isEqual( id0 ) ) {
2175 if ( !id0.isEqual( id1 ) ) {
2182 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2183 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2184 if ( !pd1.isEqual( pd1 ) ) {
2187 if ( !pd1.isEqual( pd0 ) ) {
2192 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2193 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2194 if ( !pd3.isEqual( pd3 ) ) {
2197 if ( !pd2.isEqual( pd3 ) ) {
2200 if ( !pd0.isEqual( pd3 ) ) {
2205 // DomainArchitecture
2206 // ------------------
2207 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2208 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2209 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2210 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2211 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2212 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2217 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2218 if ( ds0.getNumberOfDomains() != 4 ) {
2221 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2222 if ( !ds0.isEqual( ds0 ) ) {
2225 if ( !ds0.isEqual( ds1 ) ) {
2228 if ( ds1.getNumberOfDomains() != 4 ) {
2231 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2236 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2237 if ( ds0.isEqual( ds2 ) ) {
2243 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2244 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2245 System.out.println( ds3.toNHX() );
2248 if ( ds3.getNumberOfDomains() != 3 ) {
2253 final Event e1 = new Event( Event.EventType.fusion );
2254 if ( e1.isDuplication() ) {
2257 if ( !e1.isFusion() ) {
2260 if ( !e1.asText().toString().equals( "fusion" ) ) {
2263 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2266 final Event e11 = new Event( Event.EventType.fusion );
2267 if ( !e11.isEqual( e1 ) ) {
2270 if ( !e11.toNHX().toString().equals( "" ) ) {
2273 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2274 if ( e2.isDuplication() ) {
2277 if ( !e2.isSpeciationOrDuplication() ) {
2280 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2283 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2286 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2289 if ( e11.isEqual( e2 ) ) {
2292 final Event e2c = ( Event ) e2.copy();
2293 if ( !e2c.isEqual( e2 ) ) {
2296 Event e3 = new Event( 1, 2, 3 );
2297 if ( e3.isDuplication() ) {
2300 if ( e3.isSpeciation() ) {
2303 if ( e3.isGeneLoss() ) {
2306 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2309 final Event e3c = ( Event ) e3.copy();
2310 final Event e3cc = ( Event ) e3c.copy();
2311 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2315 if ( !e3c.isEqual( e3cc ) ) {
2318 Event e4 = new Event( 1, 2, 3 );
2319 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2322 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2325 final Event e4c = ( Event ) e4.copy();
2327 final Event e4cc = ( Event ) e4c.copy();
2328 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2331 if ( !e4c.isEqual( e4cc ) ) {
2334 final Event e5 = new Event();
2335 if ( !e5.isUnassigned() ) {
2338 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2341 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2344 final Event e6 = new Event( 1, 0, 0 );
2345 if ( !e6.asText().toString().equals( "duplication" ) ) {
2348 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2351 final Event e7 = new Event( 0, 1, 0 );
2352 if ( !e7.asText().toString().equals( "speciation" ) ) {
2355 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2358 final Event e8 = new Event( 0, 0, 1 );
2359 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2362 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2366 catch ( final Exception e ) {
2367 e.printStackTrace( System.out );
2373 private static boolean testDeletionOfExternalNodes() {
2375 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2376 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2377 final PhylogenyWriter w = new PhylogenyWriter();
2378 if ( t0.isEmpty() ) {
2381 if ( t0.getNumberOfExternalNodes() != 1 ) {
2384 t0.deleteSubtree( t0.getNode( "A" ), false );
2385 if ( t0.getNumberOfExternalNodes() != 0 ) {
2388 if ( !t0.isEmpty() ) {
2391 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2392 if ( t1.getNumberOfExternalNodes() != 2 ) {
2395 t1.deleteSubtree( t1.getNode( "A" ), false );
2396 if ( t1.getNumberOfExternalNodes() != 1 ) {
2399 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2402 t1.deleteSubtree( t1.getNode( "B" ), false );
2403 if ( t1.getNumberOfExternalNodes() != 1 ) {
2406 t1.deleteSubtree( t1.getNode( "r" ), false );
2407 if ( !t1.isEmpty() ) {
2410 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2411 if ( t2.getNumberOfExternalNodes() != 3 ) {
2414 t2.deleteSubtree( t2.getNode( "B" ), false );
2415 if ( t2.getNumberOfExternalNodes() != 2 ) {
2418 t2.toNewHampshireX();
2419 PhylogenyNode n = t2.getNode( "A" );
2420 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2423 t2.deleteSubtree( t2.getNode( "A" ), false );
2424 if ( t2.getNumberOfExternalNodes() != 2 ) {
2427 t2.deleteSubtree( t2.getNode( "C" ), true );
2428 if ( t2.getNumberOfExternalNodes() != 1 ) {
2431 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2432 if ( t3.getNumberOfExternalNodes() != 4 ) {
2435 t3.deleteSubtree( t3.getNode( "B" ), true );
2436 if ( t3.getNumberOfExternalNodes() != 3 ) {
2439 n = t3.getNode( "A" );
2440 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2443 n = n.getNextExternalNode();
2444 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2447 t3.deleteSubtree( t3.getNode( "A" ), true );
2448 if ( t3.getNumberOfExternalNodes() != 2 ) {
2451 n = t3.getNode( "C" );
2452 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2455 t3.deleteSubtree( t3.getNode( "C" ), true );
2456 if ( t3.getNumberOfExternalNodes() != 1 ) {
2459 t3.deleteSubtree( t3.getNode( "D" ), true );
2460 if ( t3.getNumberOfExternalNodes() != 0 ) {
2463 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2464 if ( t4.getNumberOfExternalNodes() != 6 ) {
2467 t4.deleteSubtree( t4.getNode( "B2" ), true );
2468 if ( t4.getNumberOfExternalNodes() != 5 ) {
2471 String s = w.toNewHampshire( t4, false, true ).toString();
2472 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2475 t4.deleteSubtree( t4.getNode( "B11" ), true );
2476 if ( t4.getNumberOfExternalNodes() != 4 ) {
2479 t4.deleteSubtree( t4.getNode( "C" ), true );
2480 if ( t4.getNumberOfExternalNodes() != 3 ) {
2483 n = t4.getNode( "A" );
2484 n = n.getNextExternalNode();
2485 if ( !n.getName().equals( "B12" ) ) {
2488 n = n.getNextExternalNode();
2489 if ( !n.getName().equals( "D" ) ) {
2492 s = w.toNewHampshire( t4, false, true ).toString();
2493 if ( !s.equals( "((A,B12),D);" ) ) {
2496 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2497 t5.deleteSubtree( t5.getNode( "A" ), true );
2498 if ( t5.getNumberOfExternalNodes() != 5 ) {
2501 s = w.toNewHampshire( t5, false, true ).toString();
2502 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2505 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2506 t6.deleteSubtree( t6.getNode( "B11" ), true );
2507 if ( t6.getNumberOfExternalNodes() != 5 ) {
2510 s = w.toNewHampshire( t6, false, false ).toString();
2511 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2514 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2515 t7.deleteSubtree( t7.getNode( "B12" ), true );
2516 if ( t7.getNumberOfExternalNodes() != 5 ) {
2519 s = w.toNewHampshire( t7, false, true ).toString();
2520 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2523 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2524 t8.deleteSubtree( t8.getNode( "B2" ), true );
2525 if ( t8.getNumberOfExternalNodes() != 5 ) {
2528 s = w.toNewHampshire( t8, false, false ).toString();
2529 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2532 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2533 t9.deleteSubtree( t9.getNode( "C" ), true );
2534 if ( t9.getNumberOfExternalNodes() != 5 ) {
2537 s = w.toNewHampshire( t9, false, true ).toString();
2538 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2541 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2542 t10.deleteSubtree( t10.getNode( "D" ), true );
2543 if ( t10.getNumberOfExternalNodes() != 5 ) {
2546 s = w.toNewHampshire( t10, false, true ).toString();
2547 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2550 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2551 t11.deleteSubtree( t11.getNode( "A" ), true );
2552 if ( t11.getNumberOfExternalNodes() != 2 ) {
2555 s = w.toNewHampshire( t11, false, true ).toString();
2556 if ( !s.equals( "(B,C);" ) ) {
2559 t11.deleteSubtree( t11.getNode( "C" ), true );
2560 if ( t11.getNumberOfExternalNodes() != 1 ) {
2563 s = w.toNewHampshire( t11, false, false ).toString();
2564 if ( !s.equals( "B;" ) ) {
2567 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2568 t12.deleteSubtree( t12.getNode( "B2" ), true );
2569 if ( t12.getNumberOfExternalNodes() != 8 ) {
2572 s = w.toNewHampshire( t12, false, true ).toString();
2573 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2576 t12.deleteSubtree( t12.getNode( "B3" ), true );
2577 if ( t12.getNumberOfExternalNodes() != 7 ) {
2580 s = w.toNewHampshire( t12, false, true ).toString();
2581 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2584 t12.deleteSubtree( t12.getNode( "C3" ), true );
2585 if ( t12.getNumberOfExternalNodes() != 6 ) {
2588 s = w.toNewHampshire( t12, false, true ).toString();
2589 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2592 t12.deleteSubtree( t12.getNode( "A1" ), true );
2593 if ( t12.getNumberOfExternalNodes() != 5 ) {
2596 s = w.toNewHampshire( t12, false, true ).toString();
2597 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2600 t12.deleteSubtree( t12.getNode( "B1" ), true );
2601 if ( t12.getNumberOfExternalNodes() != 4 ) {
2604 s = w.toNewHampshire( t12, false, true ).toString();
2605 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2608 t12.deleteSubtree( t12.getNode( "A3" ), true );
2609 if ( t12.getNumberOfExternalNodes() != 3 ) {
2612 s = w.toNewHampshire( t12, false, true ).toString();
2613 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2616 t12.deleteSubtree( t12.getNode( "A2" ), true );
2617 if ( t12.getNumberOfExternalNodes() != 2 ) {
2620 s = w.toNewHampshire( t12, false, true ).toString();
2621 if ( !s.equals( "(C1,C2);" ) ) {
2624 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2625 t13.deleteSubtree( t13.getNode( "D" ), true );
2626 if ( t13.getNumberOfExternalNodes() != 4 ) {
2629 s = w.toNewHampshire( t13, false, true ).toString();
2630 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2633 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2634 t14.deleteSubtree( t14.getNode( "E" ), true );
2635 if ( t14.getNumberOfExternalNodes() != 5 ) {
2638 s = w.toNewHampshire( t14, false, true ).toString();
2639 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2642 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2643 t15.deleteSubtree( t15.getNode( "B2" ), true );
2644 if ( t15.getNumberOfExternalNodes() != 11 ) {
2647 t15.deleteSubtree( t15.getNode( "B1" ), true );
2648 if ( t15.getNumberOfExternalNodes() != 10 ) {
2651 t15.deleteSubtree( t15.getNode( "B3" ), true );
2652 if ( t15.getNumberOfExternalNodes() != 9 ) {
2655 t15.deleteSubtree( t15.getNode( "B4" ), true );
2656 if ( t15.getNumberOfExternalNodes() != 8 ) {
2659 t15.deleteSubtree( t15.getNode( "A1" ), true );
2660 if ( t15.getNumberOfExternalNodes() != 7 ) {
2663 t15.deleteSubtree( t15.getNode( "C4" ), true );
2664 if ( t15.getNumberOfExternalNodes() != 6 ) {
2668 catch ( final Exception e ) {
2669 e.printStackTrace( System.out );
2675 private static boolean testDescriptiveStatistics() {
2677 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2678 dss1.addValue( 82 );
2679 dss1.addValue( 78 );
2680 dss1.addValue( 70 );
2681 dss1.addValue( 58 );
2682 dss1.addValue( 42 );
2683 if ( dss1.getN() != 5 ) {
2686 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2689 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2692 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2695 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2698 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2701 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2704 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2707 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2710 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2713 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2716 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2719 dss1.addValue( 123 );
2720 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2723 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2726 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2729 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2730 dss2.addValue( -1.85 );
2731 dss2.addValue( 57.5 );
2732 dss2.addValue( 92.78 );
2733 dss2.addValue( 57.78 );
2734 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2737 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2740 final double[] a = dss2.getDataAsDoubleArray();
2741 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2744 dss2.addValue( -100 );
2745 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2748 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2751 final double[] ds = new double[ 14 ];
2766 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2767 if ( bins.length != 4 ) {
2770 if ( bins[ 0 ] != 2 ) {
2773 if ( bins[ 1 ] != 3 ) {
2776 if ( bins[ 2 ] != 4 ) {
2779 if ( bins[ 3 ] != 5 ) {
2782 final double[] ds1 = new double[ 9 ];
2792 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2793 if ( bins1.length != 4 ) {
2796 if ( bins1[ 0 ] != 2 ) {
2799 if ( bins1[ 1 ] != 3 ) {
2802 if ( bins1[ 2 ] != 0 ) {
2805 if ( bins1[ 3 ] != 4 ) {
2808 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2809 if ( bins1_1.length != 3 ) {
2812 if ( bins1_1[ 0 ] != 3 ) {
2815 if ( bins1_1[ 1 ] != 2 ) {
2818 if ( bins1_1[ 2 ] != 4 ) {
2821 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2822 if ( bins1_2.length != 3 ) {
2825 if ( bins1_2[ 0 ] != 2 ) {
2828 if ( bins1_2[ 1 ] != 2 ) {
2831 if ( bins1_2[ 2 ] != 2 ) {
2834 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2848 dss3.addValue( 10 );
2849 dss3.addValue( 10 );
2850 dss3.addValue( 10 );
2851 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2852 histo.toStringBuffer( 10, '=', 40, 5 );
2853 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2855 catch ( final Exception e ) {
2856 e.printStackTrace( System.out );
2862 private static boolean testDir( final String file ) {
2864 final File f = new File( file );
2865 if ( !f.exists() ) {
2868 if ( !f.isDirectory() ) {
2871 if ( !f.canRead() ) {
2875 catch ( final Exception e ) {
2881 private static boolean testExternalNodeRelatedMethods() {
2883 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2884 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2885 PhylogenyNode n = t1.getNode( "A" );
2886 n = n.getNextExternalNode();
2887 if ( !n.getName().equals( "B" ) ) {
2890 n = n.getNextExternalNode();
2891 if ( !n.getName().equals( "C" ) ) {
2894 n = n.getNextExternalNode();
2895 if ( !n.getName().equals( "D" ) ) {
2898 n = t1.getNode( "B" );
2899 while ( !n.isLastExternalNode() ) {
2900 n = n.getNextExternalNode();
2902 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2903 n = t2.getNode( "A" );
2904 n = n.getNextExternalNode();
2905 if ( !n.getName().equals( "B" ) ) {
2908 n = n.getNextExternalNode();
2909 if ( !n.getName().equals( "C" ) ) {
2912 n = n.getNextExternalNode();
2913 if ( !n.getName().equals( "D" ) ) {
2916 n = t2.getNode( "B" );
2917 while ( !n.isLastExternalNode() ) {
2918 n = n.getNextExternalNode();
2920 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2921 n = t3.getNode( "A" );
2922 n = n.getNextExternalNode();
2923 if ( !n.getName().equals( "B" ) ) {
2926 n = n.getNextExternalNode();
2927 if ( !n.getName().equals( "C" ) ) {
2930 n = n.getNextExternalNode();
2931 if ( !n.getName().equals( "D" ) ) {
2934 n = n.getNextExternalNode();
2935 if ( !n.getName().equals( "E" ) ) {
2938 n = n.getNextExternalNode();
2939 if ( !n.getName().equals( "F" ) ) {
2942 n = n.getNextExternalNode();
2943 if ( !n.getName().equals( "G" ) ) {
2946 n = n.getNextExternalNode();
2947 if ( !n.getName().equals( "H" ) ) {
2950 n = t3.getNode( "B" );
2951 while ( !n.isLastExternalNode() ) {
2952 n = n.getNextExternalNode();
2954 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2955 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2956 final PhylogenyNode node = iter.next();
2958 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2959 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2960 final PhylogenyNode node = iter.next();
2963 catch ( final Exception e ) {
2964 e.printStackTrace( System.out );
2970 private static boolean testGeneralTable() {
2972 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2973 t0.setValue( 3, 2, "23" );
2974 t0.setValue( 10, 1, "error" );
2975 t0.setValue( 10, 1, "110" );
2976 t0.setValue( 9, 1, "19" );
2977 t0.setValue( 1, 10, "101" );
2978 t0.setValue( 10, 10, "1010" );
2979 t0.setValue( 100, 10, "10100" );
2980 t0.setValue( 0, 0, "00" );
2981 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2984 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2987 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2990 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2993 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2996 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2999 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3002 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3005 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3008 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3009 t1.setValue( "3", "2", "23" );
3010 t1.setValue( "10", "1", "error" );
3011 t1.setValue( "10", "1", "110" );
3012 t1.setValue( "9", "1", "19" );
3013 t1.setValue( "1", "10", "101" );
3014 t1.setValue( "10", "10", "1010" );
3015 t1.setValue( "100", "10", "10100" );
3016 t1.setValue( "0", "0", "00" );
3017 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3018 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3021 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3024 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3027 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3030 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3033 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3036 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3039 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3042 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3045 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3049 catch ( final Exception e ) {
3050 e.printStackTrace( System.out );
3056 private static boolean testGetDistance() {
3058 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3059 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",
3060 new NHXParser() )[ 0 ];
3061 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3062 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3065 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3068 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3071 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3074 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3077 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3080 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3083 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3086 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3089 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3092 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3095 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3098 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3101 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3104 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3107 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3110 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3113 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3116 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3119 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3122 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3125 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3128 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3131 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3134 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3137 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3140 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3143 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3146 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3149 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3152 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3155 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",
3156 new NHXParser() )[ 0 ];
3157 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3160 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3163 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3166 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3169 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3172 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3175 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3178 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3181 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3184 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3187 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3191 catch ( final Exception e ) {
3192 e.printStackTrace( System.out );
3198 private static boolean testGetLCA() {
3200 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3201 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3202 new NHXParser() )[ 0 ];
3203 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3204 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3205 if ( !A.getName().equals( "A" ) ) {
3208 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3209 if ( !gh.getName().equals( "gh" ) ) {
3212 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3213 if ( !ab.getName().equals( "ab" ) ) {
3216 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3217 if ( !ab2.getName().equals( "ab" ) ) {
3220 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3221 if ( !gh2.getName().equals( "gh" ) ) {
3224 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3225 if ( !gh3.getName().equals( "gh" ) ) {
3228 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3229 if ( !abc.getName().equals( "abc" ) ) {
3232 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3233 if ( !abc2.getName().equals( "abc" ) ) {
3236 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3237 if ( !abcd.getName().equals( "abcd" ) ) {
3240 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3241 if ( !abcd2.getName().equals( "abcd" ) ) {
3244 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3245 if ( !abcdef.getName().equals( "abcdef" ) ) {
3248 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3249 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3252 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3253 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3256 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3257 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3260 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3261 if ( !abcde.getName().equals( "abcde" ) ) {
3264 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3265 if ( !abcde2.getName().equals( "abcde" ) ) {
3268 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3269 if ( !r.getName().equals( "abcdefgh" ) ) {
3272 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3273 if ( !r2.getName().equals( "abcdefgh" ) ) {
3276 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3277 if ( !r3.getName().equals( "abcdefgh" ) ) {
3280 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3281 if ( !abcde3.getName().equals( "abcde" ) ) {
3284 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3285 if ( !abcde4.getName().equals( "abcde" ) ) {
3288 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3289 if ( !ab3.getName().equals( "ab" ) ) {
3292 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3293 if ( !ab4.getName().equals( "ab" ) ) {
3296 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3297 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3298 if ( !cd.getName().equals( "cd" ) ) {
3301 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3302 if ( !cd2.getName().equals( "cd" ) ) {
3305 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3306 if ( !cde.getName().equals( "cde" ) ) {
3309 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3310 if ( !cde2.getName().equals( "cde" ) ) {
3313 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3314 if ( !cdef.getName().equals( "cdef" ) ) {
3317 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3318 if ( !cdef2.getName().equals( "cdef" ) ) {
3321 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3322 if ( !cdef3.getName().equals( "cdef" ) ) {
3325 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3326 if ( !rt.getName().equals( "r" ) ) {
3329 final Phylogeny p3 = factory
3330 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3331 new NHXParser() )[ 0 ];
3332 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3333 if ( !bc_3.getName().equals( "bc" ) ) {
3336 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3337 if ( !ac_3.getName().equals( "abc" ) ) {
3340 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3341 if ( !ad_3.getName().equals( "abcde" ) ) {
3344 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3345 if ( !af_3.getName().equals( "abcdef" ) ) {
3348 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3349 if ( !ag_3.getName().equals( "" ) ) {
3352 if ( !ag_3.isRoot() ) {
3355 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3356 if ( !al_3.getName().equals( "" ) ) {
3359 if ( !al_3.isRoot() ) {
3362 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3363 if ( !kl_3.getName().equals( "" ) ) {
3366 if ( !kl_3.isRoot() ) {
3369 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3370 if ( !fl_3.getName().equals( "" ) ) {
3373 if ( !fl_3.isRoot() ) {
3376 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3377 if ( !gk_3.getName().equals( "ghijk" ) ) {
3380 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3381 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3382 if ( !r_4.getName().equals( "r" ) ) {
3385 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3386 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3387 if ( !r_5.getName().equals( "root" ) ) {
3390 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3391 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3392 if ( !r_6.getName().equals( "rot" ) ) {
3395 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3396 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3397 if ( !r_7.getName().equals( "rott" ) ) {
3401 catch ( final Exception e ) {
3402 e.printStackTrace( System.out );
3408 private static boolean testHmmscanOutputParser() {
3409 final String test_dir = Test.PATH_TO_TEST_DATA;
3411 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3412 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3414 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3415 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3416 final List<Protein> proteins = parser2.parse();
3417 if ( parser2.getProteinsEncountered() != 4 ) {
3420 if ( proteins.size() != 4 ) {
3423 if ( parser2.getDomainsEncountered() != 69 ) {
3426 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3429 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3432 final Protein p1 = proteins.get( 0 );
3433 if ( p1.getNumberOfProteinDomains() != 15 ) {
3436 final Protein p2 = proteins.get( 1 );
3437 if ( p2.getNumberOfProteinDomains() != 51 ) {
3440 final Protein p3 = proteins.get( 2 );
3441 if ( p3.getNumberOfProteinDomains() != 2 ) {
3444 final Protein p4 = proteins.get( 3 );
3445 if ( p4.getNumberOfProteinDomains() != 1 ) {
3448 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3451 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3454 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3457 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3460 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3463 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3466 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3469 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3472 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3476 catch ( final Exception e ) {
3477 e.printStackTrace( System.out );
3483 private static boolean testLastExternalNodeMethods() {
3485 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3486 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3487 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3488 final PhylogenyNode n1 = t0.getNode( "A" );
3489 if ( n1.isLastExternalNode() ) {
3492 final PhylogenyNode n2 = t0.getNode( "B" );
3493 if ( n2.isLastExternalNode() ) {
3496 final PhylogenyNode n3 = t0.getNode( "C" );
3497 if ( n3.isLastExternalNode() ) {
3500 final PhylogenyNode n4 = t0.getNode( "D" );
3501 if ( !n4.isLastExternalNode() ) {
3505 catch ( final Exception e ) {
3506 e.printStackTrace( System.out );
3512 private static boolean testLevelOrderIterator() {
3514 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3515 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3516 PhylogenyNodeIterator it0;
3517 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3520 for( it0.reset(); it0.hasNext(); ) {
3523 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3524 if ( !it.next().getName().equals( "r" ) ) {
3527 if ( !it.next().getName().equals( "ab" ) ) {
3530 if ( !it.next().getName().equals( "cd" ) ) {
3533 if ( !it.next().getName().equals( "A" ) ) {
3536 if ( !it.next().getName().equals( "B" ) ) {
3539 if ( !it.next().getName().equals( "C" ) ) {
3542 if ( !it.next().getName().equals( "D" ) ) {
3545 if ( it.hasNext() ) {
3548 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",
3549 new NHXParser() )[ 0 ];
3550 PhylogenyNodeIterator it2;
3551 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3554 for( it2.reset(); it2.hasNext(); ) {
3557 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3558 if ( !it3.next().getName().equals( "r" ) ) {
3561 if ( !it3.next().getName().equals( "abc" ) ) {
3564 if ( !it3.next().getName().equals( "defg" ) ) {
3567 if ( !it3.next().getName().equals( "A" ) ) {
3570 if ( !it3.next().getName().equals( "B" ) ) {
3573 if ( !it3.next().getName().equals( "C" ) ) {
3576 if ( !it3.next().getName().equals( "D" ) ) {
3579 if ( !it3.next().getName().equals( "E" ) ) {
3582 if ( !it3.next().getName().equals( "F" ) ) {
3585 if ( !it3.next().getName().equals( "G" ) ) {
3588 if ( !it3.next().getName().equals( "1" ) ) {
3591 if ( !it3.next().getName().equals( "2" ) ) {
3594 if ( !it3.next().getName().equals( "3" ) ) {
3597 if ( !it3.next().getName().equals( "4" ) ) {
3600 if ( !it3.next().getName().equals( "5" ) ) {
3603 if ( !it3.next().getName().equals( "6" ) ) {
3606 if ( !it3.next().getName().equals( "f1" ) ) {
3609 if ( !it3.next().getName().equals( "f2" ) ) {
3612 if ( !it3.next().getName().equals( "f3" ) ) {
3615 if ( !it3.next().getName().equals( "a" ) ) {
3618 if ( !it3.next().getName().equals( "b" ) ) {
3621 if ( !it3.next().getName().equals( "f21" ) ) {
3624 if ( !it3.next().getName().equals( "X" ) ) {
3627 if ( !it3.next().getName().equals( "Y" ) ) {
3630 if ( !it3.next().getName().equals( "Z" ) ) {
3633 if ( it3.hasNext() ) {
3636 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3637 PhylogenyNodeIterator it4;
3638 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3641 for( it4.reset(); it4.hasNext(); ) {
3644 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3645 if ( !it5.next().getName().equals( "r" ) ) {
3648 if ( !it5.next().getName().equals( "A" ) ) {
3651 if ( !it5.next().getName().equals( "B" ) ) {
3654 if ( !it5.next().getName().equals( "C" ) ) {
3657 if ( !it5.next().getName().equals( "D" ) ) {
3660 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3661 PhylogenyNodeIterator it6;
3662 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3665 for( it6.reset(); it6.hasNext(); ) {
3668 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3669 if ( !it7.next().getName().equals( "A" ) ) {
3672 if ( it.hasNext() ) {
3676 catch ( final Exception e ) {
3677 e.printStackTrace( System.out );
3683 private static boolean testMidpointrooting() {
3685 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3686 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",
3687 new NHXParser() )[ 0 ];
3688 if ( !t1.isRooted() ) {
3691 PhylogenyMethods.midpointRoot( t1 );
3692 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3695 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3698 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3701 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3704 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3707 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3710 t1.reRoot( t1.getNode( "A" ) );
3711 PhylogenyMethods.midpointRoot( t1 );
3712 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3715 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3718 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3721 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3724 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3727 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3731 catch ( final Exception e ) {
3732 e.printStackTrace( System.out );
3738 private static boolean testNexusCharactersParsing() {
3740 final NexusCharactersParser parser = new NexusCharactersParser();
3741 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3743 String[] labels = parser.getCharStateLabels();
3744 if ( labels.length != 7 ) {
3747 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3750 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3753 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3756 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3759 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3762 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3765 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3768 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3770 labels = parser.getCharStateLabels();
3771 if ( labels.length != 7 ) {
3774 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3777 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3780 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3783 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3786 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3789 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3792 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3796 catch ( final Exception e ) {
3797 e.printStackTrace( System.out );
3803 private static boolean testNexusMatrixParsing() {
3805 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3806 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3808 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3809 if ( m.getNumberOfCharacters() != 9 ) {
3812 if ( m.getNumberOfIdentifiers() != 5 ) {
3815 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3818 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3821 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3824 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3827 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3830 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3833 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3836 // if ( labels.length != 7 ) {
3839 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3842 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3845 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3848 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3851 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3854 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3857 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3860 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3862 // labels = parser.getCharStateLabels();
3863 // if ( labels.length != 7 ) {
3866 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3869 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3872 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3875 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3878 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3881 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3884 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3888 catch ( final Exception e ) {
3889 e.printStackTrace( System.out );
3895 private static boolean testNexusTreeParsing() {
3897 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3898 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3899 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3900 if ( phylogenies.length != 1 ) {
3903 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3906 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3910 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3911 if ( phylogenies.length != 1 ) {
3914 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3917 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3921 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3922 if ( phylogenies.length != 1 ) {
3925 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3928 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3931 if ( phylogenies[ 0 ].isRooted() ) {
3935 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3936 if ( phylogenies.length != 18 ) {
3939 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3942 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3945 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3948 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3951 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3954 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3957 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3960 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3963 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3966 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3969 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3972 if ( phylogenies[ 8 ].isRooted() ) {
3975 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3978 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3981 if ( !phylogenies[ 9 ].isRooted() ) {
3984 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3987 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3990 if ( !phylogenies[ 10 ].isRooted() ) {
3993 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3996 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3999 if ( phylogenies[ 11 ].isRooted() ) {
4002 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4005 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4008 if ( !phylogenies[ 12 ].isRooted() ) {
4011 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4014 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4017 if ( !phylogenies[ 13 ].isRooted() ) {
4020 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4023 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4026 if ( !phylogenies[ 14 ].isRooted() ) {
4029 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4032 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4035 if ( phylogenies[ 15 ].isRooted() ) {
4038 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4041 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4044 if ( !phylogenies[ 16 ].isRooted() ) {
4047 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4050 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4053 if ( phylogenies[ 17 ].isRooted() ) {
4056 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4060 catch ( final Exception e ) {
4061 e.printStackTrace( System.out );
4067 private static boolean testNexusTreeParsingTranslating() {
4069 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4070 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4071 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4072 if ( phylogenies.length != 1 ) {
4075 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4078 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4081 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4084 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4087 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4088 .equals( "Aranaeus" ) ) {
4092 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4093 if ( phylogenies.length != 3 ) {
4096 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4099 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4102 if ( phylogenies[ 0 ].isRooted() ) {
4105 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4108 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4111 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4112 .equals( "Aranaeus" ) ) {
4115 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4118 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4121 if ( phylogenies[ 1 ].isRooted() ) {
4124 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4127 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4130 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4131 .equals( "Aranaeus" ) ) {
4134 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4137 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4140 if ( !phylogenies[ 2 ].isRooted() ) {
4143 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4146 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4149 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4150 .equals( "Aranaeus" ) ) {
4154 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4155 if ( phylogenies.length != 3 ) {
4158 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4161 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4164 if ( phylogenies[ 0 ].isRooted() ) {
4167 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4170 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4173 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4174 .equals( "Aranaeus" ) ) {
4177 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4180 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4183 if ( phylogenies[ 1 ].isRooted() ) {
4186 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4189 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4192 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4193 .equals( "Aranaeus" ) ) {
4196 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4199 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4202 if ( !phylogenies[ 2 ].isRooted() ) {
4205 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4208 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4211 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4212 .equals( "Aranaeus" ) ) {
4216 catch ( final Exception e ) {
4217 e.printStackTrace( System.out );
4223 private static boolean testNHParsing() {
4225 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4226 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4227 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4230 final NHXParser nhxp = new NHXParser();
4231 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4232 nhxp.setReplaceUnderscores( true );
4233 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4234 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4237 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4240 final Phylogeny p1b = factory
4241 .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 ",
4242 new NHXParser() )[ 0 ];
4243 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4246 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4249 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4250 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4251 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4252 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4253 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4254 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4255 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4256 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4257 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4258 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4259 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4260 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4261 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4263 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4266 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4269 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4272 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4275 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4276 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4277 final String p16_S = "((A,B),C)";
4278 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4279 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4282 final String p17_S = "(C,(A,B))";
4283 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4284 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4287 final String p18_S = "((A,B),(C,D))";
4288 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4289 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4292 final String p19_S = "(((A,B),C),D)";
4293 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4294 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4297 final String p20_S = "(A,(B,(C,D)))";
4298 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4299 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4302 final String p21_S = "(A,(B,(C,(D,E))))";
4303 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4304 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4307 final String p22_S = "((((A,B),C),D),E)";
4308 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4309 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4312 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4313 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4314 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4317 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4318 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4319 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4322 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4323 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4324 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4325 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4328 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4331 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4332 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4333 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4334 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4335 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4336 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4337 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4338 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4339 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4340 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4343 final String p26_S = "(A,B)ab";
4344 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4345 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4348 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4349 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4351 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4354 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4355 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4356 final String p28_S3 = "(A,B)ab";
4357 final String p28_S4 = "((((A,B),C),D),;E;)";
4358 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4360 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4363 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4366 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4369 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4372 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";
4373 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4374 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4377 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";
4378 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4379 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4382 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4383 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4384 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4387 final String p33_S = "A";
4388 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4389 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4392 final String p34_S = "B;";
4393 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4394 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4397 final String p35_S = "B:0.2";
4398 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4399 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4402 final String p36_S = "(A)";
4403 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4404 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4407 final String p37_S = "((A))";
4408 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4409 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4412 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4413 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4414 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4417 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4418 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4419 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4422 final String p40_S = "(A,B,C)";
4423 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4424 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4427 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4428 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4429 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4432 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4433 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4434 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4437 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)";
4438 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4439 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4442 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)))";
4443 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4444 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4447 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4448 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4449 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4452 final String p46_S = "";
4453 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4454 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4457 final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
4458 if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4461 final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4462 if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4465 final Phylogeny p49 = factory
4466 .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
4467 new NHXParser() )[ 0 ];
4468 if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
4471 final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4472 if ( p50.getNode( "A" ) == null ) {
4475 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
4476 .equals( "((A,B)ab:2.0[88.0],C);" ) ) {
4479 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
4482 if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
4483 .equals( "((A,B)88.0:2.0,C);" ) ) {
4486 final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4487 if ( p51.getNode( "A(A" ) == null ) {
4490 final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
4491 if ( p52.getNode( "A(A" ) == null ) {
4494 final Phylogeny p53 = factory
4495 .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
4496 new NHXParser() )[ 0 ];
4497 if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
4501 catch ( final Exception e ) {
4502 e.printStackTrace( System.out );
4508 private static boolean testNHXconversion() {
4510 final PhylogenyNode n1 = new PhylogenyNode();
4511 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4512 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4513 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4514 final PhylogenyNode n5 = PhylogenyNode
4515 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4516 final PhylogenyNode n6 = PhylogenyNode
4517 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4518 if ( !n1.toNewHampshireX().equals( "" ) ) {
4521 if ( !n2.toNewHampshireX().equals( "" ) ) {
4524 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4527 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4530 if ( !n5.toNewHampshireX()
4531 .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56.0:W=2.0:C=10.20.30]" ) ) {
4534 if ( !n6.toNewHampshireX()
4535 .equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100.0:W=2.0:C=0.0.0]" ) ) {
4539 catch ( final Exception e ) {
4540 e.printStackTrace( System.out );
4546 private static boolean testNHXNodeParsing() {
4548 final PhylogenyNode n1 = new PhylogenyNode();
4549 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4550 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4551 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4552 final PhylogenyNode n5 = PhylogenyNode
4553 .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]" );
4554 if ( !n3.getName().equals( "n3" ) ) {
4557 if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4560 if ( n3.isDuplication() ) {
4563 if ( n3.isHasAssignedEvent() ) {
4566 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4569 if ( !n4.getName().equals( "n4" ) ) {
4572 if ( n4.getDistanceToParent() != 0.01 ) {
4575 if ( !n5.getName().equals( "n5" ) ) {
4578 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4581 if ( n5.getDistanceToParent() != 0.1 ) {
4584 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4587 if ( !n5.isDuplication() ) {
4590 if ( !n5.isHasAssignedEvent() ) {
4593 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4596 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4599 final PhylogenyNode n8 = PhylogenyNode
4600 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4601 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4602 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4605 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4608 final PhylogenyNode n9 = PhylogenyNode
4609 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4610 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4611 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4614 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4617 final PhylogenyNode n10 = PhylogenyNode
4618 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4619 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4622 final PhylogenyNode n20 = PhylogenyNode
4623 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4624 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4627 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4630 final PhylogenyNode n20x = PhylogenyNode
4631 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4632 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4635 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4638 final PhylogenyNode n20xx = PhylogenyNode
4639 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4640 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4643 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4646 final PhylogenyNode n20xxx = PhylogenyNode
4647 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4648 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4651 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4654 final PhylogenyNode n20xxxx = PhylogenyNode
4655 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4656 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4659 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4662 final PhylogenyNode n21 = PhylogenyNode
4663 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4664 if ( !n21.getName().equals( "n21_PIG" ) ) {
4667 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4670 final PhylogenyNode n21x = PhylogenyNode
4671 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4672 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4675 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4678 final PhylogenyNode n22 = PhylogenyNode
4679 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4680 if ( !n22.getName().equals( "n22/PIG" ) ) {
4683 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4686 final PhylogenyNode n23 = PhylogenyNode
4687 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4688 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4691 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4694 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4695 final PhylogenyNode a = PhylogenyNode
4696 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4697 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4698 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4701 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4704 final PhylogenyNode b = PhylogenyNode
4705 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4706 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4707 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4710 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4713 final PhylogenyNode c = PhylogenyNode
4714 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4715 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4716 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4719 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4722 final PhylogenyNode d = PhylogenyNode
4723 .createInstanceFromNhxString( "n10_RAT1/1-2",
4724 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4725 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4728 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4731 final PhylogenyNode e = PhylogenyNode
4732 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4733 if ( !e.getName().equals( "n10_RAT1" ) ) {
4736 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4740 final PhylogenyNode n11 = PhylogenyNode
4741 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4742 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4743 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4746 if ( n11.getDistanceToParent() != 0.4 ) {
4749 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4752 final PhylogenyNode n12 = PhylogenyNode
4753 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4754 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4755 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4758 if ( n12.getDistanceToParent() != 0.4 ) {
4761 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4764 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4765 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4766 if ( !tvu1.getRef().equals( "tag1" ) ) {
4769 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4772 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4775 if ( !tvu1.getValue().equals( "value1" ) ) {
4778 if ( !tvu3.getRef().equals( "tag3" ) ) {
4781 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4784 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4787 if ( !tvu3.getValue().equals( "value3" ) ) {
4790 if ( n1.getName().compareTo( "" ) != 0 ) {
4793 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4796 if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4799 if ( n2.getName().compareTo( "" ) != 0 ) {
4802 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4805 if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
4808 final PhylogenyNode n00 = PhylogenyNode
4809 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
4810 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4813 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4816 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4819 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4822 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4825 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4828 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4831 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4834 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4835 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4838 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4839 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4842 final PhylogenyNode n13 = PhylogenyNode
4843 .createInstanceFromNhxString( "blah_12345/1-2",
4844 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4845 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4848 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4851 final PhylogenyNode n14 = PhylogenyNode
4852 .createInstanceFromNhxString( "blah_12X45/1-2",
4853 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4854 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4857 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4860 final PhylogenyNode n15 = PhylogenyNode
4861 .createInstanceFromNhxString( "something_wicked[123]",
4862 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4863 if ( !n15.getName().equals( "something_wicked" ) ) {
4866 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4869 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4872 final PhylogenyNode n16 = PhylogenyNode
4873 .createInstanceFromNhxString( "something_wicked2[9]",
4874 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4875 if ( !n16.getName().equals( "something_wicked2" ) ) {
4878 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4881 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4884 final PhylogenyNode n17 = PhylogenyNode
4885 .createInstanceFromNhxString( "something_wicked3[a]",
4886 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4887 if ( !n17.getName().equals( "something_wicked3" ) ) {
4890 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4893 final PhylogenyNode n18 = PhylogenyNode
4894 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4895 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4898 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4901 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4905 catch ( final Exception e ) {
4906 e.printStackTrace( System.out );
4912 private static boolean testNHXParsing() {
4914 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4915 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4916 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4919 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]";
4920 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4921 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4924 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]";
4925 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4926 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4929 final Phylogeny[] p3 = factory
4930 .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]",
4932 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4935 final Phylogeny[] p4 = factory
4936 .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(]",
4938 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4941 final Phylogeny[] p5 = factory
4942 .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(((]",
4944 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4947 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)";
4948 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)";
4949 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4950 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4953 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)))";
4954 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)))";
4955 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4956 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4959 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]) ))[,,, ])))))))";
4960 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4961 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4962 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4965 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4966 if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) {
4969 final Phylogeny p10 = factory
4970 .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]",
4971 new NHXParser() )[ 0 ];
4972 if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91.0],C:0.1)root:0.1[&&NHX:B=100.0]" ) ) {
4976 catch ( final Exception e ) {
4977 e.printStackTrace( System.out );
4983 private static boolean testNHXParsingQuotes() {
4985 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4986 final NHXParser p = new NHXParser();
4987 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4988 if ( phylogenies_0.length != 5 ) {
4991 final Phylogeny phy = phylogenies_0[ 4 ];
4992 if ( phy.getNumberOfExternalNodes() != 7 ) {
4995 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4998 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
5001 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
5002 .getScientificName().equals( "hsapiens" ) ) {
5005 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
5008 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
5011 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
5014 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
5017 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
5020 final NHXParser p1p = new NHXParser();
5021 p1p.setIgnoreQuotes( true );
5022 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
5023 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
5026 final NHXParser p2p = new NHXParser();
5027 p1p.setIgnoreQuotes( false );
5028 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
5029 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
5032 final NHXParser p3p = new NHXParser();
5033 p3p.setIgnoreQuotes( false );
5034 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
5035 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
5038 final NHXParser p4p = new NHXParser();
5039 p4p.setIgnoreQuotes( false );
5040 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
5041 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
5044 final Phylogeny p10 = factory
5045 .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]",
5046 new NHXParser() )[ 0 ];
5047 final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]";
5048 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5051 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5052 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5056 final Phylogeny p12 = factory
5057 .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]",
5058 new NHXParser() )[ 0 ];
5059 final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91.0],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100.0]";
5060 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5063 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5064 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5067 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;";
5068 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5071 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5072 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5076 catch ( final Exception e ) {
5077 e.printStackTrace( System.out );
5083 private static boolean testNHXParsingMB() {
5085 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5086 final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
5087 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5088 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5089 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5090 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5091 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5092 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5093 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5094 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5095 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5098 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
5101 if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
5102 0.1100000000000000e+00 ) ) {
5105 if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
5108 if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
5111 final Phylogeny p2 = factory
5112 .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
5113 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5114 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5115 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5116 + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
5117 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5118 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5119 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5120 + "7.369400000000000e-02}])",
5121 new NHXParser() )[ 0 ];
5122 if ( p2.getNode( "1" ) == null ) {
5125 if ( p2.getNode( "2" ) == null ) {
5129 catch ( final Exception e ) {
5130 e.printStackTrace( System.out );
5137 private static boolean testPhylogenyBranch() {
5139 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5140 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5141 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5142 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5143 if ( !a1b1.equals( a1b1 ) ) {
5146 if ( !a1b1.equals( b1a1 ) ) {
5149 if ( !b1a1.equals( a1b1 ) ) {
5152 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5153 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5154 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5155 if ( a1_b1.equals( b1_a1 ) ) {
5158 if ( a1_b1.equals( a1_b1_ ) ) {
5161 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5162 if ( !a1_b1.equals( b1_a1_ ) ) {
5165 if ( a1_b1_.equals( b1_a1_ ) ) {
5168 if ( !a1_b1_.equals( b1_a1 ) ) {
5172 catch ( final Exception e ) {
5173 e.printStackTrace( System.out );
5179 private static boolean testPhyloXMLparsingOfDistributionElement() {
5181 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5182 PhyloXmlParser xml_parser = null;
5184 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5186 catch ( final Exception e ) {
5187 // Do nothing -- means were not running from jar.
5189 if ( xml_parser == null ) {
5190 xml_parser = new PhyloXmlParser();
5191 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5192 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5195 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5198 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5200 if ( xml_parser.getErrorCount() > 0 ) {
5201 System.out.println( xml_parser.getErrorMessages().toString() );
5204 if ( phylogenies_0.length != 1 ) {
5207 final Phylogeny t1 = phylogenies_0[ 0 ];
5208 PhylogenyNode n = null;
5209 Distribution d = null;
5210 n = t1.getNode( "root node" );
5211 if ( !n.getNodeData().isHasDistribution() ) {
5214 if ( n.getNodeData().getDistributions().size() != 1 ) {
5217 d = n.getNodeData().getDistribution();
5218 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5221 if ( d.getPoints().size() != 1 ) {
5224 if ( d.getPolygons() != null ) {
5227 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5230 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5233 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5236 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5239 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5242 n = t1.getNode( "node a" );
5243 if ( !n.getNodeData().isHasDistribution() ) {
5246 if ( n.getNodeData().getDistributions().size() != 2 ) {
5249 d = n.getNodeData().getDistribution( 1 );
5250 if ( !d.getDesc().equals( "San Diego" ) ) {
5253 if ( d.getPoints().size() != 1 ) {
5256 if ( d.getPolygons() != null ) {
5259 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5262 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5265 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5268 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5271 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5274 n = t1.getNode( "node bb" );
5275 if ( !n.getNodeData().isHasDistribution() ) {
5278 if ( n.getNodeData().getDistributions().size() != 1 ) {
5281 d = n.getNodeData().getDistribution( 0 );
5282 if ( d.getPoints().size() != 3 ) {
5285 if ( d.getPolygons().size() != 2 ) {
5288 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5291 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5294 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5297 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5300 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5303 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5306 Polygon p = d.getPolygons().get( 0 );
5307 if ( p.getPoints().size() != 3 ) {
5310 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5313 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5316 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5319 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5322 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5325 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5328 p = d.getPolygons().get( 1 );
5329 if ( p.getPoints().size() != 3 ) {
5332 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5335 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5338 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5342 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5343 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5344 if ( rt.length != 1 ) {
5347 final Phylogeny t1_rt = rt[ 0 ];
5348 n = t1_rt.getNode( "root node" );
5349 if ( !n.getNodeData().isHasDistribution() ) {
5352 if ( n.getNodeData().getDistributions().size() != 1 ) {
5355 d = n.getNodeData().getDistribution();
5356 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5359 if ( d.getPoints().size() != 1 ) {
5362 if ( d.getPolygons() != null ) {
5365 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5368 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5371 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5374 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5377 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5380 n = t1_rt.getNode( "node a" );
5381 if ( !n.getNodeData().isHasDistribution() ) {
5384 if ( n.getNodeData().getDistributions().size() != 2 ) {
5387 d = n.getNodeData().getDistribution( 1 );
5388 if ( !d.getDesc().equals( "San Diego" ) ) {
5391 if ( d.getPoints().size() != 1 ) {
5394 if ( d.getPolygons() != null ) {
5397 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5400 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5403 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5406 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5409 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5412 n = t1_rt.getNode( "node bb" );
5413 if ( !n.getNodeData().isHasDistribution() ) {
5416 if ( n.getNodeData().getDistributions().size() != 1 ) {
5419 d = n.getNodeData().getDistribution( 0 );
5420 if ( d.getPoints().size() != 3 ) {
5423 if ( d.getPolygons().size() != 2 ) {
5426 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5429 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5432 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5435 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5438 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5441 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5444 p = d.getPolygons().get( 0 );
5445 if ( p.getPoints().size() != 3 ) {
5448 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5451 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5454 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5457 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5460 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5463 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5466 p = d.getPolygons().get( 1 );
5467 if ( p.getPoints().size() != 3 ) {
5470 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5473 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5476 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5480 catch ( final Exception e ) {
5481 e.printStackTrace( System.out );
5487 private static boolean testPostOrderIterator() {
5489 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5490 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5491 PhylogenyNodeIterator it0;
5492 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5495 for( it0.reset(); it0.hasNext(); ) {
5498 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5499 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5500 if ( !it.next().getName().equals( "A" ) ) {
5503 if ( !it.next().getName().equals( "B" ) ) {
5506 if ( !it.next().getName().equals( "ab" ) ) {
5509 if ( !it.next().getName().equals( "C" ) ) {
5512 if ( !it.next().getName().equals( "D" ) ) {
5515 if ( !it.next().getName().equals( "cd" ) ) {
5518 if ( !it.next().getName().equals( "abcd" ) ) {
5521 if ( !it.next().getName().equals( "E" ) ) {
5524 if ( !it.next().getName().equals( "F" ) ) {
5527 if ( !it.next().getName().equals( "ef" ) ) {
5530 if ( !it.next().getName().equals( "G" ) ) {
5533 if ( !it.next().getName().equals( "H" ) ) {
5536 if ( !it.next().getName().equals( "gh" ) ) {
5539 if ( !it.next().getName().equals( "efgh" ) ) {
5542 if ( !it.next().getName().equals( "r" ) ) {
5545 if ( it.hasNext() ) {
5549 catch ( final Exception e ) {
5550 e.printStackTrace( System.out );
5556 private static boolean testPreOrderIterator() {
5558 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5559 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5560 PhylogenyNodeIterator it0;
5561 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5564 for( it0.reset(); it0.hasNext(); ) {
5567 PhylogenyNodeIterator it = t0.iteratorPreorder();
5568 if ( !it.next().getName().equals( "r" ) ) {
5571 if ( !it.next().getName().equals( "ab" ) ) {
5574 if ( !it.next().getName().equals( "A" ) ) {
5577 if ( !it.next().getName().equals( "B" ) ) {
5580 if ( !it.next().getName().equals( "cd" ) ) {
5583 if ( !it.next().getName().equals( "C" ) ) {
5586 if ( !it.next().getName().equals( "D" ) ) {
5589 if ( it.hasNext() ) {
5592 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5593 it = t1.iteratorPreorder();
5594 if ( !it.next().getName().equals( "r" ) ) {
5597 if ( !it.next().getName().equals( "abcd" ) ) {
5600 if ( !it.next().getName().equals( "ab" ) ) {
5603 if ( !it.next().getName().equals( "A" ) ) {
5606 if ( !it.next().getName().equals( "B" ) ) {
5609 if ( !it.next().getName().equals( "cd" ) ) {
5612 if ( !it.next().getName().equals( "C" ) ) {
5615 if ( !it.next().getName().equals( "D" ) ) {
5618 if ( !it.next().getName().equals( "efgh" ) ) {
5621 if ( !it.next().getName().equals( "ef" ) ) {
5624 if ( !it.next().getName().equals( "E" ) ) {
5627 if ( !it.next().getName().equals( "F" ) ) {
5630 if ( !it.next().getName().equals( "gh" ) ) {
5633 if ( !it.next().getName().equals( "G" ) ) {
5636 if ( !it.next().getName().equals( "H" ) ) {
5639 if ( it.hasNext() ) {
5643 catch ( final Exception e ) {
5644 e.printStackTrace( System.out );
5650 private static boolean testPropertiesMap() {
5652 final PropertiesMap pm = new PropertiesMap();
5653 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5654 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5655 final Property p2 = new Property( "something:else",
5657 "improbable:research",
5660 pm.addProperty( p0 );
5661 pm.addProperty( p1 );
5662 pm.addProperty( p2 );
5663 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5666 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5669 if ( pm.getProperties().size() != 3 ) {
5672 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5675 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5678 if ( pm.getProperties().size() != 3 ) {
5681 pm.removeProperty( "dimensions:diameter" );
5682 if ( pm.getProperties().size() != 2 ) {
5685 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5688 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5692 catch ( final Exception e ) {
5693 e.printStackTrace( System.out );
5699 private static boolean testReIdMethods() {
5701 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5702 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5703 final int count = PhylogenyNode.getNodeCount();
5705 if ( p.getNode( "r" ).getId() != count ) {
5708 if ( p.getNode( "A" ).getId() != count + 1 ) {
5711 if ( p.getNode( "B" ).getId() != count + 1 ) {
5714 if ( p.getNode( "C" ).getId() != count + 1 ) {
5717 if ( p.getNode( "1" ).getId() != count + 2 ) {
5720 if ( p.getNode( "2" ).getId() != count + 2 ) {
5723 if ( p.getNode( "3" ).getId() != count + 2 ) {
5726 if ( p.getNode( "4" ).getId() != count + 2 ) {
5729 if ( p.getNode( "5" ).getId() != count + 2 ) {
5732 if ( p.getNode( "6" ).getId() != count + 2 ) {
5735 if ( p.getNode( "a" ).getId() != count + 3 ) {
5738 if ( p.getNode( "b" ).getId() != count + 3 ) {
5741 if ( p.getNode( "X" ).getId() != count + 4 ) {
5744 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5747 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5751 catch ( final Exception e ) {
5752 e.printStackTrace( System.out );
5758 private static boolean testRerooting() {
5760 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5761 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",
5762 new NHXParser() )[ 0 ];
5763 if ( !t1.isRooted() ) {
5766 t1.reRoot( t1.getNode( "D" ) );
5767 t1.reRoot( t1.getNode( "CD" ) );
5768 t1.reRoot( t1.getNode( "A" ) );
5769 t1.reRoot( t1.getNode( "B" ) );
5770 t1.reRoot( t1.getNode( "AB" ) );
5771 t1.reRoot( t1.getNode( "D" ) );
5772 t1.reRoot( t1.getNode( "C" ) );
5773 t1.reRoot( t1.getNode( "CD" ) );
5774 t1.reRoot( t1.getNode( "A" ) );
5775 t1.reRoot( t1.getNode( "B" ) );
5776 t1.reRoot( t1.getNode( "AB" ) );
5777 t1.reRoot( t1.getNode( "D" ) );
5778 t1.reRoot( t1.getNode( "D" ) );
5779 t1.reRoot( t1.getNode( "C" ) );
5780 t1.reRoot( t1.getNode( "A" ) );
5781 t1.reRoot( t1.getNode( "B" ) );
5782 t1.reRoot( t1.getNode( "AB" ) );
5783 t1.reRoot( t1.getNode( "C" ) );
5784 t1.reRoot( t1.getNode( "D" ) );
5785 t1.reRoot( t1.getNode( "CD" ) );
5786 t1.reRoot( t1.getNode( "D" ) );
5787 t1.reRoot( t1.getNode( "A" ) );
5788 t1.reRoot( t1.getNode( "B" ) );
5789 t1.reRoot( t1.getNode( "AB" ) );
5790 t1.reRoot( t1.getNode( "C" ) );
5791 t1.reRoot( t1.getNode( "D" ) );
5792 t1.reRoot( t1.getNode( "CD" ) );
5793 t1.reRoot( t1.getNode( "D" ) );
5794 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5797 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5800 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5803 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5806 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5809 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5812 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",
5813 new NHXParser() )[ 0 ];
5814 t2.reRoot( t2.getNode( "A" ) );
5815 t2.reRoot( t2.getNode( "D" ) );
5816 t2.reRoot( t2.getNode( "ABC" ) );
5817 t2.reRoot( t2.getNode( "A" ) );
5818 t2.reRoot( t2.getNode( "B" ) );
5819 t2.reRoot( t2.getNode( "D" ) );
5820 t2.reRoot( t2.getNode( "C" ) );
5821 t2.reRoot( t2.getNode( "ABC" ) );
5822 t2.reRoot( t2.getNode( "A" ) );
5823 t2.reRoot( t2.getNode( "B" ) );
5824 t2.reRoot( t2.getNode( "AB" ) );
5825 t2.reRoot( t2.getNode( "AB" ) );
5826 t2.reRoot( t2.getNode( "D" ) );
5827 t2.reRoot( t2.getNode( "C" ) );
5828 t2.reRoot( t2.getNode( "B" ) );
5829 t2.reRoot( t2.getNode( "AB" ) );
5830 t2.reRoot( t2.getNode( "D" ) );
5831 t2.reRoot( t2.getNode( "D" ) );
5832 t2.reRoot( t2.getNode( "ABC" ) );
5833 t2.reRoot( t2.getNode( "A" ) );
5834 t2.reRoot( t2.getNode( "B" ) );
5835 t2.reRoot( t2.getNode( "AB" ) );
5836 t2.reRoot( t2.getNode( "D" ) );
5837 t2.reRoot( t2.getNode( "C" ) );
5838 t2.reRoot( t2.getNode( "ABC" ) );
5839 t2.reRoot( t2.getNode( "A" ) );
5840 t2.reRoot( t2.getNode( "B" ) );
5841 t2.reRoot( t2.getNode( "AB" ) );
5842 t2.reRoot( t2.getNode( "D" ) );
5843 t2.reRoot( t2.getNode( "D" ) );
5844 t2.reRoot( t2.getNode( "C" ) );
5845 t2.reRoot( t2.getNode( "A" ) );
5846 t2.reRoot( t2.getNode( "B" ) );
5847 t2.reRoot( t2.getNode( "AB" ) );
5848 t2.reRoot( t2.getNode( "C" ) );
5849 t2.reRoot( t2.getNode( "D" ) );
5850 t2.reRoot( t2.getNode( "ABC" ) );
5851 t2.reRoot( t2.getNode( "D" ) );
5852 t2.reRoot( t2.getNode( "A" ) );
5853 t2.reRoot( t2.getNode( "B" ) );
5854 t2.reRoot( t2.getNode( "AB" ) );
5855 t2.reRoot( t2.getNode( "C" ) );
5856 t2.reRoot( t2.getNode( "D" ) );
5857 t2.reRoot( t2.getNode( "ABC" ) );
5858 t2.reRoot( t2.getNode( "D" ) );
5859 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5862 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5865 t2.reRoot( t2.getNode( "ABC" ) );
5866 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5869 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5872 t2.reRoot( t2.getNode( "AB" ) );
5873 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5876 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5879 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5882 t2.reRoot( t2.getNode( "AB" ) );
5883 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5886 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5889 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5892 t2.reRoot( t2.getNode( "D" ) );
5893 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5896 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5899 t2.reRoot( t2.getNode( "ABC" ) );
5900 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5903 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5906 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5907 new NHXParser() )[ 0 ];
5908 t3.reRoot( t3.getNode( "B" ) );
5909 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5912 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5915 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5918 t3.reRoot( t3.getNode( "B" ) );
5919 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5922 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5925 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5928 t3.reRoot( t3.getRoot() );
5929 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5932 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5935 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5939 catch ( final Exception e ) {
5940 e.printStackTrace( System.out );
5946 private static boolean testSDIse() {
5948 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5949 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5950 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5951 gene1.setRooted( true );
5952 species1.setRooted( true );
5953 final SDI sdi = new SDIse( gene1, species1 );
5954 if ( !gene1.getRoot().isDuplication() ) {
5957 final Phylogeny species2 = factory
5958 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5959 new NHXParser() )[ 0 ];
5960 final Phylogeny gene2 = factory
5961 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5962 new NHXParser() )[ 0 ];
5963 species2.setRooted( true );
5964 gene2.setRooted( true );
5965 final SDI sdi2 = new SDIse( gene2, species2 );
5966 if ( sdi2.getDuplicationsSum() != 0 ) {
5969 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5972 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5975 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5978 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5981 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5984 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5987 final Phylogeny species3 = factory
5988 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5989 new NHXParser() )[ 0 ];
5990 final Phylogeny gene3 = factory
5991 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5992 new NHXParser() )[ 0 ];
5993 species3.setRooted( true );
5994 gene3.setRooted( true );
5995 final SDI sdi3 = new SDIse( gene3, species3 );
5996 if ( sdi3.getDuplicationsSum() != 1 ) {
5999 if ( !gene3.getNode( "aa" ).isDuplication() ) {
6002 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
6005 final Phylogeny species4 = factory
6006 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6007 new NHXParser() )[ 0 ];
6008 final Phylogeny gene4 = factory
6009 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6010 new NHXParser() )[ 0 ];
6011 species4.setRooted( true );
6012 gene4.setRooted( true );
6013 final SDI sdi4 = new SDIse( gene4, species4 );
6014 if ( sdi4.getDuplicationsSum() != 1 ) {
6017 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
6020 if ( !gene4.getNode( "abc" ).isDuplication() ) {
6023 if ( gene4.getNode( "abcd" ).isDuplication() ) {
6026 if ( species4.getNumberOfExternalNodes() != 6 ) {
6029 if ( gene4.getNumberOfExternalNodes() != 6 ) {
6032 final Phylogeny species5 = factory
6033 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6034 new NHXParser() )[ 0 ];
6035 final Phylogeny gene5 = factory
6036 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
6037 new NHXParser() )[ 0 ];
6038 species5.setRooted( true );
6039 gene5.setRooted( true );
6040 final SDI sdi5 = new SDIse( gene5, species5 );
6041 if ( sdi5.getDuplicationsSum() != 2 ) {
6044 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
6047 if ( !gene5.getNode( "adc" ).isDuplication() ) {
6050 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
6053 if ( species5.getNumberOfExternalNodes() != 6 ) {
6056 if ( gene5.getNumberOfExternalNodes() != 6 ) {
6059 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
6060 // Conjecture for Comparing Molecular Phylogenies"
6061 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
6062 final Phylogeny species6 = factory
6063 .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,"
6064 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6065 new NHXParser() )[ 0 ];
6066 final Phylogeny gene6 = factory
6067 .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,"
6068 + "((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,"
6069 + "(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;",
6070 new NHXParser() )[ 0 ];
6071 species6.setRooted( true );
6072 gene6.setRooted( true );
6073 final SDI sdi6 = new SDIse( gene6, species6 );
6074 if ( sdi6.getDuplicationsSum() != 3 ) {
6077 if ( !gene6.getNode( "r" ).isDuplication() ) {
6080 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6083 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6086 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6089 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6092 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6095 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6098 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6101 sdi6.computeMappingCostL();
6102 if ( sdi6.computeMappingCostL() != 17 ) {
6105 if ( species6.getNumberOfExternalNodes() != 9 ) {
6108 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6111 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6112 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6113 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6114 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6115 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6116 species7.setRooted( true );
6117 final Phylogeny gene7_1 = Test
6118 .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])" );
6119 gene7_1.setRooted( true );
6120 final SDI sdi7 = new SDIse( gene7_1, species7 );
6121 if ( sdi7.getDuplicationsSum() != 0 ) {
6124 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6127 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6130 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6133 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6136 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6139 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6142 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6145 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6148 final Phylogeny gene7_2 = Test
6149 .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])" );
6150 gene7_2.setRooted( true );
6151 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6152 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6155 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6158 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6161 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6164 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6167 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6170 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6173 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6176 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6179 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6183 catch ( final Exception e ) {
6189 private static boolean testSDIunrooted() {
6191 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6192 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6193 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6194 final Iterator<PhylogenyBranch> iter = l.iterator();
6195 PhylogenyBranch br = iter.next();
6196 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6199 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6203 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6206 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6210 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6213 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6217 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6220 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6224 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6227 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6231 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6234 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6238 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6241 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6245 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6248 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6252 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6255 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6259 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6262 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6266 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6269 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6273 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6276 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6280 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6283 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6287 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6290 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6294 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6297 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6300 if ( iter.hasNext() ) {
6303 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6304 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6305 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6307 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6310 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6314 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6317 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6321 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6324 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6327 if ( iter1.hasNext() ) {
6330 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6331 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6332 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6334 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6337 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6341 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6344 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6348 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6351 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6354 if ( iter2.hasNext() ) {
6357 final Phylogeny species0 = factory
6358 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6359 new NHXParser() )[ 0 ];
6360 final Phylogeny gene1 = factory
6361 .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])",
6362 new NHXParser() )[ 0 ];
6363 species0.setRooted( true );
6364 gene1.setRooted( true );
6365 final SDIR sdi_unrooted = new SDIR();
6366 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6367 if ( sdi_unrooted.getCount() != 1 ) {
6370 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6373 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6376 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6379 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6382 final Phylogeny gene2 = factory
6383 .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])",
6384 new NHXParser() )[ 0 ];
6385 gene2.setRooted( true );
6386 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6387 if ( sdi_unrooted.getCount() != 1 ) {
6390 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6393 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6396 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6399 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6402 final Phylogeny species6 = factory
6403 .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,"
6404 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6405 new NHXParser() )[ 0 ];
6406 final Phylogeny gene6 = factory
6407 .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],"
6408 + "(((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],"
6409 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6410 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6411 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6412 new NHXParser() )[ 0 ];
6413 species6.setRooted( true );
6414 gene6.setRooted( true );
6415 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6416 if ( sdi_unrooted.getCount() != 1 ) {
6419 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6422 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6425 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6428 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6431 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6434 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6437 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6440 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6443 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6446 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6449 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6452 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6456 final Phylogeny species7 = factory
6457 .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,"
6458 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6459 new NHXParser() )[ 0 ];
6460 final Phylogeny gene7 = factory
6461 .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],"
6462 + "(((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],"
6463 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6464 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6465 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6466 new NHXParser() )[ 0 ];
6467 species7.setRooted( true );
6468 gene7.setRooted( true );
6469 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6470 if ( sdi_unrooted.getCount() != 1 ) {
6473 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6476 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6479 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6482 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6485 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6488 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6491 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6494 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6497 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6500 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6503 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6506 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6510 final Phylogeny species8 = factory
6511 .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,"
6512 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6513 new NHXParser() )[ 0 ];
6514 final Phylogeny gene8 = factory
6515 .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],"
6516 + "(((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],"
6517 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6518 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6519 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6520 new NHXParser() )[ 0 ];
6521 species8.setRooted( true );
6522 gene8.setRooted( true );
6523 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6524 if ( sdi_unrooted.getCount() != 1 ) {
6527 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6530 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6533 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6536 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6539 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6542 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6545 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6548 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6551 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6554 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6557 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6560 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6565 catch ( final Exception e ) {
6566 e.printStackTrace( System.out );
6572 private static boolean testSplit() {
6574 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6575 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6576 //Archaeopteryx.createApplication( p0 );
6577 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6578 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6579 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6580 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6581 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6582 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6583 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6584 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6585 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6586 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6587 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6588 // System.out.println( s0.toString() );
6590 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6593 if ( s0.match( query_nodes ) ) {
6596 query_nodes = new HashSet<PhylogenyNode>();
6597 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6602 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6603 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6604 if ( !s0.match( query_nodes ) ) {
6608 query_nodes = new HashSet<PhylogenyNode>();
6609 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6610 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6611 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6612 if ( !s0.match( query_nodes ) ) {
6616 query_nodes = new HashSet<PhylogenyNode>();
6617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6618 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6619 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6620 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6621 if ( !s0.match( query_nodes ) ) {
6625 query_nodes = new HashSet<PhylogenyNode>();
6626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6628 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6629 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6630 if ( !s0.match( query_nodes ) ) {
6634 query_nodes = new HashSet<PhylogenyNode>();
6635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6636 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6637 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6638 if ( !s0.match( query_nodes ) ) {
6642 query_nodes = new HashSet<PhylogenyNode>();
6643 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6644 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6645 if ( !s0.match( query_nodes ) ) {
6649 query_nodes = new HashSet<PhylogenyNode>();
6650 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6651 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6652 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6653 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6654 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6655 if ( !s0.match( query_nodes ) ) {
6659 query_nodes = new HashSet<PhylogenyNode>();
6660 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6661 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6663 if ( !s0.match( query_nodes ) ) {
6667 query_nodes = new HashSet<PhylogenyNode>();
6668 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6671 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6672 if ( !s0.match( query_nodes ) ) {
6676 query_nodes = new HashSet<PhylogenyNode>();
6677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6678 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6679 if ( s0.match( query_nodes ) ) {
6683 query_nodes = new HashSet<PhylogenyNode>();
6684 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6686 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6687 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6688 if ( s0.match( query_nodes ) ) {
6692 query_nodes = new HashSet<PhylogenyNode>();
6693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6694 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6695 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6696 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6697 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6698 if ( s0.match( query_nodes ) ) {
6702 query_nodes = new HashSet<PhylogenyNode>();
6703 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6704 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6705 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6706 if ( s0.match( query_nodes ) ) {
6710 query_nodes = new HashSet<PhylogenyNode>();
6711 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6712 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6713 if ( s0.match( query_nodes ) ) {
6717 query_nodes = new HashSet<PhylogenyNode>();
6718 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6719 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6720 if ( s0.match( query_nodes ) ) {
6724 query_nodes = new HashSet<PhylogenyNode>();
6725 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6726 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6727 if ( s0.match( query_nodes ) ) {
6731 query_nodes = new HashSet<PhylogenyNode>();
6732 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6733 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6734 if ( s0.match( query_nodes ) ) {
6738 query_nodes = new HashSet<PhylogenyNode>();
6739 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6740 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6741 if ( s0.match( query_nodes ) ) {
6745 query_nodes = new HashSet<PhylogenyNode>();
6746 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6747 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6748 if ( s0.match( query_nodes ) ) {
6752 query_nodes = new HashSet<PhylogenyNode>();
6753 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6754 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6755 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6756 if ( s0.match( query_nodes ) ) {
6760 query_nodes = new HashSet<PhylogenyNode>();
6761 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6762 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6763 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6764 if ( s0.match( query_nodes ) ) {
6768 query_nodes = new HashSet<PhylogenyNode>();
6769 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6770 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6771 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6772 if ( s0.match( query_nodes ) ) {
6776 query_nodes = new HashSet<PhylogenyNode>();
6777 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6778 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6779 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6780 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6781 if ( s0.match( query_nodes ) ) {
6785 // query_nodes = new HashSet<PhylogenyNode>();
6786 // query_nodes.add( new PhylogenyNode( "X" ) );
6787 // query_nodes.add( new PhylogenyNode( "Y" ) );
6788 // query_nodes.add( new PhylogenyNode( "A" ) );
6789 // query_nodes.add( new PhylogenyNode( "B" ) );
6790 // query_nodes.add( new PhylogenyNode( "C" ) );
6791 // query_nodes.add( new PhylogenyNode( "D" ) );
6792 // query_nodes.add( new PhylogenyNode( "E" ) );
6793 // query_nodes.add( new PhylogenyNode( "F" ) );
6794 // query_nodes.add( new PhylogenyNode( "G" ) );
6795 // if ( !s0.match( query_nodes ) ) {
6798 // query_nodes = new HashSet<PhylogenyNode>();
6799 // query_nodes.add( new PhylogenyNode( "X" ) );
6800 // query_nodes.add( new PhylogenyNode( "Y" ) );
6801 // query_nodes.add( new PhylogenyNode( "A" ) );
6802 // query_nodes.add( new PhylogenyNode( "B" ) );
6803 // query_nodes.add( new PhylogenyNode( "C" ) );
6804 // if ( !s0.match( query_nodes ) ) {
6808 // query_nodes = new HashSet<PhylogenyNode>();
6809 // query_nodes.add( new PhylogenyNode( "X" ) );
6810 // query_nodes.add( new PhylogenyNode( "Y" ) );
6811 // query_nodes.add( new PhylogenyNode( "D" ) );
6812 // query_nodes.add( new PhylogenyNode( "E" ) );
6813 // query_nodes.add( new PhylogenyNode( "F" ) );
6814 // query_nodes.add( new PhylogenyNode( "G" ) );
6815 // if ( !s0.match( query_nodes ) ) {
6819 // query_nodes = new HashSet<PhylogenyNode>();
6820 // query_nodes.add( new PhylogenyNode( "X" ) );
6821 // query_nodes.add( new PhylogenyNode( "Y" ) );
6822 // query_nodes.add( new PhylogenyNode( "A" ) );
6823 // query_nodes.add( new PhylogenyNode( "B" ) );
6824 // query_nodes.add( new PhylogenyNode( "C" ) );
6825 // query_nodes.add( new PhylogenyNode( "D" ) );
6826 // if ( !s0.match( query_nodes ) ) {
6830 // query_nodes = new HashSet<PhylogenyNode>();
6831 // query_nodes.add( new PhylogenyNode( "X" ) );
6832 // query_nodes.add( new PhylogenyNode( "Y" ) );
6833 // query_nodes.add( new PhylogenyNode( "E" ) );
6834 // query_nodes.add( new PhylogenyNode( "F" ) );
6835 // query_nodes.add( new PhylogenyNode( "G" ) );
6836 // if ( !s0.match( query_nodes ) ) {
6840 // query_nodes = new HashSet<PhylogenyNode>();
6841 // query_nodes.add( new PhylogenyNode( "X" ) );
6842 // query_nodes.add( new PhylogenyNode( "Y" ) );
6843 // query_nodes.add( new PhylogenyNode( "F" ) );
6844 // query_nodes.add( new PhylogenyNode( "G" ) );
6845 // if ( !s0.match( query_nodes ) ) {
6849 query_nodes = new HashSet<PhylogenyNode>();
6850 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6851 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6854 if ( s0.match( query_nodes ) ) {
6858 query_nodes = new HashSet<PhylogenyNode>();
6859 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6860 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6861 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6863 if ( s0.match( query_nodes ) ) {
6866 ///////////////////////////
6868 query_nodes = new HashSet<PhylogenyNode>();
6869 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6870 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6871 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6873 if ( s0.match( query_nodes ) ) {
6877 query_nodes = new HashSet<PhylogenyNode>();
6878 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6879 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6880 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6881 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6882 if ( s0.match( query_nodes ) ) {
6886 query_nodes = new HashSet<PhylogenyNode>();
6887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6888 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6889 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6890 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6891 if ( s0.match( query_nodes ) ) {
6895 query_nodes = new HashSet<PhylogenyNode>();
6896 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6897 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6898 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6899 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6900 if ( s0.match( query_nodes ) ) {
6904 query_nodes = new HashSet<PhylogenyNode>();
6905 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6906 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6907 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6908 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6909 if ( s0.match( query_nodes ) ) {
6913 query_nodes = new HashSet<PhylogenyNode>();
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6915 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6916 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6917 if ( s0.match( query_nodes ) ) {
6921 query_nodes = new HashSet<PhylogenyNode>();
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6926 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6927 if ( s0.match( query_nodes ) ) {
6931 query_nodes = new HashSet<PhylogenyNode>();
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6933 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6934 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6935 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6936 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6937 if ( s0.match( query_nodes ) ) {
6941 query_nodes = new HashSet<PhylogenyNode>();
6942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6943 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6944 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6945 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6946 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6947 if ( s0.match( query_nodes ) ) {
6951 query_nodes = new HashSet<PhylogenyNode>();
6952 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6953 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6954 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6955 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6956 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6958 if ( s0.match( query_nodes ) ) {
6962 catch ( final Exception e ) {
6963 e.printStackTrace();
6969 private static boolean testSplitStrict() {
6971 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6972 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6973 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6974 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6975 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6976 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6977 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6978 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6979 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6980 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6981 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6982 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6985 if ( s0.match( query_nodes ) ) {
6988 query_nodes = new HashSet<PhylogenyNode>();
6989 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6994 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6995 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6996 if ( !s0.match( query_nodes ) ) {
7000 query_nodes = new HashSet<PhylogenyNode>();
7001 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7002 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7003 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7004 if ( !s0.match( query_nodes ) ) {
7008 query_nodes = new HashSet<PhylogenyNode>();
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7010 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7011 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7012 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7013 if ( !s0.match( query_nodes ) ) {
7017 query_nodes = new HashSet<PhylogenyNode>();
7018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7019 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7020 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7021 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7022 if ( !s0.match( query_nodes ) ) {
7026 query_nodes = new HashSet<PhylogenyNode>();
7027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7028 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7029 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7030 if ( !s0.match( query_nodes ) ) {
7034 query_nodes = new HashSet<PhylogenyNode>();
7035 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7036 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7037 if ( !s0.match( query_nodes ) ) {
7041 query_nodes = new HashSet<PhylogenyNode>();
7042 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7043 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7044 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7045 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7046 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7047 if ( !s0.match( query_nodes ) ) {
7051 query_nodes = new HashSet<PhylogenyNode>();
7052 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7053 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7055 if ( !s0.match( query_nodes ) ) {
7059 query_nodes = new HashSet<PhylogenyNode>();
7060 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7063 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7064 if ( !s0.match( query_nodes ) ) {
7068 query_nodes = new HashSet<PhylogenyNode>();
7069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7070 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7071 if ( s0.match( query_nodes ) ) {
7075 query_nodes = new HashSet<PhylogenyNode>();
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7077 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7078 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7079 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7080 if ( s0.match( query_nodes ) ) {
7084 query_nodes = new HashSet<PhylogenyNode>();
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7086 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7087 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7088 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7089 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7090 if ( s0.match( query_nodes ) ) {
7094 query_nodes = new HashSet<PhylogenyNode>();
7095 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7096 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7097 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7098 if ( s0.match( query_nodes ) ) {
7102 query_nodes = new HashSet<PhylogenyNode>();
7103 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7104 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7105 if ( s0.match( query_nodes ) ) {
7109 query_nodes = new HashSet<PhylogenyNode>();
7110 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7111 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7112 if ( s0.match( query_nodes ) ) {
7116 query_nodes = new HashSet<PhylogenyNode>();
7117 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7118 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7119 if ( s0.match( query_nodes ) ) {
7123 query_nodes = new HashSet<PhylogenyNode>();
7124 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7125 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7126 if ( s0.match( query_nodes ) ) {
7130 query_nodes = new HashSet<PhylogenyNode>();
7131 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7132 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7133 if ( s0.match( query_nodes ) ) {
7137 query_nodes = new HashSet<PhylogenyNode>();
7138 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7139 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7140 if ( s0.match( query_nodes ) ) {
7144 query_nodes = new HashSet<PhylogenyNode>();
7145 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7146 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7147 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7148 if ( s0.match( query_nodes ) ) {
7152 query_nodes = new HashSet<PhylogenyNode>();
7153 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7154 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7155 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7156 if ( s0.match( query_nodes ) ) {
7160 query_nodes = new HashSet<PhylogenyNode>();
7161 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7162 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7163 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7164 if ( s0.match( query_nodes ) ) {
7168 query_nodes = new HashSet<PhylogenyNode>();
7169 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7170 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7171 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7172 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7173 if ( s0.match( query_nodes ) ) {
7177 catch ( final Exception e ) {
7178 e.printStackTrace();
7184 private static boolean testSubtreeDeletion() {
7186 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7187 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7188 t1.deleteSubtree( t1.getNode( "A" ), false );
7189 if ( t1.getNumberOfExternalNodes() != 5 ) {
7192 t1.toNewHampshireX();
7193 t1.deleteSubtree( t1.getNode( "E" ), false );
7194 if ( t1.getNumberOfExternalNodes() != 4 ) {
7197 t1.toNewHampshireX();
7198 t1.deleteSubtree( t1.getNode( "F" ), false );
7199 if ( t1.getNumberOfExternalNodes() != 3 ) {
7202 t1.toNewHampshireX();
7203 t1.deleteSubtree( t1.getNode( "D" ), false );
7204 t1.toNewHampshireX();
7205 if ( t1.getNumberOfExternalNodes() != 3 ) {
7208 t1.deleteSubtree( t1.getNode( "def" ), false );
7209 t1.toNewHampshireX();
7210 if ( t1.getNumberOfExternalNodes() != 2 ) {
7213 t1.deleteSubtree( t1.getNode( "B" ), false );
7214 t1.toNewHampshireX();
7215 if ( t1.getNumberOfExternalNodes() != 1 ) {
7218 t1.deleteSubtree( t1.getNode( "C" ), false );
7219 t1.toNewHampshireX();
7220 if ( t1.getNumberOfExternalNodes() != 1 ) {
7223 t1.deleteSubtree( t1.getNode( "abc" ), false );
7224 t1.toNewHampshireX();
7225 if ( t1.getNumberOfExternalNodes() != 1 ) {
7228 t1.deleteSubtree( t1.getNode( "r" ), false );
7229 if ( t1.getNumberOfExternalNodes() != 0 ) {
7232 if ( !t1.isEmpty() ) {
7235 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7236 t2.deleteSubtree( t2.getNode( "A" ), false );
7237 t2.toNewHampshireX();
7238 if ( t2.getNumberOfExternalNodes() != 5 ) {
7241 t2.deleteSubtree( t2.getNode( "abc" ), false );
7242 t2.toNewHampshireX();
7243 if ( t2.getNumberOfExternalNodes() != 3 ) {
7246 t2.deleteSubtree( t2.getNode( "def" ), false );
7247 t2.toNewHampshireX();
7248 if ( t2.getNumberOfExternalNodes() != 1 ) {
7252 catch ( final Exception e ) {
7253 e.printStackTrace( System.out );
7259 private static boolean testSupportCount() {
7261 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7262 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7263 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7264 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7265 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7266 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7267 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7269 SupportCount.count( t0_1, phylogenies_1, true, false );
7270 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7271 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7272 + "(((((A,B),C),D),E),((F,G),X))"
7273 + "(((((A,Y),B),C),D),((F,G),E))"
7274 + "(((((A,B),C),D),E),(F,G))"
7275 + "(((((A,B),C),D),E),(F,G))"
7276 + "(((((A,B),C),D),E),(F,G))"
7277 + "(((((A,B),C),D),E),(F,G),Z)"
7278 + "(((((A,B),C),D),E),(F,G))"
7279 + "((((((A,B),C),D),E),F),G)"
7280 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7282 SupportCount.count( t0_2, phylogenies_2, true, false );
7283 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7284 while ( it.hasNext() ) {
7285 final PhylogenyNode n = it.next();
7286 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7290 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7291 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7292 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7293 SupportCount.count( t0_3, phylogenies_3, true, false );
7294 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7295 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7298 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7301 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7304 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7307 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7310 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7313 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7316 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7319 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7322 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7325 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7326 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7327 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7328 SupportCount.count( t0_4, phylogenies_4, true, false );
7329 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7330 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7333 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7336 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7339 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7342 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7345 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7348 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7351 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7354 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7357 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7360 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7361 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7362 double d = SupportCount.compare( b1, a, true, true, true );
7363 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7366 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7367 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7368 d = SupportCount.compare( b2, a, true, true, true );
7369 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7372 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7373 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7374 d = SupportCount.compare( b3, a, true, true, true );
7375 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7378 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7379 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7380 d = SupportCount.compare( b4, a, true, true, false );
7381 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7385 catch ( final Exception e ) {
7386 e.printStackTrace( System.out );
7392 private static boolean testSupportTransfer() {
7394 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7395 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)",
7396 new NHXParser() )[ 0 ];
7397 final Phylogeny p2 = factory
7398 .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 ];
7399 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7402 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7405 support_transfer.moveBranchLengthsToBootstrap( p1 );
7406 support_transfer.transferSupportValues( p1, p2 );
7407 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7410 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7413 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7416 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7419 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7422 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7425 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7428 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7432 catch ( final Exception e ) {
7433 e.printStackTrace( System.out );
7439 private static boolean testTaxonomyAssigner() {
7441 String s0_str = "(((([&&NHX:S=A],[&&NHX:S=B])[&&NHX:S=AB],[&&NHX:S=C])[&&NHX:S=ABC],[&&NHX:S=D])[&&NHX:S=ABCD],[&&NHX:S=E])[&&NHX:S=ABCDE]";
7442 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7443 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7444 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7445 s0.setRooted( true );
7446 g0.setRooted( true );
7447 TaxonomyAssigner.execute( g0, s0 );
7448 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7451 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7454 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7457 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7458 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7459 g0.setRooted( true );
7460 TaxonomyAssigner.execute( g0, s0 );
7461 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7464 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7467 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7470 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7471 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7472 g0.setRooted( true );
7473 TaxonomyAssigner.execute( g0, s0 );
7474 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7477 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7480 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7483 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7484 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7485 g0.setRooted( true );
7486 TaxonomyAssigner.execute( g0, s0 );
7487 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7490 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7493 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7496 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7497 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7498 g0.setRooted( true );
7499 TaxonomyAssigner.execute( g0, s0 );
7500 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7503 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7506 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7509 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7510 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7511 g0.setRooted( true );
7512 TaxonomyAssigner.execute( g0, s0 );
7513 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7516 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7519 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7522 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7523 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7524 g0.setRooted( true );
7525 TaxonomyAssigner.execute( g0, s0 );
7526 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7529 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7532 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7535 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7536 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7537 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7538 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7539 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7540 s0.setRooted( true );
7541 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7542 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7543 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7544 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7545 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7546 g0.setRooted( true );
7547 TaxonomyAssigner.execute( g0, s0 );
7548 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7551 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7554 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7557 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7560 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7563 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7564 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7565 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7566 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7567 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7568 g0.setRooted( true );
7569 TaxonomyAssigner.execute( g0, s0 );
7570 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7573 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7576 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7579 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7582 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7585 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7586 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7587 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7588 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7589 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7590 g0.setRooted( true );
7591 TaxonomyAssigner.execute( g0, s0 );
7592 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7595 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7598 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7601 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7604 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7607 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7608 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7609 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7610 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7611 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7612 g0.setRooted( true );
7613 TaxonomyAssigner.execute( g0, s0 );
7614 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7617 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7620 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7623 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7626 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7629 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7630 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7631 g0.setRooted( true );
7632 TaxonomyAssigner.execute( g0, s0 );
7633 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7636 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7639 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7642 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7643 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7644 g0.setRooted( true );
7645 TaxonomyAssigner.execute( g0, s0 );
7646 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7649 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7652 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7655 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7656 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7657 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7658 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7659 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7660 g0.setRooted( true );
7661 TaxonomyAssigner.execute( g0, s0 );
7662 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7665 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7668 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7671 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7674 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7677 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7680 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7683 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7684 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7685 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7686 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7687 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7688 g0.setRooted( true );
7689 TaxonomyAssigner.execute( g0, s0 );
7690 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7693 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7696 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7699 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7702 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7705 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7708 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7711 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7712 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7713 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7714 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7715 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7716 g0.setRooted( true );
7717 TaxonomyAssigner.execute( g0, s0 );
7718 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7721 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7724 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7727 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7730 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7733 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7736 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7739 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7740 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7741 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7742 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7743 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7744 g0.setRooted( true );
7745 TaxonomyAssigner.execute( g0, s0 );
7746 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7749 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7752 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7755 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7758 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7761 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7764 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7767 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7768 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7769 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7770 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7771 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7772 s0.setRooted( true );
7773 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7774 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7775 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7776 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7777 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7778 g0.setRooted( true );
7779 TaxonomyAssigner.execute( g0, s0 );
7780 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7783 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7787 catch ( final Exception e ) {
7788 e.printStackTrace( System.out );
7794 private static boolean testUniprotTaxonomySearch() {
7796 List<UniProtTaxonomy> results = UniProtWsTools
7797 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7798 if ( results.size() != 1 ) {
7801 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7804 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7807 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7810 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7813 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7817 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7818 if ( results.size() != 1 ) {
7821 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7824 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7827 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7830 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7833 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7837 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7838 if ( results.size() != 1 ) {
7841 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7844 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7847 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7850 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7853 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7857 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7858 if ( results.size() != 1 ) {
7861 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7864 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7867 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7870 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7873 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7876 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7879 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7882 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7883 .equals( "Nematostella vectensis" ) ) {
7884 System.out.println( results.get( 0 ).getLineage() );
7888 catch ( final IOException e ) {
7889 System.out.println();
7890 System.out.println( "the following might be due to absence internet connection:" );
7891 e.printStackTrace( System.out );
7894 catch ( final Exception e ) {
7900 private static boolean testEmblEntryRetrieval() {
7901 //The format for GenBank Accession numbers are:
7902 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7903 //Protein: 3 letters + 5 numerals
7904 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7905 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7908 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7911 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7914 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7917 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7920 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7923 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7926 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7929 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7932 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7935 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7938 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7941 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7947 private static boolean testUniprotEntryRetrieval() {
7948 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7951 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7954 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7957 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7960 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7963 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7966 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7969 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7972 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7975 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7978 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7981 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7984 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7988 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7989 if ( !entry.getAccession().equals( "P12345" ) ) {
7992 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7995 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7998 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
8001 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
8005 catch ( final IOException e ) {
8006 System.out.println();
8007 System.out.println( "the following might be due to absence internet connection:" );
8008 e.printStackTrace( System.out );
8011 catch ( final Exception e ) {
8017 private static boolean testWabiTxSearch() {
8020 result = TxSearch.searchSimple( "nematostella" );
8021 result = TxSearch.getTxId( "nematostella" );
8022 if ( !result.equals( "45350" ) ) {
8025 result = TxSearch.getTxName( "45350" );
8026 if ( !result.equals( "Nematostella" ) ) {
8029 result = TxSearch.getTxId( "nematostella vectensis" );
8030 if ( !result.equals( "45351" ) ) {
8033 result = TxSearch.getTxName( "45351" );
8034 if ( !result.equals( "Nematostella vectensis" ) ) {
8037 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
8038 if ( !result.equals( "536089" ) ) {
8041 result = TxSearch.getTxName( "536089" );
8042 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
8045 final List<String> queries = new ArrayList<String>();
8046 queries.add( "Campylobacter coli" );
8047 queries.add( "Escherichia coli" );
8048 queries.add( "Arabidopsis" );
8049 queries.add( "Trichoplax" );
8050 queries.add( "Samanea saman" );
8051 queries.add( "Kluyveromyces marxianus" );
8052 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
8053 queries.add( "Bornavirus parrot/PDD/2008" );
8054 final List<RANKS> ranks = new ArrayList<RANKS>();
8055 ranks.add( RANKS.SUPERKINGDOM );
8056 ranks.add( RANKS.KINGDOM );
8057 ranks.add( RANKS.FAMILY );
8058 ranks.add( RANKS.GENUS );
8059 ranks.add( RANKS.TRIBE );
8060 result = TxSearch.searchLineage( queries, ranks );
8061 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
8062 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
8064 catch ( final Exception e ) {
8065 System.out.println();
8066 System.out.println( "the following might be due to absence internet connection:" );
8067 e.printStackTrace( System.out );
8073 private static boolean testAminoAcidSequence() {
8075 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8076 if ( aa1.getLength() != 13 ) {
8079 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8082 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8085 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8088 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8089 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8092 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8093 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8096 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8097 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8101 catch ( final Exception e ) {
8102 e.printStackTrace();
8108 private static boolean testCreateBalancedPhylogeny() {
8110 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8111 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8114 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8117 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8118 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8121 if ( p1.getNumberOfExternalNodes() != 100 ) {
8125 catch ( final Exception e ) {
8126 e.printStackTrace();
8132 private static boolean testFastaParser() {
8134 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8137 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8140 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8141 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8144 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8147 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8150 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8153 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8156 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8160 catch ( final Exception e ) {
8161 e.printStackTrace();
8167 private static boolean testGeneralMsaParser() {
8169 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8170 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8171 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
8172 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8173 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8174 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8175 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8176 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8177 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8178 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8181 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8184 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8187 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8188 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8191 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8194 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8197 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8198 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8201 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8204 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8208 catch ( final Exception e ) {
8209 e.printStackTrace();
8215 private static boolean testMafft() {
8217 final List<String> opts = new ArrayList<String>();
8218 opts.add( "--maxiterate" );
8220 opts.add( "--localpair" );
8221 opts.add( "--quiet" );
8223 final MsaInferrer mafft = Mafft.createInstance();
8224 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
8225 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8229 catch ( final Exception e ) {
8230 e.printStackTrace( System.out );
8236 private static boolean testNextNodeWithCollapsing() {
8238 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8240 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8241 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8242 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8243 t0.getNode( "cd" ).setCollapse( true );
8244 t0.getNode( "cde" ).setCollapse( true );
8245 n = t0.getFirstExternalNode();
8246 while ( n != null ) {
8248 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8250 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8253 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8256 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8259 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8262 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8265 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8269 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8270 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8271 t1.getNode( "ab" ).setCollapse( true );
8272 t1.getNode( "cd" ).setCollapse( true );
8273 t1.getNode( "cde" ).setCollapse( true );
8274 n = t1.getNode( "ab" );
8275 ext = new ArrayList<PhylogenyNode>();
8276 while ( n != null ) {
8278 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8280 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8283 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8286 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8289 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8292 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8298 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8299 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8300 t2.getNode( "ab" ).setCollapse( true );
8301 t2.getNode( "cd" ).setCollapse( true );
8302 t2.getNode( "cde" ).setCollapse( true );
8303 t2.getNode( "c" ).setCollapse( true );
8304 t2.getNode( "d" ).setCollapse( true );
8305 t2.getNode( "e" ).setCollapse( true );
8306 t2.getNode( "gh" ).setCollapse( true );
8307 n = t2.getNode( "ab" );
8308 ext = new ArrayList<PhylogenyNode>();
8309 while ( n != null ) {
8311 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8313 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8316 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8319 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8322 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8328 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8329 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8330 t3.getNode( "ab" ).setCollapse( true );
8331 t3.getNode( "cd" ).setCollapse( true );
8332 t3.getNode( "cde" ).setCollapse( true );
8333 t3.getNode( "c" ).setCollapse( true );
8334 t3.getNode( "d" ).setCollapse( true );
8335 t3.getNode( "e" ).setCollapse( true );
8336 t3.getNode( "gh" ).setCollapse( true );
8337 t3.getNode( "fgh" ).setCollapse( true );
8338 n = t3.getNode( "ab" );
8339 ext = new ArrayList<PhylogenyNode>();
8340 while ( n != null ) {
8342 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8344 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8347 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8350 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8356 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8357 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8358 t4.getNode( "ab" ).setCollapse( true );
8359 t4.getNode( "cd" ).setCollapse( true );
8360 t4.getNode( "cde" ).setCollapse( true );
8361 t4.getNode( "c" ).setCollapse( true );
8362 t4.getNode( "d" ).setCollapse( true );
8363 t4.getNode( "e" ).setCollapse( true );
8364 t4.getNode( "gh" ).setCollapse( true );
8365 t4.getNode( "fgh" ).setCollapse( true );
8366 t4.getNode( "abcdefgh" ).setCollapse( true );
8367 n = t4.getNode( "abcdefgh" );
8368 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8373 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8374 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8376 n = t5.getFirstExternalNode();
8377 while ( n != null ) {
8379 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8381 if ( ext.size() != 8 ) {
8384 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8387 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8390 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8393 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8396 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8399 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8402 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8405 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8410 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8411 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8413 t6.getNode( "ab" ).setCollapse( true );
8414 n = t6.getNode( "ab" );
8415 while ( n != null ) {
8417 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8419 if ( ext.size() != 7 ) {
8422 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8425 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8428 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8431 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8434 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8437 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8440 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8445 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8446 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8448 t7.getNode( "cd" ).setCollapse( true );
8449 n = t7.getNode( "a" );
8450 while ( n != null ) {
8452 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8454 if ( ext.size() != 7 ) {
8457 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8460 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8463 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8466 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8469 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8472 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8475 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8480 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8481 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8483 t8.getNode( "cd" ).setCollapse( true );
8484 t8.getNode( "c" ).setCollapse( true );
8485 t8.getNode( "d" ).setCollapse( true );
8486 n = t8.getNode( "a" );
8487 while ( n != null ) {
8489 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8491 if ( ext.size() != 7 ) {
8494 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8497 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8500 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8501 System.out.println( "2 fail" );
8504 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8507 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8510 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8513 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8518 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8519 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8521 t9.getNode( "gh" ).setCollapse( true );
8522 n = t9.getNode( "a" );
8523 while ( n != null ) {
8525 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8527 if ( ext.size() != 7 ) {
8530 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8533 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8536 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8539 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8542 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8545 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8548 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8553 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8554 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8556 t10.getNode( "gh" ).setCollapse( true );
8557 t10.getNode( "g" ).setCollapse( true );
8558 t10.getNode( "h" ).setCollapse( true );
8559 n = t10.getNode( "a" );
8560 while ( n != null ) {
8562 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8564 if ( ext.size() != 7 ) {
8567 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8570 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8573 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8576 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8579 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8582 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8585 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8590 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8591 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8593 t11.getNode( "gh" ).setCollapse( true );
8594 t11.getNode( "fgh" ).setCollapse( true );
8595 n = t11.getNode( "a" );
8596 while ( n != null ) {
8598 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8600 if ( ext.size() != 6 ) {
8603 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8606 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8609 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8612 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8615 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8618 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8623 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8624 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8626 t12.getNode( "gh" ).setCollapse( true );
8627 t12.getNode( "fgh" ).setCollapse( true );
8628 t12.getNode( "g" ).setCollapse( true );
8629 t12.getNode( "h" ).setCollapse( true );
8630 t12.getNode( "f" ).setCollapse( true );
8631 n = t12.getNode( "a" );
8632 while ( n != null ) {
8634 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8636 if ( ext.size() != 6 ) {
8639 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8642 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8645 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8648 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8651 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8654 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8659 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8660 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8662 t13.getNode( "ab" ).setCollapse( true );
8663 t13.getNode( "b" ).setCollapse( true );
8664 t13.getNode( "fgh" ).setCollapse( true );
8665 t13.getNode( "gh" ).setCollapse( true );
8666 n = t13.getNode( "ab" );
8667 while ( n != null ) {
8669 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8671 if ( ext.size() != 5 ) {
8674 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8677 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8680 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8683 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8686 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8691 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8692 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8694 t14.getNode( "ab" ).setCollapse( true );
8695 t14.getNode( "a" ).setCollapse( true );
8696 t14.getNode( "fgh" ).setCollapse( true );
8697 t14.getNode( "gh" ).setCollapse( true );
8698 n = t14.getNode( "ab" );
8699 while ( n != null ) {
8701 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8703 if ( ext.size() != 5 ) {
8706 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8709 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8712 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8715 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8718 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8723 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" );
8724 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8726 t15.getNode( "ab" ).setCollapse( true );
8727 t15.getNode( "a" ).setCollapse( true );
8728 t15.getNode( "fgh" ).setCollapse( true );
8729 t15.getNode( "gh" ).setCollapse( true );
8730 n = t15.getNode( "ab" );
8731 while ( n != null ) {
8733 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8735 if ( ext.size() != 6 ) {
8738 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8741 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8744 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8747 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8750 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8753 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8758 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" );
8759 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8761 t16.getNode( "ab" ).setCollapse( true );
8762 t16.getNode( "a" ).setCollapse( true );
8763 t16.getNode( "fgh" ).setCollapse( true );
8764 t16.getNode( "gh" ).setCollapse( true );
8765 t16.getNode( "cd" ).setCollapse( true );
8766 t16.getNode( "cde" ).setCollapse( true );
8767 t16.getNode( "d" ).setCollapse( true );
8768 t16.getNode( "x" ).setCollapse( true );
8769 n = t16.getNode( "ab" );
8770 while ( n != null ) {
8772 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8774 if ( ext.size() != 4 ) {
8777 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8780 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8783 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8786 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8790 catch ( final Exception e ) {
8791 e.printStackTrace( System.out );