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.data.BinaryCharacters;
66 import org.forester.phylogeny.data.BranchWidth;
67 import org.forester.phylogeny.data.Confidence;
68 import org.forester.phylogeny.data.Distribution;
69 import org.forester.phylogeny.data.DomainArchitecture;
70 import org.forester.phylogeny.data.Event;
71 import org.forester.phylogeny.data.Identifier;
72 import org.forester.phylogeny.data.PhylogenyData;
73 import org.forester.phylogeny.data.Polygon;
74 import org.forester.phylogeny.data.PropertiesMap;
75 import org.forester.phylogeny.data.Property;
76 import org.forester.phylogeny.data.Property.AppliesTo;
77 import org.forester.phylogeny.data.ProteinDomain;
78 import org.forester.phylogeny.data.Taxonomy;
79 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
80 import org.forester.phylogeny.factories.PhylogenyFactory;
81 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
82 import org.forester.sdi.SDI;
83 import org.forester.sdi.SDIR;
84 import org.forester.sdi.SDIse;
85 import org.forester.sdi.TaxonomyAssigner;
86 import org.forester.sdi.TestGSDI;
87 import org.forester.sequence.BasicSequence;
88 import org.forester.sequence.Sequence;
89 import org.forester.surfacing.Protein;
90 import org.forester.surfacing.TestSurfacing;
91 import org.forester.tools.ConfidenceAssessor;
92 import org.forester.tools.SupportCount;
93 import org.forester.tools.TreeSplitMatrix;
94 import org.forester.util.AsciiHistogram;
95 import org.forester.util.BasicDescriptiveStatistics;
96 import org.forester.util.BasicTable;
97 import org.forester.util.BasicTableParser;
98 import org.forester.util.DescriptiveStatistics;
99 import org.forester.util.ForesterConstants;
100 import org.forester.util.ForesterUtil;
101 import org.forester.util.GeneralTable;
102 import org.forester.ws.uniprot.UniProtTaxonomy;
103 import org.forester.ws.uniprot.UniProtWsTools;
104 import org.forester.ws.wabi.TxSearch;
105 import org.forester.ws.wabi.TxSearch.RANKS;
106 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
107 import org.forester.ws.wabi.TxSearch.TAX_RANK;
109 @SuppressWarnings( "unused")
110 public final class Test {
112 private final static double ZERO_DIFF = 1.0E-9;
113 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
114 + ForesterUtil.getFileSeparator() + "test_data"
115 + ForesterUtil.getFileSeparator();
116 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
117 + ForesterUtil.getFileSeparator() + "resources"
118 + ForesterUtil.getFileSeparator();
119 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
120 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
121 + ForesterConstants.PHYLO_XML_VERSION + "/"
122 + ForesterConstants.PHYLO_XML_XSD;
123 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
124 + ForesterConstants.PHYLO_XML_VERSION + "/"
125 + ForesterConstants.PHYLO_XML_XSD;
127 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
128 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
132 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
133 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
134 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
137 public static boolean isEqual( final double a, final double b ) {
138 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
141 public static void main( final String[] args ) {
142 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
143 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
145 Locale.setDefault( Locale.US );
146 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
149 System.out.print( "[Test if directory with files for testing exists/is readable: " );
150 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
151 System.out.println( "OK.]" );
154 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
155 System.out.println( "Testing aborted." );
158 System.out.print( "[Test if resources directory exists/is readable: " );
159 if ( testDir( PATH_TO_RESOURCES ) ) {
160 System.out.println( "OK.]" );
163 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
164 System.out.println( "Testing aborted." );
167 final long start_time = new Date().getTime();
168 System.out.print( "Hmmscan output parser: " );
169 if ( testHmmscanOutputParser() ) {
170 System.out.println( "OK." );
174 System.out.println( "failed." );
177 System.out.print( "Basic node methods: " );
178 if ( Test.testBasicNodeMethods() ) {
179 System.out.println( "OK." );
183 System.out.println( "failed." );
186 System.out.print( "Basic node construction and parsing of NHX (node level): " );
187 if ( Test.testNHXNodeParsing() ) {
188 System.out.println( "OK." );
192 System.out.println( "failed." );
195 System.out.print( "NH parsing: " );
196 if ( Test.testNHParsing() ) {
197 System.out.println( "OK." );
201 System.out.println( "failed." );
204 System.out.print( "Conversion to NHX (node level): " );
205 if ( Test.testNHXconversion() ) {
206 System.out.println( "OK." );
210 System.out.println( "failed." );
213 System.out.print( "NHX parsing: " );
214 if ( Test.testNHXParsing() ) {
215 System.out.println( "OK." );
219 System.out.println( "failed." );
222 System.out.print( "NHX parsing with quotes: " );
223 if ( Test.testNHXParsingQuotes() ) {
224 System.out.println( "OK." );
228 System.out.println( "failed." );
231 System.out.print( "Nexus characters parsing: " );
232 if ( Test.testNexusCharactersParsing() ) {
233 System.out.println( "OK." );
237 System.out.println( "failed." );
240 System.out.print( "Nexus tree parsing: " );
241 if ( Test.testNexusTreeParsing() ) {
242 System.out.println( "OK." );
246 System.out.println( "failed." );
249 System.out.print( "Nexus tree parsing (translating): " );
250 if ( Test.testNexusTreeParsingTranslating() ) {
251 System.out.println( "OK." );
255 System.out.println( "failed." );
258 System.out.print( "Nexus matrix parsing: " );
259 if ( Test.testNexusMatrixParsing() ) {
260 System.out.println( "OK." );
264 System.out.println( "failed." );
267 System.out.print( "Basic phyloXML parsing: " );
268 if ( Test.testBasicPhyloXMLparsing() ) {
269 System.out.println( "OK." );
273 System.out.println( "failed." );
276 System.out.print( "Basic phyloXML parsing (validating against schema): " );
277 if ( testBasicPhyloXMLparsingValidating() ) {
278 System.out.println( "OK." );
282 System.out.println( "failed." );
285 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
286 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
287 System.out.println( "OK." );
291 System.out.println( "failed." );
294 System.out.print( "phyloXML Distribution Element: " );
295 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
296 System.out.println( "OK." );
300 System.out.println( "failed." );
303 System.out.print( "Tol XML parsing: " );
304 if ( Test.testBasicTolXMLparsing() ) {
305 System.out.println( "OK." );
309 System.out.println( "failed." );
312 System.out.print( "Copying of node data: " );
313 if ( Test.testCopyOfNodeData() ) {
314 System.out.println( "OK." );
318 System.out.println( "failed." );
321 System.out.print( "Basic tree methods: " );
322 if ( Test.testBasicTreeMethods() ) {
323 System.out.println( "OK." );
327 System.out.println( "failed." );
330 System.out.print( "Postorder Iterator: " );
331 if ( Test.testPostOrderIterator() ) {
332 System.out.println( "OK." );
336 System.out.println( "failed." );
339 System.out.print( "Preorder Iterator: " );
340 if ( Test.testPreOrderIterator() ) {
341 System.out.println( "OK." );
345 System.out.println( "failed." );
348 System.out.print( "Levelorder Iterator: " );
349 if ( Test.testLevelOrderIterator() ) {
350 System.out.println( "OK." );
354 System.out.println( "failed." );
357 System.out.print( "Re-id methods: " );
358 if ( Test.testReIdMethods() ) {
359 System.out.println( "OK." );
363 System.out.println( "failed." );
366 System.out.print( "Methods on last external nodes: " );
367 if ( Test.testLastExternalNodeMethods() ) {
368 System.out.println( "OK." );
372 System.out.println( "failed." );
375 System.out.print( "Methods on external nodes: " );
376 if ( Test.testExternalNodeRelatedMethods() ) {
377 System.out.println( "OK." );
381 System.out.println( "failed." );
384 System.out.print( "Deletion of external nodes: " );
385 if ( Test.testDeletionOfExternalNodes() ) {
386 System.out.println( "OK." );
390 System.out.println( "failed." );
393 System.out.print( "Subtree deletion: " );
394 if ( Test.testSubtreeDeletion() ) {
395 System.out.println( "OK." );
399 System.out.println( "failed." );
402 System.out.print( "Phylogeny branch: " );
403 if ( Test.testPhylogenyBranch() ) {
404 System.out.println( "OK." );
408 System.out.println( "failed." );
411 System.out.print( "Rerooting: " );
412 if ( Test.testRerooting() ) {
413 System.out.println( "OK." );
417 System.out.println( "failed." );
420 System.out.print( "Mipoint rooting: " );
421 if ( Test.testMidpointrooting() ) {
422 System.out.println( "OK." );
426 System.out.println( "failed." );
429 System.out.print( "Support count: " );
430 if ( Test.testSupportCount() ) {
431 System.out.println( "OK." );
435 System.out.println( "failed." );
438 System.out.print( "Support transfer: " );
439 if ( Test.testSupportTransfer() ) {
440 System.out.println( "OK." );
444 System.out.println( "failed." );
447 System.out.print( "Finding of LCA: " );
448 if ( Test.testGetLCA() ) {
449 System.out.println( "OK." );
453 System.out.println( "failed." );
456 System.out.print( "Calculation of distance between nodes: " );
457 if ( Test.testGetDistance() ) {
458 System.out.println( "OK." );
462 System.out.println( "failed." );
465 System.out.print( "SDIse: " );
466 if ( Test.testSDIse() ) {
467 System.out.println( "OK." );
471 System.out.println( "failed." );
474 System.out.print( "Taxonomy assigner: " );
475 if ( Test.testTaxonomyAssigner() ) {
476 System.out.println( "OK." );
480 System.out.println( "failed." );
483 System.out.print( "SDIunrooted: " );
484 if ( Test.testSDIunrooted() ) {
485 System.out.println( "OK." );
489 System.out.println( "failed." );
492 System.out.print( "GSDI: " );
493 if ( TestGSDI.test() ) {
494 System.out.println( "OK." );
498 System.out.println( "failed." );
501 System.out.print( "Descriptive statistics: " );
502 if ( Test.testDescriptiveStatistics() ) {
503 System.out.println( "OK." );
507 System.out.println( "failed." );
510 System.out.print( "Data objects and methods: " );
511 if ( Test.testDataObjects() ) {
512 System.out.println( "OK." );
516 System.out.println( "failed." );
519 System.out.print( "Properties map: " );
520 if ( Test.testPropertiesMap() ) {
521 System.out.println( "OK." );
525 System.out.println( "failed." );
528 System.out.print( "Phylogeny reconstruction:" );
529 System.out.println();
530 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
531 System.out.println( "OK." );
535 System.out.println( "failed." );
538 System.out.print( "Analysis of domain architectures: " );
539 System.out.println();
540 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
541 System.out.println( "OK." );
545 System.out.println( "failed." );
548 System.out.print( "GO: " );
549 System.out.println();
550 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
551 System.out.println( "OK." );
555 System.out.println( "failed." );
558 System.out.print( "Modeling tools: " );
559 if ( TestPccx.test() ) {
560 System.out.println( "OK." );
564 System.out.println( "failed." );
567 System.out.print( "Split Matrix strict: " );
568 if ( Test.testSplitStrict() ) {
569 System.out.println( "OK." );
573 System.out.println( "failed." );
576 System.out.print( "Split Matrix: " );
577 if ( Test.testSplit() ) {
578 System.out.println( "OK." );
582 System.out.println( "failed." );
585 System.out.print( "Confidence Assessor: " );
586 if ( Test.testConfidenceAssessor() ) {
587 System.out.println( "OK." );
591 System.out.println( "failed." );
594 System.out.print( "Basic table: " );
595 if ( Test.testBasicTable() ) {
596 System.out.println( "OK." );
600 System.out.println( "failed." );
603 System.out.print( "General table: " );
604 if ( Test.testGeneralTable() ) {
605 System.out.println( "OK." );
609 System.out.println( "failed." );
612 System.out.print( "Amino acid sequence: " );
613 if ( Test.testAminoAcidSequence() ) {
614 System.out.println( "OK." );
618 System.out.println( "failed." );
621 System.out.print( "General MSA parser: " );
622 if ( Test.testGeneralMsaParser() ) {
623 System.out.println( "OK." );
627 System.out.println( "failed." );
630 System.out.print( "Fasta parser for msa: " );
631 if ( Test.testFastaParser() ) {
632 System.out.println( "OK." );
636 System.out.println( "failed." );
639 System.out.print( "Creation of balanced phylogeny: " );
640 if ( Test.testCreateBalancedPhylogeny() ) {
641 System.out.println( "OK." );
645 System.out.println( "failed." );
648 System.out.print( "Uniprot Taxonomy Search: " );
649 if ( Test.testUniprotTaxonomySearch() ) {
650 System.out.println( "OK." );
655 .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
657 if ( Mafft.isInstalled() ) {
658 System.out.print( "MAFFT (external program): " );
659 if ( Test.testMafft() ) {
660 System.out.println( "OK." );
664 System.out.println( "failed [will not count towards failed tests]" );
667 // System.out.print( "WABI TxSearch: " );
668 // if ( Test.testWabiTxSearch() ) {
669 // System.out.println( "OK." );
674 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
676 System.out.println();
677 final Runtime rt = java.lang.Runtime.getRuntime();
678 final long free_memory = rt.freeMemory() / 1000000;
679 final long total_memory = rt.totalMemory() / 1000000;
680 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
681 + free_memory + "MB, total memory: " + total_memory + "MB)" );
682 System.out.println();
683 System.out.println( "Successful tests: " + succeeded );
684 System.out.println( "Failed tests: " + failed );
685 System.out.println();
687 System.out.println( "OK." );
690 System.out.println( "Not OK." );
692 // System.out.println();
693 // Development.setTime( true );
695 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
696 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
697 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
698 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
699 // "multifurcations_ex_1.nhx";
700 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
701 // final Phylogeny t1 = factory.create( new File( domains ), new
702 // NHXParser() )[ 0 ];
703 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
705 // catch ( final Exception e ) {
706 // e.printStackTrace();
708 // t1.getRoot().preorderPrint();
709 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
713 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
714 // + "\\AtNBSpos.nhx" ) );
716 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
717 // new NHXParser() );
718 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
719 // + "\\AtNBSpos.nhx" ) );
721 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
722 // new NHXParser() );
725 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
726 // + "\\big_tree.nhx" ) );
727 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
728 // + "\\big_tree.nhx" ) );
730 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
731 // new NHXParser() );
733 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
734 // new NHXParser() );
736 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
737 // + "\\big_tree.nhx" ) );
738 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
739 // + "\\big_tree.nhx" ) );
742 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
743 // new NHXParser() );
745 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
746 // new NHXParser() );
748 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
749 // + "\\AtNBSpos.nhx" ) );
751 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
752 // new NHXParser() );
755 // catch ( IOException e ) {
756 // // TODO Auto-generated catch block
757 // e.printStackTrace();
761 private static boolean testBasicNodeMethods() {
763 if ( PhylogenyNode.getNodeCount() != 0 ) {
766 final PhylogenyNode n1 = new PhylogenyNode();
767 final PhylogenyNode n2 = new PhylogenyNode( "", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
768 final PhylogenyNode n3 = new PhylogenyNode( "n3", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
769 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
770 if ( n1.isHasAssignedEvent() ) {
773 if ( PhylogenyNode.getNodeCount() != 4 ) {
776 if ( n3.getIndicator() != 0 ) {
779 if ( n3.getNumberOfExternalNodes() != 1 ) {
782 if ( !n3.isExternal() ) {
785 if ( !n3.isRoot() ) {
788 if ( !n4.getName().equals( "n4" ) ) {
792 catch ( final Exception e ) {
793 e.printStackTrace( System.out );
799 private static boolean testBasicPhyloXMLparsing() {
801 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
802 final PhyloXmlParser xml_parser = new PhyloXmlParser();
803 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
805 if ( xml_parser.getErrorCount() > 0 ) {
806 System.out.println( xml_parser.getErrorMessages().toString() );
809 if ( phylogenies_0.length != 4 ) {
812 final Phylogeny t1 = phylogenies_0[ 0 ];
813 final Phylogeny t2 = phylogenies_0[ 1 ];
814 final Phylogeny t3 = phylogenies_0[ 2 ];
815 final Phylogeny t4 = phylogenies_0[ 3 ];
816 if ( t1.getNumberOfExternalNodes() != 1 ) {
819 if ( !t1.isRooted() ) {
822 if ( t1.isRerootable() ) {
825 if ( !t1.getType().equals( "gene_tree" ) ) {
828 if ( t2.getNumberOfExternalNodes() != 2 ) {
831 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
834 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
837 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
840 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
843 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
846 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
849 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
850 .startsWith( "actgtgggggt" ) ) {
853 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
854 .startsWith( "ctgtgatgcat" ) ) {
857 if ( t3.getNumberOfExternalNodes() != 4 ) {
860 if ( !t1.getName().equals( "t1" ) ) {
863 if ( !t2.getName().equals( "t2" ) ) {
866 if ( !t3.getName().equals( "t3" ) ) {
869 if ( !t4.getName().equals( "t4" ) ) {
872 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
875 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
878 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
881 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
882 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
885 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
888 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
891 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
894 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
895 .equals( "apoptosis" ) ) {
898 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
899 .equals( "GO:0006915" ) ) {
902 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
903 .equals( "UniProtKB" ) ) {
906 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
907 .equals( "experimental" ) ) {
910 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
911 .equals( "function" ) ) {
914 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
918 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
919 .getType().equals( "ml" ) ) {
922 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
923 .equals( "apoptosis" ) ) {
926 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
927 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
930 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
931 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
934 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
935 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
938 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
939 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
942 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
943 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
946 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
947 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
950 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
951 .equals( "GO:0005829" ) ) {
954 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
955 .equals( "intracellular organelle" ) ) {
958 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
961 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
962 .equals( "UniProt link" ) ) ) {
965 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
968 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
971 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
974 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
977 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
980 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
983 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
986 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
989 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
992 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
995 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
996 // .equals( "B" ) ) {
999 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1002 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1005 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1008 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1009 // .getConfidence() != 2144 ) {
1012 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1013 // .equals( "pfam" ) ) {
1016 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1019 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1022 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1025 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1028 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1029 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1033 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1036 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1039 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1042 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1045 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1048 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1051 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1054 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1056 // if ( xml_parser.getErrorCount() > 0 ) {
1057 // System.out.println( xml_parser.getErrorMessages().toString() );
1060 // if ( phylogenies_1.length != 2 ) {
1063 // final Phylogeny a = phylogenies_1[ 0 ];
1064 // if ( !a.getName().equals( "tree 4" ) ) {
1067 // if ( a.getNumberOfExternalNodes() != 3 ) {
1070 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1073 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1077 catch ( final Exception e ) {
1078 e.printStackTrace( System.out );
1084 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1086 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1087 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1088 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1089 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1092 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1094 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1096 if ( xml_parser.getErrorCount() > 0 ) {
1097 System.out.println( xml_parser.getErrorMessages().toString() );
1100 if ( phylogenies_0.length != 4 ) {
1103 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1104 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1105 if ( phylogenies_t1.length != 1 ) {
1108 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1109 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1112 if ( !t1_rt.isRooted() ) {
1115 if ( t1_rt.isRerootable() ) {
1118 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1121 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1122 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1123 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1124 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1127 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1130 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1133 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1136 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1137 .startsWith( "actgtgggggt" ) ) {
1140 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1141 .startsWith( "ctgtgatgcat" ) ) {
1144 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1145 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1146 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1147 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1148 if ( phylogenies_1.length != 1 ) {
1151 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1152 if ( !t3_rt.getName().equals( "t3" ) ) {
1155 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1158 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1161 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1164 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1167 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1168 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1171 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1174 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1177 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1178 .equals( "UniProtKB" ) ) {
1181 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1182 .equals( "apoptosis" ) ) {
1185 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1186 .equals( "GO:0006915" ) ) {
1189 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1190 .equals( "UniProtKB" ) ) {
1193 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1194 .equals( "experimental" ) ) {
1197 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1198 .equals( "function" ) ) {
1201 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1202 .getValue() != 1 ) {
1205 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1206 .getType().equals( "ml" ) ) {
1209 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1210 .equals( "apoptosis" ) ) {
1213 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1214 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1217 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1218 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1221 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1222 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1225 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1226 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1229 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1230 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1233 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1234 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1237 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1238 .equals( "GO:0005829" ) ) {
1241 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1242 .equals( "intracellular organelle" ) ) {
1245 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1248 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1249 .equals( "UniProt link" ) ) ) {
1252 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1255 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1258 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1259 .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." ) ) ) {
1262 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1265 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1268 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1271 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1274 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1275 .equals( "ncbi" ) ) {
1278 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1281 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1282 .getName().equals( "B" ) ) {
1285 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1286 .getFrom() != 21 ) {
1289 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1292 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1293 .getLength() != 24 ) {
1296 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1297 .getConfidence() != 2144 ) {
1300 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1301 .equals( "pfam" ) ) {
1304 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1307 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1310 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1313 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1316 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1317 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1320 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1323 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1326 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1329 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1332 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1335 if ( taxbb.getSynonyms().size() != 2 ) {
1338 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1341 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1344 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1347 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1350 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1353 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1354 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1358 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1361 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1364 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1367 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1370 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1373 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1376 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1380 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1383 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1384 .equalsIgnoreCase( "435" ) ) {
1387 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1390 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1391 .equalsIgnoreCase( "443.7" ) ) {
1394 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1397 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1400 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1401 .equalsIgnoreCase( "433" ) ) {
1405 catch ( final Exception e ) {
1406 e.printStackTrace( System.out );
1412 private static boolean testBasicPhyloXMLparsingValidating() {
1414 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1415 PhyloXmlParser xml_parser = null;
1417 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1419 catch ( final Exception e ) {
1420 // Do nothing -- means were not running from jar.
1422 if ( xml_parser == null ) {
1423 xml_parser = new PhyloXmlParser();
1424 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1425 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1428 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1431 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1433 if ( xml_parser.getErrorCount() > 0 ) {
1434 System.out.println( xml_parser.getErrorMessages().toString() );
1437 if ( phylogenies_0.length != 4 ) {
1440 final Phylogeny t1 = phylogenies_0[ 0 ];
1441 final Phylogeny t2 = phylogenies_0[ 1 ];
1442 final Phylogeny t3 = phylogenies_0[ 2 ];
1443 final Phylogeny t4 = phylogenies_0[ 3 ];
1444 if ( !t1.getName().equals( "t1" ) ) {
1447 if ( !t2.getName().equals( "t2" ) ) {
1450 if ( !t3.getName().equals( "t3" ) ) {
1453 if ( !t4.getName().equals( "t4" ) ) {
1456 if ( t1.getNumberOfExternalNodes() != 1 ) {
1459 if ( t2.getNumberOfExternalNodes() != 2 ) {
1462 if ( t3.getNumberOfExternalNodes() != 4 ) {
1465 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1466 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1467 if ( xml_parser.getErrorCount() > 0 ) {
1468 System.out.println( "errors:" );
1469 System.out.println( xml_parser.getErrorMessages().toString() );
1472 if ( phylogenies_1.length != 4 ) {
1475 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1477 if ( xml_parser.getErrorCount() > 0 ) {
1478 System.out.println( "errors:" );
1479 System.out.println( xml_parser.getErrorMessages().toString() );
1482 if ( phylogenies_2.length != 1 ) {
1485 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1488 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1490 if ( xml_parser.getErrorCount() > 0 ) {
1491 System.out.println( xml_parser.getErrorMessages().toString() );
1494 if ( phylogenies_3.length != 2 ) {
1497 final Phylogeny a = phylogenies_3[ 0 ];
1498 if ( !a.getName().equals( "tree 4" ) ) {
1501 if ( a.getNumberOfExternalNodes() != 3 ) {
1504 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1507 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1510 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1512 if ( xml_parser.getErrorCount() > 0 ) {
1513 System.out.println( xml_parser.getErrorMessages().toString() );
1516 if ( phylogenies_4.length != 1 ) {
1519 final Phylogeny s = phylogenies_4[ 0 ];
1520 if ( s.getNumberOfExternalNodes() != 6 ) {
1523 s.getNode( "first" );
1525 s.getNode( "\"<a'b&c'd\">\"" );
1526 s.getNode( "'''\"" );
1527 s.getNode( "\"\"\"" );
1528 s.getNode( "dick & doof" );
1530 catch ( final Exception e ) {
1531 e.printStackTrace( System.out );
1537 private static boolean testBasicTable() {
1539 final BasicTable<String> t0 = new BasicTable<String>();
1540 if ( t0.getNumberOfColumns() != 0 ) {
1543 if ( t0.getNumberOfRows() != 0 ) {
1546 t0.setValue( 3, 2, "23" );
1547 t0.setValue( 10, 1, "error" );
1548 t0.setValue( 10, 1, "110" );
1549 t0.setValue( 9, 1, "19" );
1550 t0.setValue( 1, 10, "101" );
1551 t0.setValue( 10, 10, "1010" );
1552 t0.setValue( 100, 10, "10100" );
1553 t0.setValue( 0, 0, "00" );
1554 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1557 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1560 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1563 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1566 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1569 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1572 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1575 if ( t0.getNumberOfColumns() != 101 ) {
1578 if ( t0.getNumberOfRows() != 11 ) {
1581 if ( t0.getValueAsString( 49, 4 ) != null ) {
1584 final String l = ForesterUtil.getLineSeparator();
1585 final StringBuffer source = new StringBuffer();
1586 source.append( "" + l );
1587 source.append( "# 1 1 1 1 1 1 1 1" + l );
1588 source.append( " 00 01 02 03" + l );
1589 source.append( " 10 11 12 13 " + l );
1590 source.append( "20 21 22 23 " + l );
1591 source.append( " 30 31 32 33" + l );
1592 source.append( "40 41 42 43" + l );
1593 source.append( " # 1 1 1 1 1 " + l );
1594 source.append( "50 51 52 53 54" + l );
1595 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1596 if ( t1.getNumberOfColumns() != 5 ) {
1599 if ( t1.getNumberOfRows() != 6 ) {
1602 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1605 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1608 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1611 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1614 final StringBuffer source1 = new StringBuffer();
1615 source1.append( "" + l );
1616 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1617 source1.append( " 00; 01 ;02;03" + l );
1618 source1.append( " 10; 11; 12; 13 " + l );
1619 source1.append( "20; 21; 22; 23 " + l );
1620 source1.append( " 30; 31; 32; 33" + l );
1621 source1.append( "40;41;42;43" + l );
1622 source1.append( " # 1 1 1 1 1 " + l );
1623 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1624 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1625 if ( t2.getNumberOfColumns() != 5 ) {
1628 if ( t2.getNumberOfRows() != 6 ) {
1631 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1634 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1637 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1640 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1643 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1646 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1649 final StringBuffer source2 = new StringBuffer();
1650 source2.append( "" + l );
1651 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1652 source2.append( " 00; 01 ;02;03" + l );
1653 source2.append( " 10; 11; 12; 13 " + l );
1654 source2.append( "20; 21; 22; 23 " + l );
1655 source2.append( " " + l );
1656 source2.append( " 30; 31; 32; 33" + l );
1657 source2.append( "40;41;42;43" + l );
1658 source2.append( " comment: 1 1 1 1 1 " + l );
1659 source2.append( ";;;50 ; 52; 53;;54 " + l );
1660 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1665 if ( tl.size() != 2 ) {
1668 final BasicTable<String> t3 = tl.get( 0 );
1669 final BasicTable<String> t4 = tl.get( 1 );
1670 if ( t3.getNumberOfColumns() != 4 ) {
1673 if ( t3.getNumberOfRows() != 3 ) {
1676 if ( t4.getNumberOfColumns() != 4 ) {
1679 if ( t4.getNumberOfRows() != 3 ) {
1682 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1685 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1689 catch ( final Exception e ) {
1690 e.printStackTrace( System.out );
1696 private static boolean testBasicTolXMLparsing() {
1698 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1699 final TolParser parser = new TolParser();
1700 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1701 if ( parser.getErrorCount() > 0 ) {
1702 System.out.println( parser.getErrorMessages().toString() );
1705 if ( phylogenies_0.length != 1 ) {
1708 final Phylogeny t1 = phylogenies_0[ 0 ];
1709 if ( t1.getNumberOfExternalNodes() != 5 ) {
1712 if ( !t1.isRooted() ) {
1715 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1718 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1721 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1724 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1727 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1728 if ( parser.getErrorCount() > 0 ) {
1729 System.out.println( parser.getErrorMessages().toString() );
1732 if ( phylogenies_1.length != 1 ) {
1735 final Phylogeny t2 = phylogenies_1[ 0 ];
1736 if ( t2.getNumberOfExternalNodes() != 664 ) {
1739 if ( !t2.isRooted() ) {
1742 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1745 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1748 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1751 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1754 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1757 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1758 .equals( "Aquifex" ) ) {
1761 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1762 if ( parser.getErrorCount() > 0 ) {
1763 System.out.println( parser.getErrorMessages().toString() );
1766 if ( phylogenies_2.length != 1 ) {
1769 final Phylogeny t3 = phylogenies_2[ 0 ];
1770 if ( t3.getNumberOfExternalNodes() != 184 ) {
1773 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1776 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1779 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1782 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1783 if ( parser.getErrorCount() > 0 ) {
1784 System.out.println( parser.getErrorMessages().toString() );
1787 if ( phylogenies_3.length != 1 ) {
1790 final Phylogeny t4 = phylogenies_3[ 0 ];
1791 if ( t4.getNumberOfExternalNodes() != 1 ) {
1794 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1797 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1800 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1803 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1804 if ( parser.getErrorCount() > 0 ) {
1805 System.out.println( parser.getErrorMessages().toString() );
1808 if ( phylogenies_4.length != 1 ) {
1811 final Phylogeny t5 = phylogenies_4[ 0 ];
1812 if ( t5.getNumberOfExternalNodes() != 13 ) {
1815 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1818 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1821 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1825 catch ( final Exception e ) {
1826 e.printStackTrace( System.out );
1832 private static boolean testBasicTreeMethods() {
1834 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1835 final Phylogeny t1 = factory.create();
1836 if ( !t1.isEmpty() ) {
1839 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1840 if ( t2.getNumberOfExternalNodes() != 4 ) {
1843 if ( t2.getHeight() != 8.5 ) {
1846 if ( !t2.isCompletelyBinary() ) {
1849 if ( t2.isEmpty() ) {
1852 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1853 if ( t3.getNumberOfExternalNodes() != 5 ) {
1856 if ( t3.getHeight() != 11 ) {
1859 if ( t3.isCompletelyBinary() ) {
1862 final PhylogenyNode n = t3.getNode( "ABC" );
1863 PhylogenyNodeIterator it;
1864 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1867 for( it.reset(); it.hasNext(); ) {
1870 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1871 if ( !it2.next().getName().equals( "A" ) ) {
1874 if ( !it2.next().getName().equals( "B" ) ) {
1877 if ( !it2.next().getName().equals( "C" ) ) {
1880 if ( it2.hasNext() ) {
1883 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 ];
1884 if ( t4.getNumberOfExternalNodes() != 9 ) {
1887 if ( t4.getHeight() != 11 ) {
1890 if ( t4.isCompletelyBinary() ) {
1893 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)" );
1894 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1895 if ( t5.getNumberOfExternalNodes() != 8 ) {
1898 if ( t5.getHeight() != 15 ) {
1901 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)" );
1902 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1903 if ( t6.getHeight() != 15 ) {
1906 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)" );
1907 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1908 if ( t7.getHeight() != 15 ) {
1911 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)" );
1912 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1913 if ( t8.getNumberOfExternalNodes() != 10 ) {
1916 if ( t8.getHeight() != 15 ) {
1919 final char[] a9 = new char[] {};
1920 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1921 if ( t9.getHeight() != 0 ) {
1924 final char[] a10 = new char[] { 'a', ':', '6' };
1925 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1926 if ( t10.getHeight() != 6 ) {
1930 catch ( final Exception e ) {
1931 e.printStackTrace( System.out );
1937 private static boolean testConfidenceAssessor() {
1939 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1940 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1941 final Phylogeny[] ev0 = factory
1942 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1944 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1945 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1948 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1951 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1952 final Phylogeny[] ev1 = factory
1953 .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)));",
1955 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1956 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1959 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1962 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1963 final Phylogeny[] ev_b = factory
1964 .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",
1966 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1967 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
1968 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1971 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1975 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1976 final Phylogeny[] ev1x = factory
1977 .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)));",
1979 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1980 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1983 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1986 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1987 final Phylogeny[] ev_bx = factory
1988 .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",
1990 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
1991 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1994 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1998 final Phylogeny[] t2 = factory
1999 .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);",
2001 final Phylogeny[] ev2 = factory
2002 .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);",
2004 for( final Phylogeny target : t2 ) {
2005 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2008 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2009 new NHXParser() )[ 0 ];
2010 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2011 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2012 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2015 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2018 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2022 catch ( final Exception e ) {
2023 e.printStackTrace();
2029 private static boolean testCopyOfNodeData() {
2031 final PhylogenyNode n1 = new PhylogenyNode( "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]" );
2032 final PhylogenyNode n2 = n1.copyNodeData();
2033 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2037 catch ( final Exception e ) {
2038 e.printStackTrace();
2044 private static boolean testDataObjects() {
2046 final Confidence s0 = new Confidence();
2047 final Confidence s1 = new Confidence();
2048 if ( !s0.isEqual( s1 ) ) {
2051 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2052 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2053 if ( s2.isEqual( s1 ) ) {
2056 if ( !s2.isEqual( s3 ) ) {
2059 final Confidence s4 = ( Confidence ) s3.copy();
2060 if ( !s4.isEqual( s3 ) ) {
2067 final Taxonomy t1 = new Taxonomy();
2068 final Taxonomy t2 = new Taxonomy();
2069 final Taxonomy t3 = new Taxonomy();
2070 final Taxonomy t4 = new Taxonomy();
2071 final Taxonomy t5 = new Taxonomy();
2072 t1.setIdentifier( new Identifier( "ecoli" ) );
2073 t1.setTaxonomyCode( "ECOLI" );
2074 t1.setScientificName( "E. coli" );
2075 t1.setCommonName( "coli" );
2076 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2077 if ( !t1.isEqual( t0 ) ) {
2080 t2.setIdentifier( new Identifier( "ecoli" ) );
2081 t2.setTaxonomyCode( "other" );
2082 t2.setScientificName( "what" );
2083 t2.setCommonName( "something" );
2084 if ( !t1.isEqual( t2 ) ) {
2087 t2.setIdentifier( new Identifier( "nemve" ) );
2088 if ( t1.isEqual( t2 ) ) {
2091 t1.setIdentifier( null );
2092 t3.setTaxonomyCode( "ECOLI" );
2093 t3.setScientificName( "what" );
2094 t3.setCommonName( "something" );
2095 if ( !t1.isEqual( t3 ) ) {
2098 t1.setIdentifier( null );
2099 t1.setTaxonomyCode( "" );
2100 t4.setScientificName( "E. ColI" );
2101 t4.setCommonName( "something" );
2102 if ( !t1.isEqual( t4 ) ) {
2105 t4.setScientificName( "B. subtilis" );
2106 t4.setCommonName( "something" );
2107 if ( t1.isEqual( t4 ) ) {
2110 t1.setIdentifier( null );
2111 t1.setTaxonomyCode( "" );
2112 t1.setScientificName( "" );
2113 t5.setCommonName( "COLI" );
2114 if ( !t1.isEqual( t5 ) ) {
2117 t5.setCommonName( "vibrio" );
2118 if ( t1.isEqual( t5 ) ) {
2123 final Identifier id0 = new Identifier( "123", "pfam" );
2124 final Identifier id1 = ( Identifier ) id0.copy();
2125 if ( !id1.isEqual( id1 ) ) {
2128 if ( !id1.isEqual( id0 ) ) {
2131 if ( !id0.isEqual( id1 ) ) {
2138 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2139 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2140 if ( !pd1.isEqual( pd1 ) ) {
2143 if ( !pd1.isEqual( pd0 ) ) {
2148 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2149 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2150 if ( !pd3.isEqual( pd3 ) ) {
2153 if ( !pd2.isEqual( pd3 ) ) {
2156 if ( !pd0.isEqual( pd3 ) ) {
2161 // DomainArchitecture
2162 // ------------------
2163 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2164 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2165 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2166 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2167 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2168 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2173 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2174 if ( ds0.getNumberOfDomains() != 4 ) {
2177 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2178 if ( !ds0.isEqual( ds0 ) ) {
2181 if ( !ds0.isEqual( ds1 ) ) {
2184 if ( ds1.getNumberOfDomains() != 4 ) {
2187 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2192 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2193 if ( ds0.isEqual( ds2 ) ) {
2199 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2200 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2201 System.out.println( ds3.toNHX() );
2204 if ( ds3.getNumberOfDomains() != 3 ) {
2209 final Event e1 = new Event( Event.EventType.fusion );
2210 if ( e1.isDuplication() ) {
2213 if ( !e1.isFusion() ) {
2216 if ( !e1.asText().toString().equals( "fusion" ) ) {
2219 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2222 final Event e11 = new Event( Event.EventType.fusion );
2223 if ( !e11.isEqual( e1 ) ) {
2226 if ( !e11.toNHX().toString().equals( "" ) ) {
2229 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2230 if ( e2.isDuplication() ) {
2233 if ( !e2.isSpeciationOrDuplication() ) {
2236 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2239 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2242 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2245 if ( e11.isEqual( e2 ) ) {
2248 final Event e2c = ( Event ) e2.copy();
2249 if ( !e2c.isEqual( e2 ) ) {
2252 Event e3 = new Event( 1, 2, 3 );
2253 if ( e3.isDuplication() ) {
2256 if ( e3.isSpeciation() ) {
2259 if ( e3.isGeneLoss() ) {
2262 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2265 final Event e3c = ( Event ) e3.copy();
2266 final Event e3cc = ( Event ) e3c.copy();
2267 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2271 if ( !e3c.isEqual( e3cc ) ) {
2274 Event e4 = new Event( 1, 2, 3 );
2275 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2278 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2281 final Event e4c = ( Event ) e4.copy();
2283 final Event e4cc = ( Event ) e4c.copy();
2284 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2287 if ( !e4c.isEqual( e4cc ) ) {
2290 final Event e5 = new Event();
2291 if ( !e5.isUnassigned() ) {
2294 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2297 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2300 final Event e6 = new Event( 1, 0, 0 );
2301 if ( !e6.asText().toString().equals( "duplication" ) ) {
2304 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2307 final Event e7 = new Event( 0, 1, 0 );
2308 if ( !e7.asText().toString().equals( "speciation" ) ) {
2311 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2314 final Event e8 = new Event( 0, 0, 1 );
2315 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2318 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2322 catch ( final Exception e ) {
2323 e.printStackTrace( System.out );
2329 private static boolean testDeletionOfExternalNodes() {
2331 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2332 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2333 final PhylogenyWriter w = new PhylogenyWriter();
2334 if ( t0.isEmpty() ) {
2337 if ( t0.getNumberOfExternalNodes() != 1 ) {
2340 t0.deleteSubtree( t0.getNode( "A" ), false );
2341 if ( t0.getNumberOfExternalNodes() != 0 ) {
2344 if ( !t0.isEmpty() ) {
2347 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2348 if ( t1.getNumberOfExternalNodes() != 2 ) {
2351 t1.deleteSubtree( t1.getNode( "A" ), false );
2352 if ( t1.getNumberOfExternalNodes() != 1 ) {
2355 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2358 t1.deleteSubtree( t1.getNode( "B" ), false );
2359 if ( t1.getNumberOfExternalNodes() != 1 ) {
2362 t1.deleteSubtree( t1.getNode( "r" ), false );
2363 if ( !t1.isEmpty() ) {
2366 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2367 if ( t2.getNumberOfExternalNodes() != 3 ) {
2370 t2.deleteSubtree( t2.getNode( "B" ), false );
2371 if ( t2.getNumberOfExternalNodes() != 2 ) {
2374 t2.toNewHampshireX();
2375 PhylogenyNode n = t2.getNode( "A" );
2376 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2379 t2.deleteSubtree( t2.getNode( "A" ), false );
2380 if ( t2.getNumberOfExternalNodes() != 2 ) {
2383 t2.deleteSubtree( t2.getNode( "C" ), true );
2384 if ( t2.getNumberOfExternalNodes() != 1 ) {
2387 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2388 if ( t3.getNumberOfExternalNodes() != 4 ) {
2391 t3.deleteSubtree( t3.getNode( "B" ), true );
2392 if ( t3.getNumberOfExternalNodes() != 3 ) {
2395 n = t3.getNode( "A" );
2396 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2399 n = n.getNextExternalNode();
2400 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2403 t3.deleteSubtree( t3.getNode( "A" ), true );
2404 if ( t3.getNumberOfExternalNodes() != 2 ) {
2407 n = t3.getNode( "C" );
2408 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2411 t3.deleteSubtree( t3.getNode( "C" ), true );
2412 if ( t3.getNumberOfExternalNodes() != 1 ) {
2415 t3.deleteSubtree( t3.getNode( "D" ), true );
2416 if ( t3.getNumberOfExternalNodes() != 0 ) {
2419 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2420 if ( t4.getNumberOfExternalNodes() != 6 ) {
2423 t4.deleteSubtree( t4.getNode( "B2" ), true );
2424 if ( t4.getNumberOfExternalNodes() != 5 ) {
2427 String s = w.toNewHampshire( t4, false, true ).toString();
2428 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2431 t4.deleteSubtree( t4.getNode( "B11" ), true );
2432 if ( t4.getNumberOfExternalNodes() != 4 ) {
2435 t4.deleteSubtree( t4.getNode( "C" ), true );
2436 if ( t4.getNumberOfExternalNodes() != 3 ) {
2439 n = t4.getNode( "A" );
2440 n = n.getNextExternalNode();
2441 if ( !n.getName().equals( "B12" ) ) {
2444 n = n.getNextExternalNode();
2445 if ( !n.getName().equals( "D" ) ) {
2448 s = w.toNewHampshire( t4, false, true ).toString();
2449 if ( !s.equals( "((A,B12),D);" ) ) {
2452 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2453 t5.deleteSubtree( t5.getNode( "A" ), true );
2454 if ( t5.getNumberOfExternalNodes() != 5 ) {
2457 s = w.toNewHampshire( t5, false, true ).toString();
2458 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2461 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2462 t6.deleteSubtree( t6.getNode( "B11" ), true );
2463 if ( t6.getNumberOfExternalNodes() != 5 ) {
2466 s = w.toNewHampshire( t6, false, false ).toString();
2467 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2470 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2471 t7.deleteSubtree( t7.getNode( "B12" ), true );
2472 if ( t7.getNumberOfExternalNodes() != 5 ) {
2475 s = w.toNewHampshire( t7, false, true ).toString();
2476 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2479 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2480 t8.deleteSubtree( t8.getNode( "B2" ), true );
2481 if ( t8.getNumberOfExternalNodes() != 5 ) {
2484 s = w.toNewHampshire( t8, false, false ).toString();
2485 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2488 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2489 t9.deleteSubtree( t9.getNode( "C" ), true );
2490 if ( t9.getNumberOfExternalNodes() != 5 ) {
2493 s = w.toNewHampshire( t9, false, true ).toString();
2494 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2497 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2498 t10.deleteSubtree( t10.getNode( "D" ), true );
2499 if ( t10.getNumberOfExternalNodes() != 5 ) {
2502 s = w.toNewHampshire( t10, false, true ).toString();
2503 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2506 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2507 t11.deleteSubtree( t11.getNode( "A" ), true );
2508 if ( t11.getNumberOfExternalNodes() != 2 ) {
2511 s = w.toNewHampshire( t11, false, true ).toString();
2512 if ( !s.equals( "(B,C);" ) ) {
2515 t11.deleteSubtree( t11.getNode( "C" ), true );
2516 if ( t11.getNumberOfExternalNodes() != 1 ) {
2519 s = w.toNewHampshire( t11, false, false ).toString();
2520 if ( !s.equals( "B;" ) ) {
2523 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2524 t12.deleteSubtree( t12.getNode( "B2" ), true );
2525 if ( t12.getNumberOfExternalNodes() != 8 ) {
2528 s = w.toNewHampshire( t12, false, true ).toString();
2529 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2532 t12.deleteSubtree( t12.getNode( "B3" ), true );
2533 if ( t12.getNumberOfExternalNodes() != 7 ) {
2536 s = w.toNewHampshire( t12, false, true ).toString();
2537 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2540 t12.deleteSubtree( t12.getNode( "C3" ), true );
2541 if ( t12.getNumberOfExternalNodes() != 6 ) {
2544 s = w.toNewHampshire( t12, false, true ).toString();
2545 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2548 t12.deleteSubtree( t12.getNode( "A1" ), true );
2549 if ( t12.getNumberOfExternalNodes() != 5 ) {
2552 s = w.toNewHampshire( t12, false, true ).toString();
2553 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2556 t12.deleteSubtree( t12.getNode( "B1" ), true );
2557 if ( t12.getNumberOfExternalNodes() != 4 ) {
2560 s = w.toNewHampshire( t12, false, true ).toString();
2561 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2564 t12.deleteSubtree( t12.getNode( "A3" ), true );
2565 if ( t12.getNumberOfExternalNodes() != 3 ) {
2568 s = w.toNewHampshire( t12, false, true ).toString();
2569 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2572 t12.deleteSubtree( t12.getNode( "A2" ), true );
2573 if ( t12.getNumberOfExternalNodes() != 2 ) {
2576 s = w.toNewHampshire( t12, false, true ).toString();
2577 if ( !s.equals( "(C1,C2);" ) ) {
2580 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2581 t13.deleteSubtree( t13.getNode( "D" ), true );
2582 if ( t13.getNumberOfExternalNodes() != 4 ) {
2585 s = w.toNewHampshire( t13, false, true ).toString();
2586 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2589 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2590 t14.deleteSubtree( t14.getNode( "E" ), true );
2591 if ( t14.getNumberOfExternalNodes() != 5 ) {
2594 s = w.toNewHampshire( t14, false, true ).toString();
2595 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2598 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2599 t15.deleteSubtree( t15.getNode( "B2" ), true );
2600 if ( t15.getNumberOfExternalNodes() != 11 ) {
2603 t15.deleteSubtree( t15.getNode( "B1" ), true );
2604 if ( t15.getNumberOfExternalNodes() != 10 ) {
2607 t15.deleteSubtree( t15.getNode( "B3" ), true );
2608 if ( t15.getNumberOfExternalNodes() != 9 ) {
2611 t15.deleteSubtree( t15.getNode( "B4" ), true );
2612 if ( t15.getNumberOfExternalNodes() != 8 ) {
2615 t15.deleteSubtree( t15.getNode( "A1" ), true );
2616 if ( t15.getNumberOfExternalNodes() != 7 ) {
2619 t15.deleteSubtree( t15.getNode( "C4" ), true );
2620 if ( t15.getNumberOfExternalNodes() != 6 ) {
2624 catch ( final Exception e ) {
2625 e.printStackTrace( System.out );
2631 private static boolean testDescriptiveStatistics() {
2633 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2634 dss1.addValue( 82 );
2635 dss1.addValue( 78 );
2636 dss1.addValue( 70 );
2637 dss1.addValue( 58 );
2638 dss1.addValue( 42 );
2639 if ( dss1.getN() != 5 ) {
2642 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2645 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2648 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2651 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2654 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2657 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2660 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2663 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2666 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2669 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2672 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2675 dss1.addValue( 123 );
2676 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2679 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2682 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2685 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2686 dss2.addValue( -1.85 );
2687 dss2.addValue( 57.5 );
2688 dss2.addValue( 92.78 );
2689 dss2.addValue( 57.78 );
2690 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2693 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2696 final double[] a = dss2.getDataAsDoubleArray();
2697 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2700 dss2.addValue( -100 );
2701 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2704 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2707 final double[] ds = new double[ 14 ];
2722 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2723 if ( bins.length != 4 ) {
2726 if ( bins[ 0 ] != 2 ) {
2729 if ( bins[ 1 ] != 3 ) {
2732 if ( bins[ 2 ] != 4 ) {
2735 if ( bins[ 3 ] != 5 ) {
2738 final double[] ds1 = new double[ 9 ];
2748 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2749 if ( bins1.length != 4 ) {
2752 if ( bins1[ 0 ] != 2 ) {
2755 if ( bins1[ 1 ] != 3 ) {
2758 if ( bins1[ 2 ] != 0 ) {
2761 if ( bins1[ 3 ] != 4 ) {
2764 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2765 if ( bins1_1.length != 3 ) {
2768 if ( bins1_1[ 0 ] != 3 ) {
2771 if ( bins1_1[ 1 ] != 2 ) {
2774 if ( bins1_1[ 2 ] != 4 ) {
2777 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2778 if ( bins1_2.length != 3 ) {
2781 if ( bins1_2[ 0 ] != 2 ) {
2784 if ( bins1_2[ 1 ] != 2 ) {
2787 if ( bins1_2[ 2 ] != 2 ) {
2790 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2804 dss3.addValue( 10 );
2805 dss3.addValue( 10 );
2806 dss3.addValue( 10 );
2807 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2808 histo.toStringBuffer( 10, '=', 40, 5 );
2809 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2811 catch ( final Exception e ) {
2812 e.printStackTrace( System.out );
2818 private static boolean testDir( final String file ) {
2820 final File f = new File( file );
2821 if ( !f.exists() ) {
2824 if ( !f.isDirectory() ) {
2827 if ( !f.canRead() ) {
2831 catch ( final Exception e ) {
2837 private static boolean testExternalNodeRelatedMethods() {
2839 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2840 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2841 PhylogenyNode n = t1.getNode( "A" );
2842 n = n.getNextExternalNode();
2843 if ( !n.getName().equals( "B" ) ) {
2846 n = n.getNextExternalNode();
2847 if ( !n.getName().equals( "C" ) ) {
2850 n = n.getNextExternalNode();
2851 if ( !n.getName().equals( "D" ) ) {
2854 n = t1.getNode( "B" );
2855 while ( !n.isLastExternalNode() ) {
2856 n = n.getNextExternalNode();
2858 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2859 n = t2.getNode( "A" );
2860 n = n.getNextExternalNode();
2861 if ( !n.getName().equals( "B" ) ) {
2864 n = n.getNextExternalNode();
2865 if ( !n.getName().equals( "C" ) ) {
2868 n = n.getNextExternalNode();
2869 if ( !n.getName().equals( "D" ) ) {
2872 n = t2.getNode( "B" );
2873 while ( !n.isLastExternalNode() ) {
2874 n = n.getNextExternalNode();
2876 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2877 n = t3.getNode( "A" );
2878 n = n.getNextExternalNode();
2879 if ( !n.getName().equals( "B" ) ) {
2882 n = n.getNextExternalNode();
2883 if ( !n.getName().equals( "C" ) ) {
2886 n = n.getNextExternalNode();
2887 if ( !n.getName().equals( "D" ) ) {
2890 n = n.getNextExternalNode();
2891 if ( !n.getName().equals( "E" ) ) {
2894 n = n.getNextExternalNode();
2895 if ( !n.getName().equals( "F" ) ) {
2898 n = n.getNextExternalNode();
2899 if ( !n.getName().equals( "G" ) ) {
2902 n = n.getNextExternalNode();
2903 if ( !n.getName().equals( "H" ) ) {
2906 n = t3.getNode( "B" );
2907 while ( !n.isLastExternalNode() ) {
2908 n = n.getNextExternalNode();
2910 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2911 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2912 final PhylogenyNode node = iter.next();
2914 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2915 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2916 final PhylogenyNode node = iter.next();
2919 catch ( final Exception e ) {
2920 e.printStackTrace( System.out );
2926 private static boolean testGeneralTable() {
2928 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2929 t0.setValue( 3, 2, "23" );
2930 t0.setValue( 10, 1, "error" );
2931 t0.setValue( 10, 1, "110" );
2932 t0.setValue( 9, 1, "19" );
2933 t0.setValue( 1, 10, "101" );
2934 t0.setValue( 10, 10, "1010" );
2935 t0.setValue( 100, 10, "10100" );
2936 t0.setValue( 0, 0, "00" );
2937 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2940 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2943 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2946 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2949 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2952 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2955 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2958 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2961 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2964 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2965 t1.setValue( "3", "2", "23" );
2966 t1.setValue( "10", "1", "error" );
2967 t1.setValue( "10", "1", "110" );
2968 t1.setValue( "9", "1", "19" );
2969 t1.setValue( "1", "10", "101" );
2970 t1.setValue( "10", "10", "1010" );
2971 t1.setValue( "100", "10", "10100" );
2972 t1.setValue( "0", "0", "00" );
2973 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2974 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2977 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2980 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2983 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2986 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2989 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
2992 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
2995 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
2998 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3001 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3005 catch ( final Exception e ) {
3006 e.printStackTrace( System.out );
3012 private static boolean testGetDistance() {
3014 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3015 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",
3016 new NHXParser() )[ 0 ];
3017 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3018 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3021 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3024 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3027 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3030 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3033 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3036 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3039 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3042 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3045 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3048 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3051 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3054 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3057 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3060 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3063 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3066 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3069 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3072 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3075 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3078 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3081 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3084 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3087 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3090 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3093 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3096 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3099 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3102 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3105 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3108 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3111 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",
3112 new NHXParser() )[ 0 ];
3113 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3116 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3119 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3122 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3125 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3128 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3131 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3134 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3137 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3140 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3143 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3147 catch ( final Exception e ) {
3148 e.printStackTrace( System.out );
3154 private static boolean testGetLCA() {
3156 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3157 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3158 new NHXParser() )[ 0 ];
3159 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3160 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3161 if ( !A.getName().equals( "A" ) ) {
3164 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3165 if ( !gh.getName().equals( "gh" ) ) {
3168 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3169 if ( !ab.getName().equals( "ab" ) ) {
3172 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3173 if ( !ab2.getName().equals( "ab" ) ) {
3176 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3177 if ( !gh2.getName().equals( "gh" ) ) {
3180 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3181 if ( !gh3.getName().equals( "gh" ) ) {
3184 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3185 if ( !abc.getName().equals( "abc" ) ) {
3188 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3189 if ( !abc2.getName().equals( "abc" ) ) {
3192 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3193 if ( !abcd.getName().equals( "abcd" ) ) {
3196 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3197 if ( !abcd2.getName().equals( "abcd" ) ) {
3200 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3201 if ( !abcdef.getName().equals( "abcdef" ) ) {
3204 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3205 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3208 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3209 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3212 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3213 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3216 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3217 if ( !abcde.getName().equals( "abcde" ) ) {
3220 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3221 if ( !abcde2.getName().equals( "abcde" ) ) {
3224 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3225 if ( !r.getName().equals( "abcdefgh" ) ) {
3228 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3229 if ( !r2.getName().equals( "abcdefgh" ) ) {
3232 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3233 if ( !r3.getName().equals( "abcdefgh" ) ) {
3236 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3237 if ( !abcde3.getName().equals( "abcde" ) ) {
3240 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3241 if ( !abcde4.getName().equals( "abcde" ) ) {
3244 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3245 if ( !ab3.getName().equals( "ab" ) ) {
3248 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3249 if ( !ab4.getName().equals( "ab" ) ) {
3252 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3253 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3254 if ( !cd.getName().equals( "cd" ) ) {
3257 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3258 if ( !cd2.getName().equals( "cd" ) ) {
3261 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3262 if ( !cde.getName().equals( "cde" ) ) {
3265 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3266 if ( !cde2.getName().equals( "cde" ) ) {
3269 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3270 if ( !cdef.getName().equals( "cdef" ) ) {
3273 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3274 if ( !cdef2.getName().equals( "cdef" ) ) {
3277 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3278 if ( !cdef3.getName().equals( "cdef" ) ) {
3281 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3282 if ( !rt.getName().equals( "r" ) ) {
3285 final Phylogeny p3 = factory
3286 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3287 new NHXParser() )[ 0 ];
3288 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3289 if ( !bc_3.getName().equals( "bc" ) ) {
3292 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3293 if ( !ac_3.getName().equals( "abc" ) ) {
3296 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3297 if ( !ad_3.getName().equals( "abcde" ) ) {
3300 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3301 if ( !af_3.getName().equals( "abcdef" ) ) {
3304 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3305 if ( !ag_3.getName().equals( "" ) ) {
3308 if ( !ag_3.isRoot() ) {
3311 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3312 if ( !al_3.getName().equals( "" ) ) {
3315 if ( !al_3.isRoot() ) {
3318 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3319 if ( !kl_3.getName().equals( "" ) ) {
3322 if ( !kl_3.isRoot() ) {
3325 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3326 if ( !fl_3.getName().equals( "" ) ) {
3329 if ( !fl_3.isRoot() ) {
3332 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3333 if ( !gk_3.getName().equals( "ghijk" ) ) {
3336 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3337 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3338 if ( !r_4.getName().equals( "r" ) ) {
3341 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3342 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3343 if ( !r_5.getName().equals( "root" ) ) {
3346 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3347 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3348 if ( !r_6.getName().equals( "rot" ) ) {
3351 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3352 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3353 if ( !r_7.getName().equals( "rott" ) ) {
3357 catch ( final Exception e ) {
3358 e.printStackTrace( System.out );
3364 private static boolean testHmmscanOutputParser() {
3365 final String test_dir = Test.PATH_TO_TEST_DATA;
3367 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3368 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3370 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3371 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3372 final List<Protein> domain_collections = parser2.parse();
3373 if ( parser2.getProteinsEncountered() != 4 ) {
3376 if ( domain_collections.size() != 4 ) {
3379 if ( parser2.getDomainsEncountered() != 69 ) {
3382 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3385 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3388 final Protein p1 = domain_collections.get( 0 );
3389 if ( p1.getNumberOfProteinDomains() != 15 ) {
3392 final Protein p4 = domain_collections.get( 3 );
3393 if ( p4.getNumberOfProteinDomains() != 1 ) {
3396 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3399 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3402 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3405 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3408 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3411 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3414 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3417 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3420 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3424 catch ( final Exception e ) {
3425 e.printStackTrace( System.out );
3431 private static boolean testLastExternalNodeMethods() {
3433 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3434 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3435 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3436 final PhylogenyNode n1 = t0.getNode( "A" );
3437 if ( n1.isLastExternalNode() ) {
3440 final PhylogenyNode n2 = t0.getNode( "B" );
3441 if ( n2.isLastExternalNode() ) {
3444 final PhylogenyNode n3 = t0.getNode( "C" );
3445 if ( n3.isLastExternalNode() ) {
3448 final PhylogenyNode n4 = t0.getNode( "D" );
3449 if ( !n4.isLastExternalNode() ) {
3453 catch ( final Exception e ) {
3454 e.printStackTrace( System.out );
3460 private static boolean testLevelOrderIterator() {
3462 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3463 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3464 PhylogenyNodeIterator it0;
3465 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3468 for( it0.reset(); it0.hasNext(); ) {
3471 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3472 if ( !it.next().getName().equals( "r" ) ) {
3475 if ( !it.next().getName().equals( "ab" ) ) {
3478 if ( !it.next().getName().equals( "cd" ) ) {
3481 if ( !it.next().getName().equals( "A" ) ) {
3484 if ( !it.next().getName().equals( "B" ) ) {
3487 if ( !it.next().getName().equals( "C" ) ) {
3490 if ( !it.next().getName().equals( "D" ) ) {
3493 if ( it.hasNext() ) {
3496 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",
3497 new NHXParser() )[ 0 ];
3498 PhylogenyNodeIterator it2;
3499 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3502 for( it2.reset(); it2.hasNext(); ) {
3505 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3506 if ( !it3.next().getName().equals( "r" ) ) {
3509 if ( !it3.next().getName().equals( "abc" ) ) {
3512 if ( !it3.next().getName().equals( "defg" ) ) {
3515 if ( !it3.next().getName().equals( "A" ) ) {
3518 if ( !it3.next().getName().equals( "B" ) ) {
3521 if ( !it3.next().getName().equals( "C" ) ) {
3524 if ( !it3.next().getName().equals( "D" ) ) {
3527 if ( !it3.next().getName().equals( "E" ) ) {
3530 if ( !it3.next().getName().equals( "F" ) ) {
3533 if ( !it3.next().getName().equals( "G" ) ) {
3536 if ( !it3.next().getName().equals( "1" ) ) {
3539 if ( !it3.next().getName().equals( "2" ) ) {
3542 if ( !it3.next().getName().equals( "3" ) ) {
3545 if ( !it3.next().getName().equals( "4" ) ) {
3548 if ( !it3.next().getName().equals( "5" ) ) {
3551 if ( !it3.next().getName().equals( "6" ) ) {
3554 if ( !it3.next().getName().equals( "f1" ) ) {
3557 if ( !it3.next().getName().equals( "f2" ) ) {
3560 if ( !it3.next().getName().equals( "f3" ) ) {
3563 if ( !it3.next().getName().equals( "a" ) ) {
3566 if ( !it3.next().getName().equals( "b" ) ) {
3569 if ( !it3.next().getName().equals( "f21" ) ) {
3572 if ( !it3.next().getName().equals( "X" ) ) {
3575 if ( !it3.next().getName().equals( "Y" ) ) {
3578 if ( !it3.next().getName().equals( "Z" ) ) {
3581 if ( it3.hasNext() ) {
3584 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3585 PhylogenyNodeIterator it4;
3586 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3589 for( it4.reset(); it4.hasNext(); ) {
3592 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3593 if ( !it5.next().getName().equals( "r" ) ) {
3596 if ( !it5.next().getName().equals( "A" ) ) {
3599 if ( !it5.next().getName().equals( "B" ) ) {
3602 if ( !it5.next().getName().equals( "C" ) ) {
3605 if ( !it5.next().getName().equals( "D" ) ) {
3608 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3609 PhylogenyNodeIterator it6;
3610 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3613 for( it6.reset(); it6.hasNext(); ) {
3616 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3617 if ( !it7.next().getName().equals( "A" ) ) {
3620 if ( it.hasNext() ) {
3624 catch ( final Exception e ) {
3625 e.printStackTrace( System.out );
3631 private static boolean testMidpointrooting() {
3633 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3634 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",
3635 new NHXParser() )[ 0 ];
3636 if ( !t1.isRooted() ) {
3639 PhylogenyMethods.midpointRoot( t1 );
3640 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3643 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3646 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3649 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3652 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3655 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3658 t1.reRoot( t1.getNode( "A" ) );
3659 PhylogenyMethods.midpointRoot( t1 );
3660 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3663 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3666 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3669 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3672 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3675 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3679 catch ( final Exception e ) {
3680 e.printStackTrace( System.out );
3686 private static boolean testNexusCharactersParsing() {
3688 final NexusCharactersParser parser = new NexusCharactersParser();
3689 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3691 String[] labels = parser.getCharStateLabels();
3692 if ( labels.length != 7 ) {
3695 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3698 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3701 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3704 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3707 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3710 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3713 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3716 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3718 labels = parser.getCharStateLabels();
3719 if ( labels.length != 7 ) {
3722 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3725 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3728 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3731 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3734 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3737 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3740 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3744 catch ( final Exception e ) {
3745 e.printStackTrace( System.out );
3751 private static boolean testNexusMatrixParsing() {
3753 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3754 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3756 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3757 if ( m.getNumberOfCharacters() != 9 ) {
3760 if ( m.getNumberOfIdentifiers() != 5 ) {
3763 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3766 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3769 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3772 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3775 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3778 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3781 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3784 // if ( labels.length != 7 ) {
3787 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3790 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3793 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3796 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3799 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3802 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3805 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3808 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3810 // labels = parser.getCharStateLabels();
3811 // if ( labels.length != 7 ) {
3814 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3817 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3820 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3823 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3826 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3829 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3832 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3836 catch ( final Exception e ) {
3837 e.printStackTrace( System.out );
3843 private static boolean testNexusTreeParsing() {
3845 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3846 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3847 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3848 if ( phylogenies.length != 1 ) {
3851 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3854 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3858 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3859 if ( phylogenies.length != 1 ) {
3862 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3865 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3869 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3870 if ( phylogenies.length != 1 ) {
3873 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3876 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3879 if ( phylogenies[ 0 ].isRooted() ) {
3883 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3884 if ( phylogenies.length != 18 ) {
3887 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3890 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3893 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3896 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3899 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3902 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3905 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3908 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3911 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3914 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3917 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3920 if ( phylogenies[ 8 ].isRooted() ) {
3923 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3926 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3929 if ( !phylogenies[ 9 ].isRooted() ) {
3932 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3935 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3938 if ( !phylogenies[ 10 ].isRooted() ) {
3941 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3944 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3947 if ( phylogenies[ 11 ].isRooted() ) {
3950 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
3953 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
3956 if ( !phylogenies[ 12 ].isRooted() ) {
3959 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
3962 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
3965 if ( !phylogenies[ 13 ].isRooted() ) {
3968 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
3971 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
3974 if ( !phylogenies[ 14 ].isRooted() ) {
3977 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
3980 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
3983 if ( phylogenies[ 15 ].isRooted() ) {
3986 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
3989 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
3992 if ( !phylogenies[ 16 ].isRooted() ) {
3995 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
3998 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4001 if ( phylogenies[ 17 ].isRooted() ) {
4004 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4008 catch ( final Exception e ) {
4009 e.printStackTrace( System.out );
4015 private static boolean testNexusTreeParsingTranslating() {
4017 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4018 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4019 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4020 if ( phylogenies.length != 1 ) {
4023 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4026 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4029 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4032 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4035 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4036 .equals( "Aranaeus" ) ) {
4040 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4041 if ( phylogenies.length != 3 ) {
4044 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4047 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4050 if ( phylogenies[ 0 ].isRooted() ) {
4053 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4056 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4059 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4060 .equals( "Aranaeus" ) ) {
4063 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4066 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4069 if ( phylogenies[ 1 ].isRooted() ) {
4072 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4075 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4078 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4079 .equals( "Aranaeus" ) ) {
4082 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4085 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4088 if ( !phylogenies[ 2 ].isRooted() ) {
4091 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4094 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4097 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4098 .equals( "Aranaeus" ) ) {
4102 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4103 if ( phylogenies.length != 3 ) {
4106 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4109 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4112 if ( phylogenies[ 0 ].isRooted() ) {
4115 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4118 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4121 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4122 .equals( "Aranaeus" ) ) {
4125 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4128 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4131 if ( phylogenies[ 1 ].isRooted() ) {
4134 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4137 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4140 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4141 .equals( "Aranaeus" ) ) {
4144 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4147 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4150 if ( !phylogenies[ 2 ].isRooted() ) {
4153 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4156 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4159 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4160 .equals( "Aranaeus" ) ) {
4164 catch ( final Exception e ) {
4165 e.printStackTrace( System.out );
4171 private static boolean testNHParsing() {
4173 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4174 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4175 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4178 final NHXParser nhxp = new NHXParser();
4179 nhxp.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
4180 nhxp.setReplaceUnderscores( true );
4181 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4182 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4185 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4188 final Phylogeny p1b = factory
4189 .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 ",
4190 new NHXParser() )[ 0 ];
4191 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4194 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4197 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4198 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4199 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4200 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4201 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4202 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4203 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4204 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4205 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4206 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4207 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4208 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4209 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4211 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4214 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4217 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4220 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4223 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4224 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4225 final String p16_S = "((A,B),C)";
4226 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4227 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4230 final String p17_S = "(C,(A,B))";
4231 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4232 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4235 final String p18_S = "((A,B),(C,D))";
4236 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4237 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4240 final String p19_S = "(((A,B),C),D)";
4241 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4242 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4245 final String p20_S = "(A,(B,(C,D)))";
4246 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4247 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4250 final String p21_S = "(A,(B,(C,(D,E))))";
4251 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4252 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4255 final String p22_S = "((((A,B),C),D),E)";
4256 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4257 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4260 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4261 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4262 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4265 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4266 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4267 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4270 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4271 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4272 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4273 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4276 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4279 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4280 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4281 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4282 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4283 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4284 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4285 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4286 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4287 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4288 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4291 final String p26_S = "(A,B)ab";
4292 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4293 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4296 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4297 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4299 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4302 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4303 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4304 final String p28_S3 = "(A,B)ab";
4305 final String p28_S4 = "((((A,B),C),D),;E;)";
4306 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4308 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4311 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4314 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4317 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4320 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";
4321 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4322 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4325 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";
4326 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4327 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4330 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4331 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4332 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4335 final String p33_S = "A";
4336 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4337 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4340 final String p34_S = "B;";
4341 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4342 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4345 final String p35_S = "B:0.2";
4346 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4347 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4350 final String p36_S = "(A)";
4351 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4352 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4355 final String p37_S = "((A))";
4356 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4357 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4360 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4361 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4362 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4365 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4366 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4367 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4370 final String p40_S = "(A,B,C)";
4371 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4372 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4375 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4376 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4377 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4380 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4381 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4382 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4385 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)";
4386 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4387 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4390 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)))";
4391 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4392 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4395 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4396 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4397 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4400 final String p46_S = "";
4401 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4402 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4406 catch ( final Exception e ) {
4407 e.printStackTrace( System.out );
4413 private static boolean testNHXconversion() {
4415 final PhylogenyNode n1 = new PhylogenyNode();
4416 final PhylogenyNode n2 = new PhylogenyNode( "" );
4417 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4418 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4419 final PhylogenyNode n5 = new PhylogenyNode( "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]" );
4420 final PhylogenyNode n6 = new PhylogenyNode( "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]" );
4421 if ( !n1.toNewHampshireX().equals( "" ) ) {
4424 if ( !n2.toNewHampshireX().equals( "" ) ) {
4427 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4430 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4433 if ( !n5.toNewHampshireX()
4434 .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]" ) ) {
4437 if ( !n6.toNewHampshireX()
4438 .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]" ) ) {
4442 catch ( final Exception e ) {
4443 e.printStackTrace( System.out );
4449 private static boolean testNHXNodeParsing() {
4451 final PhylogenyNode n1 = new PhylogenyNode();
4452 final PhylogenyNode n2 = new PhylogenyNode( "" );
4453 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4454 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4455 final PhylogenyNode n5 = new PhylogenyNode( "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]" );
4456 if ( !n3.getName().equals( "n3" ) ) {
4459 if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4462 if ( n3.isDuplication() ) {
4465 if ( n3.isHasAssignedEvent() ) {
4468 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4471 if ( !n4.getName().equals( "n4" ) ) {
4474 if ( n4.getDistanceToParent() != 0.01 ) {
4477 if ( !n5.getName().equals( "n5" ) ) {
4480 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4483 if ( n5.getDistanceToParent() != 0.1 ) {
4486 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4489 if ( !n5.isDuplication() ) {
4492 if ( !n5.isHasAssignedEvent() ) {
4495 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4498 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4501 final PhylogenyNode n8 = new PhylogenyNode( "n8_ECOLI/12:0.01",
4502 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4503 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4506 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4509 final PhylogenyNode n9 = new PhylogenyNode( "n9_ECOLI/12=12:0.01",
4510 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4511 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4514 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4517 final PhylogenyNode n10 = new PhylogenyNode( "n10.ECOLI", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4518 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4521 final PhylogenyNode n20 = new PhylogenyNode( "n20_ECOLI/1-2",
4522 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4523 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4526 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4529 final PhylogenyNode n20x = new PhylogenyNode( "n20_ECOL1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4530 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4533 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4536 final PhylogenyNode n20xx = new PhylogenyNode( "n20_eCOL1/1-2",
4537 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4538 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4541 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4544 final PhylogenyNode n20xxx = new PhylogenyNode( "n20_ecoli/1-2",
4545 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4546 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4549 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4552 final PhylogenyNode n20xxxx = new PhylogenyNode( "n20_Ecoli/1-2",
4553 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4554 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4557 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4560 final PhylogenyNode n21 = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4561 if ( !n21.getName().equals( "n21_PIG" ) ) {
4564 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4567 final PhylogenyNode n21x = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4568 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4571 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4574 final PhylogenyNode n22 = new PhylogenyNode( "n22/PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4575 if ( !n22.getName().equals( "n22/PIG" ) ) {
4578 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4581 final PhylogenyNode n23 = new PhylogenyNode( "n23/PIG_1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4582 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4585 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4588 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4589 final PhylogenyNode a = new PhylogenyNode( "n10_ECOLI/1-2",
4590 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4591 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4594 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4597 final PhylogenyNode b = new PhylogenyNode( "n10_ECOLI1/1-2",
4598 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4599 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4602 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4605 final PhylogenyNode c = new PhylogenyNode( "n10_RATAF12/1000-2000",
4606 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4607 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4610 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4613 final PhylogenyNode d = new PhylogenyNode( "n10_RAT1/1-2",
4614 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4615 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4618 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4621 final PhylogenyNode e = new PhylogenyNode( "n10_RAT1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4622 if ( !e.getName().equals( "n10_RAT1" ) ) {
4625 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4629 final PhylogenyNode n11 = new PhylogenyNode( "n111111_ECOLI/jdj:0.4",
4630 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4631 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4634 if ( n11.getDistanceToParent() != 0.4 ) {
4637 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4640 final PhylogenyNode n12 = new PhylogenyNode( "n111111-ECOLI---/jdj:0.4",
4641 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4642 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4645 if ( n12.getDistanceToParent() != 0.4 ) {
4648 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4651 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4652 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4653 if ( !tvu1.getRef().equals( "tag1" ) ) {
4656 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4659 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4662 if ( !tvu1.getValue().equals( "value1" ) ) {
4665 if ( !tvu3.getRef().equals( "tag3" ) ) {
4668 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4671 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4674 if ( !tvu3.getValue().equals( "value3" ) ) {
4677 if ( n1.getName().compareTo( "" ) != 0 ) {
4680 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4683 if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4686 if ( n2.getName().compareTo( "" ) != 0 ) {
4689 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4692 if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4695 final PhylogenyNode n00 = new PhylogenyNode( "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]" );
4696 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4699 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4702 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4705 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4708 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4711 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4714 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4717 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4720 final PhylogenyNode nx = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4721 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4724 final PhylogenyNode nx2 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4725 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4728 final PhylogenyNode n13 = new PhylogenyNode( "blah_12345/1-2",
4729 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4730 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4733 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4736 final PhylogenyNode n14 = new PhylogenyNode( "blah_12X45/1-2",
4737 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4738 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4741 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4744 final PhylogenyNode n15 = new PhylogenyNode( "something_wicked[123]",
4745 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4746 if ( !n15.getName().equals( "something_wicked" ) ) {
4749 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4752 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4755 final PhylogenyNode n16 = new PhylogenyNode( "something_wicked2[9]",
4756 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4757 if ( !n16.getName().equals( "something_wicked2" ) ) {
4760 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4763 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4766 final PhylogenyNode n17 = new PhylogenyNode( "something_wicked3[a]",
4767 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4768 if ( !n17.getName().equals( "something_wicked3" ) ) {
4771 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4774 final PhylogenyNode n18 = new PhylogenyNode( ":0.5[91]", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4775 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4778 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4781 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4785 catch ( final Exception e ) {
4786 e.printStackTrace( System.out );
4792 private static boolean testNHXParsing() {
4794 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4795 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4796 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4799 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]";
4800 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4801 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4804 final String p2b_S = "(((((((A:0.2[&NHX:S=qwerty]):0.2[&:S=uiop]):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]";
4805 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4806 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4809 final Phylogeny[] p3 = factory
4810 .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]",
4812 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4815 final Phylogeny[] p4 = factory
4816 .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(]",
4818 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4821 final Phylogeny[] p5 = factory
4822 .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(((]",
4824 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4827 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)";
4828 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)";
4829 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4830 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4833 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)))";
4834 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)))";
4835 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4836 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4839 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]) ))[,,, ])))))))";
4840 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4841 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4842 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4845 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4846 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]" ) ) {
4849 final Phylogeny p10 = factory
4850 .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]",
4851 new NHXParser() )[ 0 ];
4852 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]" ) ) {
4856 catch ( final Exception e ) {
4857 e.printStackTrace( System.out );
4863 private static boolean testNHXParsingQuotes() {
4865 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4866 final NHXParser p = new NHXParser();
4867 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4868 if ( phylogenies_0.length != 5 ) {
4871 final Phylogeny phy = phylogenies_0[ 4 ];
4872 if ( phy.getNumberOfExternalNodes() != 7 ) {
4875 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4878 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4881 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4882 .getScientificName().equals( "hsapiens" ) ) {
4885 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4888 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4891 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4894 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4897 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4900 final NHXParser p1p = new NHXParser();
4901 p1p.setIgnoreQuotes( true );
4902 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4903 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4906 final NHXParser p2p = new NHXParser();
4907 p1p.setIgnoreQuotes( false );
4908 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4909 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4912 final NHXParser p3p = new NHXParser();
4913 p3p.setIgnoreQuotes( false );
4914 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4915 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4918 final NHXParser p4p = new NHXParser();
4919 p4p.setIgnoreQuotes( false );
4920 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4921 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
4924 final Phylogeny p10 = factory
4925 .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]",
4926 new NHXParser() )[ 0 ];
4927 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]";
4928 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
4931 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
4932 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
4936 final Phylogeny p12 = factory
4937 .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]",
4938 new NHXParser() )[ 0 ];
4939 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]";
4940 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
4943 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
4944 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
4947 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;";
4948 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
4951 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
4952 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
4956 catch ( final Exception e ) {
4957 e.printStackTrace( System.out );
4963 private static boolean testPhylogenyBranch() {
4965 final PhylogenyNode a1 = new PhylogenyNode( "a" );
4966 final PhylogenyNode b1 = new PhylogenyNode( "b" );
4967 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
4968 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
4969 if ( !a1b1.equals( a1b1 ) ) {
4972 if ( !a1b1.equals( b1a1 ) ) {
4975 if ( !b1a1.equals( a1b1 ) ) {
4978 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
4979 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
4980 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
4981 if ( a1_b1.equals( b1_a1 ) ) {
4984 if ( a1_b1.equals( a1_b1_ ) ) {
4987 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
4988 if ( !a1_b1.equals( b1_a1_ ) ) {
4991 if ( a1_b1_.equals( b1_a1_ ) ) {
4994 if ( !a1_b1_.equals( b1_a1 ) ) {
4998 catch ( final Exception e ) {
4999 e.printStackTrace( System.out );
5005 private static boolean testPhyloXMLparsingOfDistributionElement() {
5007 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5008 PhyloXmlParser xml_parser = null;
5010 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5012 catch ( final Exception e ) {
5013 // Do nothing -- means were not running from jar.
5015 if ( xml_parser == null ) {
5016 xml_parser = new PhyloXmlParser();
5017 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5018 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5021 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5024 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5026 if ( xml_parser.getErrorCount() > 0 ) {
5027 System.out.println( xml_parser.getErrorMessages().toString() );
5030 if ( phylogenies_0.length != 1 ) {
5033 final Phylogeny t1 = phylogenies_0[ 0 ];
5034 PhylogenyNode n = null;
5035 Distribution d = null;
5036 n = t1.getNode( "root node" );
5037 if ( !n.getNodeData().isHasDistribution() ) {
5040 if ( n.getNodeData().getDistributions().size() != 1 ) {
5043 d = n.getNodeData().getDistribution();
5044 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5047 if ( d.getPoints().size() != 1 ) {
5050 if ( d.getPolygons() != null ) {
5053 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5056 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5059 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5062 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5065 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5068 n = t1.getNode( "node a" );
5069 if ( !n.getNodeData().isHasDistribution() ) {
5072 if ( n.getNodeData().getDistributions().size() != 2 ) {
5075 d = n.getNodeData().getDistribution( 1 );
5076 if ( !d.getDesc().equals( "San Diego" ) ) {
5079 if ( d.getPoints().size() != 1 ) {
5082 if ( d.getPolygons() != null ) {
5085 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5088 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5091 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5094 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5097 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5100 n = t1.getNode( "node bb" );
5101 if ( !n.getNodeData().isHasDistribution() ) {
5104 if ( n.getNodeData().getDistributions().size() != 1 ) {
5107 d = n.getNodeData().getDistribution( 0 );
5108 if ( d.getPoints().size() != 3 ) {
5111 if ( d.getPolygons().size() != 2 ) {
5114 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5117 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5120 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5123 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5126 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5129 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5132 Polygon p = d.getPolygons().get( 0 );
5133 if ( p.getPoints().size() != 3 ) {
5136 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5139 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5142 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5145 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5148 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5151 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5154 p = d.getPolygons().get( 1 );
5155 if ( p.getPoints().size() != 3 ) {
5158 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5161 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5164 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5168 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5169 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5170 if ( rt.length != 1 ) {
5173 final Phylogeny t1_rt = rt[ 0 ];
5174 n = t1_rt.getNode( "root node" );
5175 if ( !n.getNodeData().isHasDistribution() ) {
5178 if ( n.getNodeData().getDistributions().size() != 1 ) {
5181 d = n.getNodeData().getDistribution();
5182 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5185 if ( d.getPoints().size() != 1 ) {
5188 if ( d.getPolygons() != null ) {
5191 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5194 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5197 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5200 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5203 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5206 n = t1_rt.getNode( "node a" );
5207 if ( !n.getNodeData().isHasDistribution() ) {
5210 if ( n.getNodeData().getDistributions().size() != 2 ) {
5213 d = n.getNodeData().getDistribution( 1 );
5214 if ( !d.getDesc().equals( "San Diego" ) ) {
5217 if ( d.getPoints().size() != 1 ) {
5220 if ( d.getPolygons() != null ) {
5223 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5226 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5229 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5232 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5235 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5238 n = t1_rt.getNode( "node bb" );
5239 if ( !n.getNodeData().isHasDistribution() ) {
5242 if ( n.getNodeData().getDistributions().size() != 1 ) {
5245 d = n.getNodeData().getDistribution( 0 );
5246 if ( d.getPoints().size() != 3 ) {
5249 if ( d.getPolygons().size() != 2 ) {
5252 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5255 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5258 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5261 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5264 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5267 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5270 p = d.getPolygons().get( 0 );
5271 if ( p.getPoints().size() != 3 ) {
5274 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5277 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5280 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5283 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5286 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5289 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5292 p = d.getPolygons().get( 1 );
5293 if ( p.getPoints().size() != 3 ) {
5296 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5299 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5302 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5306 catch ( final Exception e ) {
5307 e.printStackTrace( System.out );
5313 private static boolean testPostOrderIterator() {
5315 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5316 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5317 PhylogenyNodeIterator it0;
5318 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5321 for( it0.reset(); it0.hasNext(); ) {
5324 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5325 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5326 if ( !it.next().getName().equals( "A" ) ) {
5329 if ( !it.next().getName().equals( "B" ) ) {
5332 if ( !it.next().getName().equals( "ab" ) ) {
5335 if ( !it.next().getName().equals( "C" ) ) {
5338 if ( !it.next().getName().equals( "D" ) ) {
5341 if ( !it.next().getName().equals( "cd" ) ) {
5344 if ( !it.next().getName().equals( "abcd" ) ) {
5347 if ( !it.next().getName().equals( "E" ) ) {
5350 if ( !it.next().getName().equals( "F" ) ) {
5353 if ( !it.next().getName().equals( "ef" ) ) {
5356 if ( !it.next().getName().equals( "G" ) ) {
5359 if ( !it.next().getName().equals( "H" ) ) {
5362 if ( !it.next().getName().equals( "gh" ) ) {
5365 if ( !it.next().getName().equals( "efgh" ) ) {
5368 if ( !it.next().getName().equals( "r" ) ) {
5371 if ( it.hasNext() ) {
5375 catch ( final Exception e ) {
5376 e.printStackTrace( System.out );
5382 private static boolean testPreOrderIterator() {
5384 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5385 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5386 PhylogenyNodeIterator it0;
5387 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5390 for( it0.reset(); it0.hasNext(); ) {
5393 PhylogenyNodeIterator it = t0.iteratorPreorder();
5394 if ( !it.next().getName().equals( "r" ) ) {
5397 if ( !it.next().getName().equals( "ab" ) ) {
5400 if ( !it.next().getName().equals( "A" ) ) {
5403 if ( !it.next().getName().equals( "B" ) ) {
5406 if ( !it.next().getName().equals( "cd" ) ) {
5409 if ( !it.next().getName().equals( "C" ) ) {
5412 if ( !it.next().getName().equals( "D" ) ) {
5415 if ( it.hasNext() ) {
5418 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5419 it = t1.iteratorPreorder();
5420 if ( !it.next().getName().equals( "r" ) ) {
5423 if ( !it.next().getName().equals( "abcd" ) ) {
5426 if ( !it.next().getName().equals( "ab" ) ) {
5429 if ( !it.next().getName().equals( "A" ) ) {
5432 if ( !it.next().getName().equals( "B" ) ) {
5435 if ( !it.next().getName().equals( "cd" ) ) {
5438 if ( !it.next().getName().equals( "C" ) ) {
5441 if ( !it.next().getName().equals( "D" ) ) {
5444 if ( !it.next().getName().equals( "efgh" ) ) {
5447 if ( !it.next().getName().equals( "ef" ) ) {
5450 if ( !it.next().getName().equals( "E" ) ) {
5453 if ( !it.next().getName().equals( "F" ) ) {
5456 if ( !it.next().getName().equals( "gh" ) ) {
5459 if ( !it.next().getName().equals( "G" ) ) {
5462 if ( !it.next().getName().equals( "H" ) ) {
5465 if ( it.hasNext() ) {
5469 catch ( final Exception e ) {
5470 e.printStackTrace( System.out );
5476 private static boolean testPropertiesMap() {
5478 final PropertiesMap pm = new PropertiesMap();
5479 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5480 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5481 final Property p2 = new Property( "something:else",
5483 "improbable:research",
5486 pm.addProperty( p0 );
5487 pm.addProperty( p1 );
5488 pm.addProperty( p2 );
5489 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5492 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5495 if ( pm.getProperties().size() != 3 ) {
5498 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5501 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5504 if ( pm.getProperties().size() != 3 ) {
5507 pm.removeProperty( "dimensions:diameter" );
5508 if ( pm.getProperties().size() != 2 ) {
5511 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5514 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5518 catch ( final Exception e ) {
5519 e.printStackTrace( System.out );
5525 private static boolean testReIdMethods() {
5527 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5528 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5529 final int count = PhylogenyNode.getNodeCount();
5531 if ( p.getNode( "r" ).getId() != count ) {
5534 if ( p.getNode( "A" ).getId() != count + 1 ) {
5537 if ( p.getNode( "B" ).getId() != count + 1 ) {
5540 if ( p.getNode( "C" ).getId() != count + 1 ) {
5543 if ( p.getNode( "1" ).getId() != count + 2 ) {
5546 if ( p.getNode( "2" ).getId() != count + 2 ) {
5549 if ( p.getNode( "3" ).getId() != count + 2 ) {
5552 if ( p.getNode( "4" ).getId() != count + 2 ) {
5555 if ( p.getNode( "5" ).getId() != count + 2 ) {
5558 if ( p.getNode( "6" ).getId() != count + 2 ) {
5561 if ( p.getNode( "a" ).getId() != count + 3 ) {
5564 if ( p.getNode( "b" ).getId() != count + 3 ) {
5567 if ( p.getNode( "X" ).getId() != count + 4 ) {
5570 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5573 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5577 catch ( final Exception e ) {
5578 e.printStackTrace( System.out );
5584 private static boolean testRerooting() {
5586 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5587 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",
5588 new NHXParser() )[ 0 ];
5589 if ( !t1.isRooted() ) {
5592 t1.reRoot( t1.getNode( "D" ) );
5593 t1.reRoot( t1.getNode( "CD" ) );
5594 t1.reRoot( t1.getNode( "A" ) );
5595 t1.reRoot( t1.getNode( "B" ) );
5596 t1.reRoot( t1.getNode( "AB" ) );
5597 t1.reRoot( t1.getNode( "D" ) );
5598 t1.reRoot( t1.getNode( "C" ) );
5599 t1.reRoot( t1.getNode( "CD" ) );
5600 t1.reRoot( t1.getNode( "A" ) );
5601 t1.reRoot( t1.getNode( "B" ) );
5602 t1.reRoot( t1.getNode( "AB" ) );
5603 t1.reRoot( t1.getNode( "D" ) );
5604 t1.reRoot( t1.getNode( "D" ) );
5605 t1.reRoot( t1.getNode( "C" ) );
5606 t1.reRoot( t1.getNode( "A" ) );
5607 t1.reRoot( t1.getNode( "B" ) );
5608 t1.reRoot( t1.getNode( "AB" ) );
5609 t1.reRoot( t1.getNode( "C" ) );
5610 t1.reRoot( t1.getNode( "D" ) );
5611 t1.reRoot( t1.getNode( "CD" ) );
5612 t1.reRoot( t1.getNode( "D" ) );
5613 t1.reRoot( t1.getNode( "A" ) );
5614 t1.reRoot( t1.getNode( "B" ) );
5615 t1.reRoot( t1.getNode( "AB" ) );
5616 t1.reRoot( t1.getNode( "C" ) );
5617 t1.reRoot( t1.getNode( "D" ) );
5618 t1.reRoot( t1.getNode( "CD" ) );
5619 t1.reRoot( t1.getNode( "D" ) );
5620 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5623 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5626 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5629 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5632 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5635 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5638 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",
5639 new NHXParser() )[ 0 ];
5640 t2.reRoot( t2.getNode( "A" ) );
5641 t2.reRoot( t2.getNode( "D" ) );
5642 t2.reRoot( t2.getNode( "ABC" ) );
5643 t2.reRoot( t2.getNode( "A" ) );
5644 t2.reRoot( t2.getNode( "B" ) );
5645 t2.reRoot( t2.getNode( "D" ) );
5646 t2.reRoot( t2.getNode( "C" ) );
5647 t2.reRoot( t2.getNode( "ABC" ) );
5648 t2.reRoot( t2.getNode( "A" ) );
5649 t2.reRoot( t2.getNode( "B" ) );
5650 t2.reRoot( t2.getNode( "AB" ) );
5651 t2.reRoot( t2.getNode( "AB" ) );
5652 t2.reRoot( t2.getNode( "D" ) );
5653 t2.reRoot( t2.getNode( "C" ) );
5654 t2.reRoot( t2.getNode( "B" ) );
5655 t2.reRoot( t2.getNode( "AB" ) );
5656 t2.reRoot( t2.getNode( "D" ) );
5657 t2.reRoot( t2.getNode( "D" ) );
5658 t2.reRoot( t2.getNode( "ABC" ) );
5659 t2.reRoot( t2.getNode( "A" ) );
5660 t2.reRoot( t2.getNode( "B" ) );
5661 t2.reRoot( t2.getNode( "AB" ) );
5662 t2.reRoot( t2.getNode( "D" ) );
5663 t2.reRoot( t2.getNode( "C" ) );
5664 t2.reRoot( t2.getNode( "ABC" ) );
5665 t2.reRoot( t2.getNode( "A" ) );
5666 t2.reRoot( t2.getNode( "B" ) );
5667 t2.reRoot( t2.getNode( "AB" ) );
5668 t2.reRoot( t2.getNode( "D" ) );
5669 t2.reRoot( t2.getNode( "D" ) );
5670 t2.reRoot( t2.getNode( "C" ) );
5671 t2.reRoot( t2.getNode( "A" ) );
5672 t2.reRoot( t2.getNode( "B" ) );
5673 t2.reRoot( t2.getNode( "AB" ) );
5674 t2.reRoot( t2.getNode( "C" ) );
5675 t2.reRoot( t2.getNode( "D" ) );
5676 t2.reRoot( t2.getNode( "ABC" ) );
5677 t2.reRoot( t2.getNode( "D" ) );
5678 t2.reRoot( t2.getNode( "A" ) );
5679 t2.reRoot( t2.getNode( "B" ) );
5680 t2.reRoot( t2.getNode( "AB" ) );
5681 t2.reRoot( t2.getNode( "C" ) );
5682 t2.reRoot( t2.getNode( "D" ) );
5683 t2.reRoot( t2.getNode( "ABC" ) );
5684 t2.reRoot( t2.getNode( "D" ) );
5685 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5688 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5691 t2.reRoot( t2.getNode( "ABC" ) );
5692 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5695 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5698 t2.reRoot( t2.getNode( "AB" ) );
5699 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5702 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5705 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5708 t2.reRoot( t2.getNode( "AB" ) );
5709 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5712 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5715 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5718 t2.reRoot( t2.getNode( "D" ) );
5719 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5722 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5725 t2.reRoot( t2.getNode( "ABC" ) );
5726 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5729 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5732 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5733 new NHXParser() )[ 0 ];
5734 t3.reRoot( t3.getNode( "B" ) );
5735 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5738 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5741 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5744 t3.reRoot( t3.getNode( "B" ) );
5745 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5748 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5751 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5754 t3.reRoot( t3.getRoot() );
5755 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5758 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5761 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5765 catch ( final Exception e ) {
5766 e.printStackTrace( System.out );
5772 private static boolean testSDIse() {
5774 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5775 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5776 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5777 gene1.setRooted( true );
5778 species1.setRooted( true );
5779 final SDI sdi = new SDIse( gene1, species1 );
5780 if ( !gene1.getRoot().isDuplication() ) {
5783 final Phylogeny species2 = factory
5784 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5785 new NHXParser() )[ 0 ];
5786 final Phylogeny gene2 = factory
5787 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5788 new NHXParser() )[ 0 ];
5789 species2.setRooted( true );
5790 gene2.setRooted( true );
5791 final SDI sdi2 = new SDIse( gene2, species2 );
5792 if ( sdi2.getDuplicationsSum() != 0 ) {
5795 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5798 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5801 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5804 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5807 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5810 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5813 final Phylogeny species3 = factory
5814 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5815 new NHXParser() )[ 0 ];
5816 final Phylogeny gene3 = factory
5817 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5818 new NHXParser() )[ 0 ];
5819 species3.setRooted( true );
5820 gene3.setRooted( true );
5821 final SDI sdi3 = new SDIse( gene3, species3 );
5822 if ( sdi3.getDuplicationsSum() != 1 ) {
5825 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5828 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5831 final Phylogeny species4 = factory
5832 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5833 new NHXParser() )[ 0 ];
5834 final Phylogeny gene4 = factory
5835 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5836 new NHXParser() )[ 0 ];
5837 species4.setRooted( true );
5838 gene4.setRooted( true );
5839 final SDI sdi4 = new SDIse( gene4, species4 );
5840 if ( sdi4.getDuplicationsSum() != 1 ) {
5843 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5846 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5849 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5852 if ( species4.getNumberOfExternalNodes() != 6 ) {
5855 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5858 final Phylogeny species5 = factory
5859 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5860 new NHXParser() )[ 0 ];
5861 final Phylogeny gene5 = factory
5862 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5863 new NHXParser() )[ 0 ];
5864 species5.setRooted( true );
5865 gene5.setRooted( true );
5866 final SDI sdi5 = new SDIse( gene5, species5 );
5867 if ( sdi5.getDuplicationsSum() != 2 ) {
5870 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
5873 if ( !gene5.getNode( "adc" ).isDuplication() ) {
5876 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
5879 if ( species5.getNumberOfExternalNodes() != 6 ) {
5882 if ( gene5.getNumberOfExternalNodes() != 6 ) {
5885 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
5886 // Conjecture for Comparing Molecular Phylogenies"
5887 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
5888 final Phylogeny species6 = factory
5889 .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,"
5890 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
5891 new NHXParser() )[ 0 ];
5892 final Phylogeny gene6 = factory
5893 .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,"
5894 + "((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,"
5895 + "(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;",
5896 new NHXParser() )[ 0 ];
5897 species6.setRooted( true );
5898 gene6.setRooted( true );
5899 final SDI sdi6 = new SDIse( gene6, species6 );
5900 if ( sdi6.getDuplicationsSum() != 3 ) {
5903 if ( !gene6.getNode( "r" ).isDuplication() ) {
5906 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
5909 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
5912 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
5915 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
5918 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
5921 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
5924 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
5927 sdi6.computeMappingCostL();
5928 if ( sdi6.computeMappingCostL() != 17 ) {
5931 if ( species6.getNumberOfExternalNodes() != 9 ) {
5934 if ( gene6.getNumberOfExternalNodes() != 9 ) {
5937 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
5938 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
5939 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
5940 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
5941 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
5942 species7.setRooted( true );
5943 final Phylogeny gene7_1 = Test
5944 .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])" );
5945 gene7_1.setRooted( true );
5946 final SDI sdi7 = new SDIse( gene7_1, species7 );
5947 if ( sdi7.getDuplicationsSum() != 0 ) {
5950 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
5953 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
5956 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
5959 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
5962 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
5965 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
5968 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
5971 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
5974 final Phylogeny gene7_2 = Test
5975 .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])" );
5976 gene7_2.setRooted( true );
5977 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
5978 if ( sdi7_2.getDuplicationsSum() != 1 ) {
5981 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
5984 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
5987 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
5990 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
5993 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
5996 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
5999 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6002 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6005 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6009 catch ( final Exception e ) {
6015 private static boolean testSDIunrooted() {
6017 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6018 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6019 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6020 final Iterator<PhylogenyBranch> iter = l.iterator();
6021 PhylogenyBranch br = iter.next();
6022 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6025 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6029 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6032 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6036 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6039 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6043 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6046 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6050 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6053 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6057 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6060 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6064 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6067 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6071 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6074 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6078 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6081 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6085 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6088 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6092 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6095 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6099 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6102 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6106 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6109 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6113 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6116 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6120 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6123 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6126 if ( iter.hasNext() ) {
6129 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6130 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6131 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6133 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6136 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6140 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6143 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6147 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6150 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6153 if ( iter1.hasNext() ) {
6156 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6157 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6158 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6160 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6163 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6167 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6170 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6174 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6177 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6180 if ( iter2.hasNext() ) {
6183 final Phylogeny species0 = factory
6184 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6185 new NHXParser() )[ 0 ];
6186 final Phylogeny gene1 = factory
6187 .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])",
6188 new NHXParser() )[ 0 ];
6189 species0.setRooted( true );
6190 gene1.setRooted( true );
6191 final SDIR sdi_unrooted = new SDIR();
6192 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6193 if ( sdi_unrooted.getCount() != 1 ) {
6196 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6199 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6202 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6205 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6208 final Phylogeny gene2 = factory
6209 .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])",
6210 new NHXParser() )[ 0 ];
6211 gene2.setRooted( true );
6212 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6213 if ( sdi_unrooted.getCount() != 1 ) {
6216 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6219 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6222 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6225 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6228 final Phylogeny species6 = factory
6229 .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,"
6230 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6231 new NHXParser() )[ 0 ];
6232 final Phylogeny gene6 = factory
6233 .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],"
6234 + "(((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],"
6235 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6236 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6237 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6238 new NHXParser() )[ 0 ];
6239 species6.setRooted( true );
6240 gene6.setRooted( true );
6241 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6242 if ( sdi_unrooted.getCount() != 1 ) {
6245 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6248 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6251 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6254 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6257 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6260 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6263 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6266 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6269 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6272 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6275 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6278 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6282 final Phylogeny species7 = factory
6283 .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,"
6284 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6285 new NHXParser() )[ 0 ];
6286 final Phylogeny gene7 = factory
6287 .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],"
6288 + "(((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],"
6289 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6290 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6291 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6292 new NHXParser() )[ 0 ];
6293 species7.setRooted( true );
6294 gene7.setRooted( true );
6295 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6296 if ( sdi_unrooted.getCount() != 1 ) {
6299 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6302 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6305 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6308 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6311 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6314 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6317 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6320 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6323 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6326 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6329 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6332 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6336 final Phylogeny species8 = factory
6337 .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,"
6338 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6339 new NHXParser() )[ 0 ];
6340 final Phylogeny gene8 = factory
6341 .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],"
6342 + "(((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],"
6343 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6344 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6345 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6346 new NHXParser() )[ 0 ];
6347 species8.setRooted( true );
6348 gene8.setRooted( true );
6349 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6350 if ( sdi_unrooted.getCount() != 1 ) {
6353 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6356 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6359 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6362 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6365 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6368 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6371 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6374 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6377 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6380 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6383 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6386 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6391 catch ( final Exception e ) {
6392 e.printStackTrace( System.out );
6398 private static boolean testSplit() {
6400 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6401 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6402 //Archaeopteryx.createApplication( p0 );
6403 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6404 ex.add( new PhylogenyNode( "A" ) );
6405 ex.add( new PhylogenyNode( "B" ) );
6406 ex.add( new PhylogenyNode( "C" ) );
6407 ex.add( new PhylogenyNode( "D" ) );
6408 ex.add( new PhylogenyNode( "E" ) );
6409 ex.add( new PhylogenyNode( "F" ) );
6410 ex.add( new PhylogenyNode( "G" ) );
6411 ex.add( new PhylogenyNode( "X" ) );
6412 ex.add( new PhylogenyNode( "Y" ) );
6413 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6414 // System.out.println( s0.toString() );
6416 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6417 query_nodes.add( new PhylogenyNode( "A" ) );
6418 query_nodes.add( new PhylogenyNode( "B" ) );
6419 if ( s0.match( query_nodes ) ) {
6422 query_nodes = new HashSet<PhylogenyNode>();
6423 query_nodes.add( new PhylogenyNode( "A" ) );
6424 query_nodes.add( new PhylogenyNode( "B" ) );
6425 query_nodes.add( new PhylogenyNode( "C" ) );
6426 query_nodes.add( new PhylogenyNode( "D" ) );
6427 query_nodes.add( new PhylogenyNode( "E" ) );
6428 query_nodes.add( new PhylogenyNode( "F" ) );
6429 query_nodes.add( new PhylogenyNode( "G" ) );
6430 if ( !s0.match( query_nodes ) ) {
6434 query_nodes = new HashSet<PhylogenyNode>();
6435 query_nodes.add( new PhylogenyNode( "A" ) );
6436 query_nodes.add( new PhylogenyNode( "B" ) );
6437 query_nodes.add( new PhylogenyNode( "C" ) );
6438 if ( !s0.match( query_nodes ) ) {
6442 query_nodes = new HashSet<PhylogenyNode>();
6443 query_nodes.add( new PhylogenyNode( "D" ) );
6444 query_nodes.add( new PhylogenyNode( "E" ) );
6445 query_nodes.add( new PhylogenyNode( "F" ) );
6446 query_nodes.add( new PhylogenyNode( "G" ) );
6447 if ( !s0.match( query_nodes ) ) {
6451 query_nodes = new HashSet<PhylogenyNode>();
6452 query_nodes.add( new PhylogenyNode( "A" ) );
6453 query_nodes.add( new PhylogenyNode( "B" ) );
6454 query_nodes.add( new PhylogenyNode( "C" ) );
6455 query_nodes.add( new PhylogenyNode( "D" ) );
6456 if ( !s0.match( query_nodes ) ) {
6460 query_nodes = new HashSet<PhylogenyNode>();
6461 query_nodes.add( new PhylogenyNode( "E" ) );
6462 query_nodes.add( new PhylogenyNode( "F" ) );
6463 query_nodes.add( new PhylogenyNode( "G" ) );
6464 if ( !s0.match( query_nodes ) ) {
6468 query_nodes = new HashSet<PhylogenyNode>();
6469 query_nodes.add( new PhylogenyNode( "F" ) );
6470 query_nodes.add( new PhylogenyNode( "G" ) );
6471 if ( !s0.match( query_nodes ) ) {
6475 query_nodes = new HashSet<PhylogenyNode>();
6476 query_nodes.add( new PhylogenyNode( "E" ) );
6477 query_nodes.add( new PhylogenyNode( "D" ) );
6478 query_nodes.add( new PhylogenyNode( "C" ) );
6479 query_nodes.add( new PhylogenyNode( "B" ) );
6480 query_nodes.add( new PhylogenyNode( "A" ) );
6481 if ( !s0.match( query_nodes ) ) {
6485 query_nodes = new HashSet<PhylogenyNode>();
6486 query_nodes.add( new PhylogenyNode( "F" ) );
6487 query_nodes.add( new PhylogenyNode( "G" ) );
6488 query_nodes.add( new PhylogenyNode( "E" ) );
6489 if ( !s0.match( query_nodes ) ) {
6493 query_nodes = new HashSet<PhylogenyNode>();
6494 query_nodes.add( new PhylogenyNode( "F" ) );
6495 query_nodes.add( new PhylogenyNode( "G" ) );
6496 query_nodes.add( new PhylogenyNode( "E" ) );
6497 query_nodes.add( new PhylogenyNode( "D" ) );
6498 if ( !s0.match( query_nodes ) ) {
6502 query_nodes = new HashSet<PhylogenyNode>();
6503 query_nodes.add( new PhylogenyNode( "F" ) );
6504 query_nodes.add( new PhylogenyNode( "A" ) );
6505 if ( s0.match( query_nodes ) ) {
6509 query_nodes = new HashSet<PhylogenyNode>();
6510 query_nodes.add( new PhylogenyNode( "A" ) );
6511 query_nodes.add( new PhylogenyNode( "E" ) );
6512 query_nodes.add( new PhylogenyNode( "B" ) );
6513 query_nodes.add( new PhylogenyNode( "C" ) );
6514 if ( s0.match( query_nodes ) ) {
6518 query_nodes = new HashSet<PhylogenyNode>();
6519 query_nodes.add( new PhylogenyNode( "F" ) );
6520 query_nodes.add( new PhylogenyNode( "G" ) );
6521 query_nodes.add( new PhylogenyNode( "E" ) );
6522 query_nodes.add( new PhylogenyNode( "D" ) );
6523 query_nodes.add( new PhylogenyNode( "C" ) );
6524 if ( s0.match( query_nodes ) ) {
6528 query_nodes = new HashSet<PhylogenyNode>();
6529 query_nodes.add( new PhylogenyNode( "A" ) );
6530 query_nodes.add( new PhylogenyNode( "B" ) );
6531 query_nodes.add( new PhylogenyNode( "D" ) );
6532 if ( s0.match( query_nodes ) ) {
6536 query_nodes = new HashSet<PhylogenyNode>();
6537 query_nodes.add( new PhylogenyNode( "A" ) );
6538 query_nodes.add( new PhylogenyNode( "D" ) );
6539 if ( s0.match( query_nodes ) ) {
6543 query_nodes = new HashSet<PhylogenyNode>();
6544 query_nodes.add( new PhylogenyNode( "A" ) );
6545 query_nodes.add( new PhylogenyNode( "B" ) );
6546 if ( s0.match( query_nodes ) ) {
6550 query_nodes = new HashSet<PhylogenyNode>();
6551 query_nodes.add( new PhylogenyNode( "A" ) );
6552 query_nodes.add( new PhylogenyNode( "C" ) );
6553 if ( s0.match( query_nodes ) ) {
6557 query_nodes = new HashSet<PhylogenyNode>();
6558 query_nodes.add( new PhylogenyNode( "A" ) );
6559 query_nodes.add( new PhylogenyNode( "E" ) );
6560 if ( s0.match( query_nodes ) ) {
6564 query_nodes = new HashSet<PhylogenyNode>();
6565 query_nodes.add( new PhylogenyNode( "A" ) );
6566 query_nodes.add( new PhylogenyNode( "F" ) );
6567 if ( s0.match( query_nodes ) ) {
6571 query_nodes = new HashSet<PhylogenyNode>();
6572 query_nodes.add( new PhylogenyNode( "A" ) );
6573 query_nodes.add( new PhylogenyNode( "G" ) );
6574 if ( s0.match( query_nodes ) ) {
6578 query_nodes = new HashSet<PhylogenyNode>();
6579 query_nodes.add( new PhylogenyNode( "A" ) );
6580 query_nodes.add( new PhylogenyNode( "F" ) );
6581 query_nodes.add( new PhylogenyNode( "G" ) );
6582 if ( s0.match( query_nodes ) ) {
6586 query_nodes = new HashSet<PhylogenyNode>();
6587 query_nodes.add( new PhylogenyNode( "A" ) );
6588 query_nodes.add( new PhylogenyNode( "B" ) );
6589 query_nodes.add( new PhylogenyNode( "D" ) );
6590 if ( s0.match( query_nodes ) ) {
6594 query_nodes = new HashSet<PhylogenyNode>();
6595 query_nodes.add( new PhylogenyNode( "E" ) );
6596 query_nodes.add( new PhylogenyNode( "D" ) );
6597 query_nodes.add( new PhylogenyNode( "A" ) );
6598 if ( s0.match( query_nodes ) ) {
6602 query_nodes = new HashSet<PhylogenyNode>();
6603 query_nodes.add( new PhylogenyNode( "E" ) );
6604 query_nodes.add( new PhylogenyNode( "D" ) );
6605 query_nodes.add( new PhylogenyNode( "A" ) );
6606 query_nodes.add( new PhylogenyNode( "G" ) );
6607 if ( s0.match( query_nodes ) ) {
6611 // query_nodes = new HashSet<PhylogenyNode>();
6612 // query_nodes.add( new PhylogenyNode( "X" ) );
6613 // query_nodes.add( new PhylogenyNode( "Y" ) );
6614 // query_nodes.add( new PhylogenyNode( "A" ) );
6615 // query_nodes.add( new PhylogenyNode( "B" ) );
6616 // query_nodes.add( new PhylogenyNode( "C" ) );
6617 // query_nodes.add( new PhylogenyNode( "D" ) );
6618 // query_nodes.add( new PhylogenyNode( "E" ) );
6619 // query_nodes.add( new PhylogenyNode( "F" ) );
6620 // query_nodes.add( new PhylogenyNode( "G" ) );
6621 // if ( !s0.match( query_nodes ) ) {
6624 // query_nodes = new HashSet<PhylogenyNode>();
6625 // query_nodes.add( new PhylogenyNode( "X" ) );
6626 // query_nodes.add( new PhylogenyNode( "Y" ) );
6627 // query_nodes.add( new PhylogenyNode( "A" ) );
6628 // query_nodes.add( new PhylogenyNode( "B" ) );
6629 // query_nodes.add( new PhylogenyNode( "C" ) );
6630 // if ( !s0.match( query_nodes ) ) {
6634 // query_nodes = new HashSet<PhylogenyNode>();
6635 // query_nodes.add( new PhylogenyNode( "X" ) );
6636 // query_nodes.add( new PhylogenyNode( "Y" ) );
6637 // query_nodes.add( new PhylogenyNode( "D" ) );
6638 // query_nodes.add( new PhylogenyNode( "E" ) );
6639 // query_nodes.add( new PhylogenyNode( "F" ) );
6640 // query_nodes.add( new PhylogenyNode( "G" ) );
6641 // if ( !s0.match( query_nodes ) ) {
6645 // query_nodes = new HashSet<PhylogenyNode>();
6646 // query_nodes.add( new PhylogenyNode( "X" ) );
6647 // query_nodes.add( new PhylogenyNode( "Y" ) );
6648 // query_nodes.add( new PhylogenyNode( "A" ) );
6649 // query_nodes.add( new PhylogenyNode( "B" ) );
6650 // query_nodes.add( new PhylogenyNode( "C" ) );
6651 // query_nodes.add( new PhylogenyNode( "D" ) );
6652 // if ( !s0.match( query_nodes ) ) {
6656 // query_nodes = new HashSet<PhylogenyNode>();
6657 // query_nodes.add( new PhylogenyNode( "X" ) );
6658 // query_nodes.add( new PhylogenyNode( "Y" ) );
6659 // query_nodes.add( new PhylogenyNode( "E" ) );
6660 // query_nodes.add( new PhylogenyNode( "F" ) );
6661 // query_nodes.add( new PhylogenyNode( "G" ) );
6662 // if ( !s0.match( query_nodes ) ) {
6666 // query_nodes = new HashSet<PhylogenyNode>();
6667 // query_nodes.add( new PhylogenyNode( "X" ) );
6668 // query_nodes.add( new PhylogenyNode( "Y" ) );
6669 // query_nodes.add( new PhylogenyNode( "F" ) );
6670 // query_nodes.add( new PhylogenyNode( "G" ) );
6671 // if ( !s0.match( query_nodes ) ) {
6675 query_nodes = new HashSet<PhylogenyNode>();
6676 query_nodes.add( new PhylogenyNode( "X" ) );
6677 query_nodes.add( new PhylogenyNode( "Y" ) );
6678 query_nodes.add( new PhylogenyNode( "E" ) );
6679 query_nodes.add( new PhylogenyNode( "G" ) );
6680 if ( s0.match( query_nodes ) ) {
6684 query_nodes = new HashSet<PhylogenyNode>();
6685 query_nodes.add( new PhylogenyNode( "X" ) );
6686 query_nodes.add( new PhylogenyNode( "Y" ) );
6687 query_nodes.add( new PhylogenyNode( "A" ) );
6688 query_nodes.add( new PhylogenyNode( "B" ) );
6689 if ( s0.match( query_nodes ) ) {
6692 ///////////////////////////
6694 query_nodes = new HashSet<PhylogenyNode>();
6695 query_nodes.add( new PhylogenyNode( "X" ) );
6696 query_nodes.add( new PhylogenyNode( "Y" ) );
6697 query_nodes.add( new PhylogenyNode( "A" ) );
6698 query_nodes.add( new PhylogenyNode( "D" ) );
6699 if ( s0.match( query_nodes ) ) {
6703 query_nodes = new HashSet<PhylogenyNode>();
6704 query_nodes.add( new PhylogenyNode( "X" ) );
6705 query_nodes.add( new PhylogenyNode( "Y" ) );
6706 query_nodes.add( new PhylogenyNode( "A" ) );
6707 query_nodes.add( new PhylogenyNode( "B" ) );
6708 if ( s0.match( query_nodes ) ) {
6712 query_nodes = new HashSet<PhylogenyNode>();
6713 query_nodes.add( new PhylogenyNode( "X" ) );
6714 query_nodes.add( new PhylogenyNode( "Y" ) );
6715 query_nodes.add( new PhylogenyNode( "A" ) );
6716 query_nodes.add( new PhylogenyNode( "C" ) );
6717 if ( s0.match( query_nodes ) ) {
6721 query_nodes = new HashSet<PhylogenyNode>();
6722 query_nodes.add( new PhylogenyNode( "X" ) );
6723 query_nodes.add( new PhylogenyNode( "Y" ) );
6724 query_nodes.add( new PhylogenyNode( "A" ) );
6725 query_nodes.add( new PhylogenyNode( "E" ) );
6726 if ( s0.match( query_nodes ) ) {
6730 query_nodes = new HashSet<PhylogenyNode>();
6731 query_nodes.add( new PhylogenyNode( "X" ) );
6732 query_nodes.add( new PhylogenyNode( "Y" ) );
6733 query_nodes.add( new PhylogenyNode( "A" ) );
6734 query_nodes.add( new PhylogenyNode( "F" ) );
6735 if ( s0.match( query_nodes ) ) {
6739 query_nodes = new HashSet<PhylogenyNode>();
6740 query_nodes.add( new PhylogenyNode( "Y" ) );
6741 query_nodes.add( new PhylogenyNode( "A" ) );
6742 query_nodes.add( new PhylogenyNode( "G" ) );
6743 if ( s0.match( query_nodes ) ) {
6747 query_nodes = new HashSet<PhylogenyNode>();
6748 query_nodes.add( new PhylogenyNode( "X" ) );
6749 query_nodes.add( new PhylogenyNode( "Y" ) );
6750 query_nodes.add( new PhylogenyNode( "A" ) );
6751 query_nodes.add( new PhylogenyNode( "F" ) );
6752 query_nodes.add( new PhylogenyNode( "G" ) );
6753 if ( s0.match( query_nodes ) ) {
6757 query_nodes = new HashSet<PhylogenyNode>();
6758 query_nodes.add( new PhylogenyNode( "X" ) );
6759 query_nodes.add( new PhylogenyNode( "Y" ) );
6760 query_nodes.add( new PhylogenyNode( "A" ) );
6761 query_nodes.add( new PhylogenyNode( "B" ) );
6762 query_nodes.add( new PhylogenyNode( "D" ) );
6763 if ( s0.match( query_nodes ) ) {
6767 query_nodes = new HashSet<PhylogenyNode>();
6768 query_nodes.add( new PhylogenyNode( "X" ) );
6769 query_nodes.add( new PhylogenyNode( "Y" ) );
6770 query_nodes.add( new PhylogenyNode( "E" ) );
6771 query_nodes.add( new PhylogenyNode( "D" ) );
6772 query_nodes.add( new PhylogenyNode( "A" ) );
6773 if ( s0.match( query_nodes ) ) {
6777 query_nodes = new HashSet<PhylogenyNode>();
6778 query_nodes.add( new PhylogenyNode( "X" ) );
6779 query_nodes.add( new PhylogenyNode( "Y" ) );
6780 query_nodes.add( new PhylogenyNode( "E" ) );
6781 query_nodes.add( new PhylogenyNode( "D" ) );
6782 query_nodes.add( new PhylogenyNode( "A" ) );
6783 query_nodes.add( new PhylogenyNode( "G" ) );
6784 if ( s0.match( query_nodes ) ) {
6788 catch ( final Exception e ) {
6789 e.printStackTrace();
6795 private static boolean testSplitStrict() {
6797 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6798 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6799 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6800 ex.add( new PhylogenyNode( "A" ) );
6801 ex.add( new PhylogenyNode( "B" ) );
6802 ex.add( new PhylogenyNode( "C" ) );
6803 ex.add( new PhylogenyNode( "D" ) );
6804 ex.add( new PhylogenyNode( "E" ) );
6805 ex.add( new PhylogenyNode( "F" ) );
6806 ex.add( new PhylogenyNode( "G" ) );
6807 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6808 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6809 query_nodes.add( new PhylogenyNode( "A" ) );
6810 query_nodes.add( new PhylogenyNode( "B" ) );
6811 if ( s0.match( query_nodes ) ) {
6814 query_nodes = new HashSet<PhylogenyNode>();
6815 query_nodes.add( new PhylogenyNode( "A" ) );
6816 query_nodes.add( new PhylogenyNode( "B" ) );
6817 query_nodes.add( new PhylogenyNode( "C" ) );
6818 query_nodes.add( new PhylogenyNode( "D" ) );
6819 query_nodes.add( new PhylogenyNode( "E" ) );
6820 query_nodes.add( new PhylogenyNode( "F" ) );
6821 query_nodes.add( new PhylogenyNode( "G" ) );
6822 if ( !s0.match( query_nodes ) ) {
6826 query_nodes = new HashSet<PhylogenyNode>();
6827 query_nodes.add( new PhylogenyNode( "A" ) );
6828 query_nodes.add( new PhylogenyNode( "B" ) );
6829 query_nodes.add( new PhylogenyNode( "C" ) );
6830 if ( !s0.match( query_nodes ) ) {
6834 query_nodes = new HashSet<PhylogenyNode>();
6835 query_nodes.add( new PhylogenyNode( "D" ) );
6836 query_nodes.add( new PhylogenyNode( "E" ) );
6837 query_nodes.add( new PhylogenyNode( "F" ) );
6838 query_nodes.add( new PhylogenyNode( "G" ) );
6839 if ( !s0.match( query_nodes ) ) {
6843 query_nodes = new HashSet<PhylogenyNode>();
6844 query_nodes.add( new PhylogenyNode( "A" ) );
6845 query_nodes.add( new PhylogenyNode( "B" ) );
6846 query_nodes.add( new PhylogenyNode( "C" ) );
6847 query_nodes.add( new PhylogenyNode( "D" ) );
6848 if ( !s0.match( query_nodes ) ) {
6852 query_nodes = new HashSet<PhylogenyNode>();
6853 query_nodes.add( new PhylogenyNode( "E" ) );
6854 query_nodes.add( new PhylogenyNode( "F" ) );
6855 query_nodes.add( new PhylogenyNode( "G" ) );
6856 if ( !s0.match( query_nodes ) ) {
6860 query_nodes = new HashSet<PhylogenyNode>();
6861 query_nodes.add( new PhylogenyNode( "F" ) );
6862 query_nodes.add( new PhylogenyNode( "G" ) );
6863 if ( !s0.match( query_nodes ) ) {
6867 query_nodes = new HashSet<PhylogenyNode>();
6868 query_nodes.add( new PhylogenyNode( "E" ) );
6869 query_nodes.add( new PhylogenyNode( "D" ) );
6870 query_nodes.add( new PhylogenyNode( "C" ) );
6871 query_nodes.add( new PhylogenyNode( "B" ) );
6872 query_nodes.add( new PhylogenyNode( "A" ) );
6873 if ( !s0.match( query_nodes ) ) {
6877 query_nodes = new HashSet<PhylogenyNode>();
6878 query_nodes.add( new PhylogenyNode( "F" ) );
6879 query_nodes.add( new PhylogenyNode( "G" ) );
6880 query_nodes.add( new PhylogenyNode( "E" ) );
6881 if ( !s0.match( query_nodes ) ) {
6885 query_nodes = new HashSet<PhylogenyNode>();
6886 query_nodes.add( new PhylogenyNode( "F" ) );
6887 query_nodes.add( new PhylogenyNode( "G" ) );
6888 query_nodes.add( new PhylogenyNode( "E" ) );
6889 query_nodes.add( new PhylogenyNode( "D" ) );
6890 if ( !s0.match( query_nodes ) ) {
6894 query_nodes = new HashSet<PhylogenyNode>();
6895 query_nodes.add( new PhylogenyNode( "F" ) );
6896 query_nodes.add( new PhylogenyNode( "A" ) );
6897 if ( s0.match( query_nodes ) ) {
6901 query_nodes = new HashSet<PhylogenyNode>();
6902 query_nodes.add( new PhylogenyNode( "A" ) );
6903 query_nodes.add( new PhylogenyNode( "E" ) );
6904 query_nodes.add( new PhylogenyNode( "B" ) );
6905 query_nodes.add( new PhylogenyNode( "C" ) );
6906 if ( s0.match( query_nodes ) ) {
6910 query_nodes = new HashSet<PhylogenyNode>();
6911 query_nodes.add( new PhylogenyNode( "F" ) );
6912 query_nodes.add( new PhylogenyNode( "G" ) );
6913 query_nodes.add( new PhylogenyNode( "E" ) );
6914 query_nodes.add( new PhylogenyNode( "D" ) );
6915 query_nodes.add( new PhylogenyNode( "C" ) );
6916 if ( s0.match( query_nodes ) ) {
6920 query_nodes = new HashSet<PhylogenyNode>();
6921 query_nodes.add( new PhylogenyNode( "A" ) );
6922 query_nodes.add( new PhylogenyNode( "B" ) );
6923 query_nodes.add( new PhylogenyNode( "D" ) );
6924 if ( s0.match( query_nodes ) ) {
6928 query_nodes = new HashSet<PhylogenyNode>();
6929 query_nodes.add( new PhylogenyNode( "A" ) );
6930 query_nodes.add( new PhylogenyNode( "D" ) );
6931 if ( s0.match( query_nodes ) ) {
6935 query_nodes = new HashSet<PhylogenyNode>();
6936 query_nodes.add( new PhylogenyNode( "A" ) );
6937 query_nodes.add( new PhylogenyNode( "B" ) );
6938 if ( s0.match( query_nodes ) ) {
6942 query_nodes = new HashSet<PhylogenyNode>();
6943 query_nodes.add( new PhylogenyNode( "A" ) );
6944 query_nodes.add( new PhylogenyNode( "C" ) );
6945 if ( s0.match( query_nodes ) ) {
6949 query_nodes = new HashSet<PhylogenyNode>();
6950 query_nodes.add( new PhylogenyNode( "A" ) );
6951 query_nodes.add( new PhylogenyNode( "E" ) );
6952 if ( s0.match( query_nodes ) ) {
6956 query_nodes = new HashSet<PhylogenyNode>();
6957 query_nodes.add( new PhylogenyNode( "A" ) );
6958 query_nodes.add( new PhylogenyNode( "F" ) );
6959 if ( s0.match( query_nodes ) ) {
6963 query_nodes = new HashSet<PhylogenyNode>();
6964 query_nodes.add( new PhylogenyNode( "A" ) );
6965 query_nodes.add( new PhylogenyNode( "G" ) );
6966 if ( s0.match( query_nodes ) ) {
6970 query_nodes = new HashSet<PhylogenyNode>();
6971 query_nodes.add( new PhylogenyNode( "A" ) );
6972 query_nodes.add( new PhylogenyNode( "F" ) );
6973 query_nodes.add( new PhylogenyNode( "G" ) );
6974 if ( s0.match( query_nodes ) ) {
6978 query_nodes = new HashSet<PhylogenyNode>();
6979 query_nodes.add( new PhylogenyNode( "A" ) );
6980 query_nodes.add( new PhylogenyNode( "B" ) );
6981 query_nodes.add( new PhylogenyNode( "D" ) );
6982 if ( s0.match( query_nodes ) ) {
6986 query_nodes = new HashSet<PhylogenyNode>();
6987 query_nodes.add( new PhylogenyNode( "E" ) );
6988 query_nodes.add( new PhylogenyNode( "D" ) );
6989 query_nodes.add( new PhylogenyNode( "A" ) );
6990 if ( s0.match( query_nodes ) ) {
6994 query_nodes = new HashSet<PhylogenyNode>();
6995 query_nodes.add( new PhylogenyNode( "E" ) );
6996 query_nodes.add( new PhylogenyNode( "D" ) );
6997 query_nodes.add( new PhylogenyNode( "A" ) );
6998 query_nodes.add( new PhylogenyNode( "G" ) );
6999 if ( s0.match( query_nodes ) ) {
7003 catch ( final Exception e ) {
7004 e.printStackTrace();
7010 private static boolean testSubtreeDeletion() {
7012 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7013 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7014 t1.deleteSubtree( t1.getNode( "A" ), false );
7015 if ( t1.getNumberOfExternalNodes() != 5 ) {
7018 t1.toNewHampshireX();
7019 t1.deleteSubtree( t1.getNode( "E" ), false );
7020 if ( t1.getNumberOfExternalNodes() != 4 ) {
7023 t1.toNewHampshireX();
7024 t1.deleteSubtree( t1.getNode( "F" ), false );
7025 if ( t1.getNumberOfExternalNodes() != 3 ) {
7028 t1.toNewHampshireX();
7029 t1.deleteSubtree( t1.getNode( "D" ), false );
7030 t1.toNewHampshireX();
7031 if ( t1.getNumberOfExternalNodes() != 3 ) {
7034 t1.deleteSubtree( t1.getNode( "def" ), false );
7035 t1.toNewHampshireX();
7036 if ( t1.getNumberOfExternalNodes() != 2 ) {
7039 t1.deleteSubtree( t1.getNode( "B" ), false );
7040 t1.toNewHampshireX();
7041 if ( t1.getNumberOfExternalNodes() != 1 ) {
7044 t1.deleteSubtree( t1.getNode( "C" ), false );
7045 t1.toNewHampshireX();
7046 if ( t1.getNumberOfExternalNodes() != 1 ) {
7049 t1.deleteSubtree( t1.getNode( "abc" ), false );
7050 t1.toNewHampshireX();
7051 if ( t1.getNumberOfExternalNodes() != 1 ) {
7054 t1.deleteSubtree( t1.getNode( "r" ), false );
7055 if ( t1.getNumberOfExternalNodes() != 0 ) {
7058 if ( !t1.isEmpty() ) {
7061 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7062 t2.deleteSubtree( t2.getNode( "A" ), false );
7063 t2.toNewHampshireX();
7064 if ( t2.getNumberOfExternalNodes() != 5 ) {
7067 t2.deleteSubtree( t2.getNode( "abc" ), false );
7068 t2.toNewHampshireX();
7069 if ( t2.getNumberOfExternalNodes() != 3 ) {
7072 t2.deleteSubtree( t2.getNode( "def" ), false );
7073 t2.toNewHampshireX();
7074 if ( t2.getNumberOfExternalNodes() != 1 ) {
7078 catch ( final Exception e ) {
7079 e.printStackTrace( System.out );
7085 private static boolean testSupportCount() {
7087 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7088 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7089 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7090 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7091 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7092 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7093 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7095 SupportCount.count( t0_1, phylogenies_1, true, false );
7096 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7097 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7098 + "(((((A,B),C),D),E),((F,G),X))"
7099 + "(((((A,Y),B),C),D),((F,G),E))"
7100 + "(((((A,B),C),D),E),(F,G))"
7101 + "(((((A,B),C),D),E),(F,G))"
7102 + "(((((A,B),C),D),E),(F,G))"
7103 + "(((((A,B),C),D),E),(F,G),Z)"
7104 + "(((((A,B),C),D),E),(F,G))"
7105 + "((((((A,B),C),D),E),F),G)"
7106 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7108 SupportCount.count( t0_2, phylogenies_2, true, false );
7109 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7110 while ( it.hasNext() ) {
7111 final PhylogenyNode n = it.next();
7112 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7116 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7117 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7118 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7119 SupportCount.count( t0_3, phylogenies_3, true, false );
7120 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7121 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7124 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7127 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7130 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7133 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7136 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7139 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7142 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7145 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7148 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7151 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7152 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7153 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7154 SupportCount.count( t0_4, phylogenies_4, true, false );
7155 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7156 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7159 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7162 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7165 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7168 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7171 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7174 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7177 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7180 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7183 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7186 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7187 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7188 double d = SupportCount.compare( b1, a, true, true, true );
7189 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7192 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7193 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7194 d = SupportCount.compare( b2, a, true, true, true );
7195 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7198 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7199 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7200 d = SupportCount.compare( b3, a, true, true, true );
7201 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7204 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7205 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7206 d = SupportCount.compare( b4, a, true, true, false );
7207 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7211 catch ( final Exception e ) {
7212 e.printStackTrace( System.out );
7218 private static boolean testSupportTransfer() {
7220 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7221 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)",
7222 new NHXParser() )[ 0 ];
7223 final Phylogeny p2 = factory
7224 .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 ];
7225 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7228 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7231 support_transfer.moveBranchLengthsToBootstrap( p1 );
7232 support_transfer.transferSupportValues( p1, p2 );
7233 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7236 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7239 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7242 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7245 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7248 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7251 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7254 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7258 catch ( final Exception e ) {
7259 e.printStackTrace( System.out );
7265 private static boolean testTaxonomyAssigner() {
7267 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]";
7268 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7269 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7270 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7271 s0.setRooted( true );
7272 g0.setRooted( true );
7273 TaxonomyAssigner.execute( g0, s0 );
7274 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7277 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7280 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7283 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7284 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7285 g0.setRooted( true );
7286 TaxonomyAssigner.execute( g0, s0 );
7287 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7290 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7293 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7296 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7297 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7298 g0.setRooted( true );
7299 TaxonomyAssigner.execute( g0, s0 );
7300 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7303 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7306 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7309 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7310 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7311 g0.setRooted( true );
7312 TaxonomyAssigner.execute( g0, s0 );
7313 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7316 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7319 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7322 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7323 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7324 g0.setRooted( true );
7325 TaxonomyAssigner.execute( g0, s0 );
7326 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7329 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7332 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7335 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7336 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7337 g0.setRooted( true );
7338 TaxonomyAssigner.execute( g0, s0 );
7339 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7342 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7345 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7348 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7349 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7350 g0.setRooted( true );
7351 TaxonomyAssigner.execute( g0, s0 );
7352 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7355 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7358 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7361 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7362 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7363 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7364 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7365 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7366 s0.setRooted( true );
7367 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7368 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7369 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7370 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7371 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7372 g0.setRooted( true );
7373 TaxonomyAssigner.execute( g0, s0 );
7374 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7377 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7380 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7383 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7386 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7389 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7390 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7391 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7392 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7393 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7394 g0.setRooted( true );
7395 TaxonomyAssigner.execute( g0, s0 );
7396 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7399 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7402 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7405 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7408 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7411 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7412 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7413 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7414 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7415 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7416 g0.setRooted( true );
7417 TaxonomyAssigner.execute( g0, s0 );
7418 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7421 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7424 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7427 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7430 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7433 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7434 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7435 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7436 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7437 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7438 g0.setRooted( true );
7439 TaxonomyAssigner.execute( g0, s0 );
7440 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7443 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7446 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7449 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7452 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7455 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7456 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7457 g0.setRooted( true );
7458 TaxonomyAssigner.execute( g0, s0 );
7459 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7462 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7465 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7468 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7469 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7470 g0.setRooted( true );
7471 TaxonomyAssigner.execute( g0, s0 );
7472 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7475 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7478 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7481 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7482 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7483 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7484 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7485 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7486 g0.setRooted( true );
7487 TaxonomyAssigner.execute( g0, s0 );
7488 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7491 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7494 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7497 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7500 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7503 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7506 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7509 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7510 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7511 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7512 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7513 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7514 g0.setRooted( true );
7515 TaxonomyAssigner.execute( g0, s0 );
7516 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7519 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7522 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7525 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7528 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7531 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7534 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7537 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7538 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7539 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7540 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7541 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7542 g0.setRooted( true );
7543 TaxonomyAssigner.execute( g0, s0 );
7544 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7547 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7550 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7553 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7556 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7559 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7562 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7565 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7566 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7567 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7568 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7569 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7570 g0.setRooted( true );
7571 TaxonomyAssigner.execute( g0, s0 );
7572 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7575 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7578 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7581 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7584 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7587 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7590 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7593 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7594 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7595 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7596 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7597 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7598 s0.setRooted( true );
7599 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7600 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7601 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7602 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7603 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7604 g0.setRooted( true );
7605 TaxonomyAssigner.execute( g0, s0 );
7606 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7609 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7613 catch ( final Exception e ) {
7614 e.printStackTrace( System.out );
7620 private static boolean testUniprotTaxonomySearch() {
7622 List<UniProtTaxonomy> results = UniProtWsTools
7623 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7624 if ( results.size() != 1 ) {
7627 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7630 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7633 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7636 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7639 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7643 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7644 if ( results.size() != 1 ) {
7647 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7650 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7653 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7656 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7659 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7663 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7664 if ( results.size() != 1 ) {
7667 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7670 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7673 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7676 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7679 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7683 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7684 if ( results.size() != 1 ) {
7687 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7690 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7693 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7696 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7699 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7702 if ( !results.get( 0 ).getLineage()[ 0 ].equals( "Eukaryota" ) ) {
7705 if ( !results.get( 0 ).getLineage()[ 1 ].equals( "Metazoa" ) ) {
7708 if ( !results.get( 0 ).getLineage()[ results.get( 0 ).getLineage().length - 1 ].equals( "Nematostella" ) ) {
7712 catch ( final Exception e ) {
7713 System.out.println();
7714 System.out.println( "the following might be due to absence internet connection:" );
7715 e.printStackTrace( System.out );
7721 private static boolean testWabiTxSearch() {
7724 result = TxSearch.searchSimple( "nematostella" );
7725 result = TxSearch.getTxId( "nematostella" );
7726 if ( !result.equals( "45350" ) ) {
7729 result = TxSearch.getTxName( "45350" );
7730 if ( !result.equals( "Nematostella" ) ) {
7733 result = TxSearch.getTxId( "nematostella vectensis" );
7734 if ( !result.equals( "45351" ) ) {
7737 result = TxSearch.getTxName( "45351" );
7738 if ( !result.equals( "Nematostella vectensis" ) ) {
7741 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7742 if ( !result.equals( "536089" ) ) {
7745 result = TxSearch.getTxName( "536089" );
7746 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7749 final List<String> queries = new ArrayList<String>();
7750 queries.add( "Campylobacter coli" );
7751 queries.add( "Escherichia coli" );
7752 queries.add( "Arabidopsis" );
7753 queries.add( "Trichoplax" );
7754 queries.add( "Samanea saman" );
7755 queries.add( "Kluyveromyces marxianus" );
7756 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7757 queries.add( "Bornavirus parrot/PDD/2008" );
7758 final List<RANKS> ranks = new ArrayList<RANKS>();
7759 ranks.add( RANKS.SUPERKINGDOM );
7760 ranks.add( RANKS.KINGDOM );
7761 ranks.add( RANKS.FAMILY );
7762 ranks.add( RANKS.GENUS );
7763 ranks.add( RANKS.TRIBE );
7764 result = TxSearch.searchLineage( queries, ranks );
7765 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7766 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7768 catch ( final Exception e ) {
7769 System.out.println();
7770 System.out.println( "the following might be due to absence internet connection:" );
7771 e.printStackTrace( System.out );
7777 private static boolean testAminoAcidSequence() {
7779 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7780 if ( aa1.getLength() != 13 ) {
7783 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7786 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7789 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7792 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7793 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7796 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7797 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7800 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7801 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7805 catch ( final Exception e ) {
7806 e.printStackTrace();
7812 private static boolean testCreateBalancedPhylogeny() {
7814 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7815 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7818 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7821 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7822 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7825 if ( p1.getNumberOfExternalNodes() != 100 ) {
7829 catch ( final Exception e ) {
7830 e.printStackTrace();
7836 private static boolean testFastaParser() {
7838 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7841 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7844 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7845 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7848 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7851 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7854 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7857 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
7860 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
7864 catch ( final Exception e ) {
7865 e.printStackTrace();
7871 private static boolean testGeneralMsaParser() {
7873 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
7874 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
7875 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
7876 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
7877 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
7878 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
7879 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
7880 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
7881 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
7882 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7885 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7888 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7891 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
7892 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
7895 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
7898 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
7901 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
7902 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7905 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7908 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7912 catch ( final Exception e ) {
7913 e.printStackTrace();
7919 private static boolean testMafft() {
7921 final List<String> opts = new ArrayList<String>();
7922 opts.add( "--maxiterate" );
7924 opts.add( "--localpair" );
7925 opts.add( "--quiet" );
7927 final MsaInferrer mafft = Mafft.createInstance();
7928 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
7929 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
7933 catch ( final Exception e ) {
7934 e.printStackTrace( System.out );