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.DatabaseTools;
103 import org.forester.ws.uniprot.SequenceDatabaseEntry;
104 import org.forester.ws.uniprot.UniProtTaxonomy;
105 import org.forester.ws.uniprot.UniProtWsTools;
106 import org.forester.ws.wabi.TxSearch;
107 import org.forester.ws.wabi.TxSearch.RANKS;
108 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
109 import org.forester.ws.wabi.TxSearch.TAX_RANK;
111 @SuppressWarnings( "unused")
112 public final class Test {
114 private final static double ZERO_DIFF = 1.0E-9;
115 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
116 + ForesterUtil.getFileSeparator() + "test_data"
117 + ForesterUtil.getFileSeparator();
118 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
119 + ForesterUtil.getFileSeparator() + "resources"
120 + ForesterUtil.getFileSeparator();
121 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
122 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
123 + ForesterConstants.PHYLO_XML_VERSION + "/"
124 + ForesterConstants.PHYLO_XML_XSD;
125 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
126 + ForesterConstants.PHYLO_XML_VERSION + "/"
127 + ForesterConstants.PHYLO_XML_XSD;
129 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
130 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
134 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
135 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
136 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
139 public static boolean isEqual( final double a, final double b ) {
140 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
143 public static void main( final String[] args ) {
144 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
145 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
147 Locale.setDefault( Locale.US );
148 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
151 System.out.print( "[Test if directory with files for testing exists/is readable: " );
152 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
153 System.out.println( "OK.]" );
156 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
157 System.out.println( "Testing aborted." );
160 System.out.print( "[Test if resources directory exists/is readable: " );
161 if ( testDir( PATH_TO_RESOURCES ) ) {
162 System.out.println( "OK.]" );
165 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
166 System.out.println( "Testing aborted." );
169 final long start_time = new Date().getTime();
170 System.out.print( "Hmmscan output parser: " );
171 if ( testHmmscanOutputParser() ) {
172 System.out.println( "OK." );
176 System.out.println( "failed." );
179 System.out.print( "Basic node methods: " );
180 if ( Test.testBasicNodeMethods() ) {
181 System.out.println( "OK." );
185 System.out.println( "failed." );
188 System.out.print( "Basic node construction and parsing of NHX (node level): " );
189 if ( Test.testNHXNodeParsing() ) {
190 System.out.println( "OK." );
194 System.out.println( "failed." );
197 System.out.print( "NH parsing: " );
198 if ( Test.testNHParsing() ) {
199 System.out.println( "OK." );
203 System.out.println( "failed." );
206 System.out.print( "Conversion to NHX (node level): " );
207 if ( Test.testNHXconversion() ) {
208 System.out.println( "OK." );
212 System.out.println( "failed." );
215 System.out.print( "NHX parsing: " );
216 if ( Test.testNHXParsing() ) {
217 System.out.println( "OK." );
221 System.out.println( "failed." );
224 System.out.print( "NHX parsing with quotes: " );
225 if ( Test.testNHXParsingQuotes() ) {
226 System.out.println( "OK." );
230 System.out.println( "failed." );
233 System.out.print( "Nexus characters parsing: " );
234 if ( Test.testNexusCharactersParsing() ) {
235 System.out.println( "OK." );
239 System.out.println( "failed." );
242 System.out.print( "Nexus tree parsing: " );
243 if ( Test.testNexusTreeParsing() ) {
244 System.out.println( "OK." );
248 System.out.println( "failed." );
251 System.out.print( "Nexus tree parsing (translating): " );
252 if ( Test.testNexusTreeParsingTranslating() ) {
253 System.out.println( "OK." );
257 System.out.println( "failed." );
260 System.out.print( "Nexus matrix parsing: " );
261 if ( Test.testNexusMatrixParsing() ) {
262 System.out.println( "OK." );
266 System.out.println( "failed." );
269 System.out.print( "Basic phyloXML parsing: " );
270 if ( Test.testBasicPhyloXMLparsing() ) {
271 System.out.println( "OK." );
275 System.out.println( "failed." );
278 System.out.print( "Basic phyloXML parsing (validating against schema): " );
279 if ( testBasicPhyloXMLparsingValidating() ) {
280 System.out.println( "OK." );
284 System.out.println( "failed." );
287 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
288 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
289 System.out.println( "OK." );
293 System.out.println( "failed." );
296 System.out.print( "phyloXML Distribution Element: " );
297 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
298 System.out.println( "OK." );
302 System.out.println( "failed." );
305 System.out.print( "Tol XML parsing: " );
306 if ( Test.testBasicTolXMLparsing() ) {
307 System.out.println( "OK." );
311 System.out.println( "failed." );
314 System.out.print( "Copying of node data: " );
315 if ( Test.testCopyOfNodeData() ) {
316 System.out.println( "OK." );
320 System.out.println( "failed." );
323 System.out.print( "Basic tree methods: " );
324 if ( Test.testBasicTreeMethods() ) {
325 System.out.println( "OK." );
329 System.out.println( "failed." );
332 System.out.print( "Postorder Iterator: " );
333 if ( Test.testPostOrderIterator() ) {
334 System.out.println( "OK." );
338 System.out.println( "failed." );
341 System.out.print( "Preorder Iterator: " );
342 if ( Test.testPreOrderIterator() ) {
343 System.out.println( "OK." );
347 System.out.println( "failed." );
350 System.out.print( "Levelorder Iterator: " );
351 if ( Test.testLevelOrderIterator() ) {
352 System.out.println( "OK." );
356 System.out.println( "failed." );
359 System.out.print( "Re-id methods: " );
360 if ( Test.testReIdMethods() ) {
361 System.out.println( "OK." );
365 System.out.println( "failed." );
368 System.out.print( "Methods on last external nodes: " );
369 if ( Test.testLastExternalNodeMethods() ) {
370 System.out.println( "OK." );
374 System.out.println( "failed." );
377 System.out.print( "Methods on external nodes: " );
378 if ( Test.testExternalNodeRelatedMethods() ) {
379 System.out.println( "OK." );
383 System.out.println( "failed." );
386 System.out.print( "Deletion of external nodes: " );
387 if ( Test.testDeletionOfExternalNodes() ) {
388 System.out.println( "OK." );
392 System.out.println( "failed." );
395 System.out.print( "Subtree deletion: " );
396 if ( Test.testSubtreeDeletion() ) {
397 System.out.println( "OK." );
401 System.out.println( "failed." );
404 System.out.print( "Phylogeny branch: " );
405 if ( Test.testPhylogenyBranch() ) {
406 System.out.println( "OK." );
410 System.out.println( "failed." );
413 System.out.print( "Rerooting: " );
414 if ( Test.testRerooting() ) {
415 System.out.println( "OK." );
419 System.out.println( "failed." );
422 System.out.print( "Mipoint rooting: " );
423 if ( Test.testMidpointrooting() ) {
424 System.out.println( "OK." );
428 System.out.println( "failed." );
431 System.out.print( "Support count: " );
432 if ( Test.testSupportCount() ) {
433 System.out.println( "OK." );
437 System.out.println( "failed." );
440 System.out.print( "Support transfer: " );
441 if ( Test.testSupportTransfer() ) {
442 System.out.println( "OK." );
446 System.out.println( "failed." );
449 System.out.print( "Finding of LCA: " );
450 if ( Test.testGetLCA() ) {
451 System.out.println( "OK." );
455 System.out.println( "failed." );
458 System.out.print( "Calculation of distance between nodes: " );
459 if ( Test.testGetDistance() ) {
460 System.out.println( "OK." );
464 System.out.println( "failed." );
467 System.out.print( "SDIse: " );
468 if ( Test.testSDIse() ) {
469 System.out.println( "OK." );
473 System.out.println( "failed." );
476 System.out.print( "Taxonomy assigner: " );
477 if ( Test.testTaxonomyAssigner() ) {
478 System.out.println( "OK." );
482 System.out.println( "failed." );
485 System.out.print( "SDIunrooted: " );
486 if ( Test.testSDIunrooted() ) {
487 System.out.println( "OK." );
491 System.out.println( "failed." );
494 System.out.print( "GSDI: " );
495 if ( TestGSDI.test() ) {
496 System.out.println( "OK." );
500 System.out.println( "failed." );
503 System.out.print( "Descriptive statistics: " );
504 if ( Test.testDescriptiveStatistics() ) {
505 System.out.println( "OK." );
509 System.out.println( "failed." );
512 System.out.print( "Data objects and methods: " );
513 if ( Test.testDataObjects() ) {
514 System.out.println( "OK." );
518 System.out.println( "failed." );
521 System.out.print( "Properties map: " );
522 if ( Test.testPropertiesMap() ) {
523 System.out.println( "OK." );
527 System.out.println( "failed." );
530 System.out.print( "Phylogeny reconstruction:" );
531 System.out.println();
532 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
533 System.out.println( "OK." );
537 System.out.println( "failed." );
540 System.out.print( "Analysis of domain architectures: " );
541 System.out.println();
542 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
543 System.out.println( "OK." );
547 System.out.println( "failed." );
550 System.out.print( "GO: " );
551 System.out.println();
552 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
553 System.out.println( "OK." );
557 System.out.println( "failed." );
560 System.out.print( "Modeling tools: " );
561 if ( TestPccx.test() ) {
562 System.out.println( "OK." );
566 System.out.println( "failed." );
569 System.out.print( "Split Matrix strict: " );
570 if ( Test.testSplitStrict() ) {
571 System.out.println( "OK." );
575 System.out.println( "failed." );
578 System.out.print( "Split Matrix: " );
579 if ( Test.testSplit() ) {
580 System.out.println( "OK." );
584 System.out.println( "failed." );
587 System.out.print( "Confidence Assessor: " );
588 if ( Test.testConfidenceAssessor() ) {
589 System.out.println( "OK." );
593 System.out.println( "failed." );
596 System.out.print( "Basic table: " );
597 if ( Test.testBasicTable() ) {
598 System.out.println( "OK." );
602 System.out.println( "failed." );
605 System.out.print( "General table: " );
606 if ( Test.testGeneralTable() ) {
607 System.out.println( "OK." );
611 System.out.println( "failed." );
614 System.out.print( "Amino acid sequence: " );
615 if ( Test.testAminoAcidSequence() ) {
616 System.out.println( "OK." );
620 System.out.println( "failed." );
623 System.out.print( "General MSA parser: " );
624 if ( Test.testGeneralMsaParser() ) {
625 System.out.println( "OK." );
629 System.out.println( "failed." );
632 System.out.print( "Fasta parser for msa: " );
633 if ( Test.testFastaParser() ) {
634 System.out.println( "OK." );
638 System.out.println( "failed." );
641 System.out.print( "Creation of balanced phylogeny: " );
642 if ( Test.testCreateBalancedPhylogeny() ) {
643 System.out.println( "OK." );
647 System.out.println( "failed." );
651 System.out.print( "EMBL Entry Retrieval: " );
652 if ( Test.testEmblEntryRetrieval() ) {
653 System.out.println( "OK." );
657 System.out.println( "failed." );
661 System.out.print( "Uniprot Entry Retrieval: " );
662 if ( Test.testUniprotEntryRetrieval() ) {
663 System.out.println( "OK." );
667 System.out.println( "failed." );
670 System.out.print( "Uniprot Taxonomy Search: " );
671 if ( Test.testUniprotTaxonomySearch() ) {
672 System.out.println( "OK." );
676 System.out.println( "failed." );
679 if ( Mafft.isInstalled() ) {
680 System.out.print( "MAFFT (external program): " );
681 if ( Test.testMafft() ) {
682 System.out.println( "OK." );
686 System.out.println( "failed [will not count towards failed tests]" );
689 // System.out.print( "WABI TxSearch: " );
690 // if ( Test.testWabiTxSearch() ) {
691 // System.out.println( "OK." );
696 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
698 System.out.println();
699 final Runtime rt = java.lang.Runtime.getRuntime();
700 final long free_memory = rt.freeMemory() / 1000000;
701 final long total_memory = rt.totalMemory() / 1000000;
702 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
703 + free_memory + "MB, total memory: " + total_memory + "MB)" );
704 System.out.println();
705 System.out.println( "Successful tests: " + succeeded );
706 System.out.println( "Failed tests: " + failed );
707 System.out.println();
709 System.out.println( "OK." );
712 System.out.println( "Not OK." );
714 // System.out.println();
715 // Development.setTime( true );
717 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
718 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
719 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
720 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
721 // "multifurcations_ex_1.nhx";
722 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
723 // final Phylogeny t1 = factory.create( new File( domains ), new
724 // NHXParser() )[ 0 ];
725 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
727 // catch ( final Exception e ) {
728 // e.printStackTrace();
730 // t1.getRoot().preorderPrint();
731 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
735 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
736 // + "\\AtNBSpos.nhx" ) );
738 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
739 // new NHXParser() );
740 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
741 // + "\\AtNBSpos.nhx" ) );
743 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
744 // new NHXParser() );
747 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
748 // + "\\big_tree.nhx" ) );
749 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
750 // + "\\big_tree.nhx" ) );
752 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
753 // new NHXParser() );
755 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
756 // new NHXParser() );
758 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
759 // + "\\big_tree.nhx" ) );
760 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
761 // + "\\big_tree.nhx" ) );
764 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
765 // new NHXParser() );
767 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
768 // new NHXParser() );
770 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
771 // + "\\AtNBSpos.nhx" ) );
773 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
774 // new NHXParser() );
777 // catch ( IOException e ) {
778 // // TODO Auto-generated catch block
779 // e.printStackTrace();
783 private static boolean testBasicNodeMethods() {
785 if ( PhylogenyNode.getNodeCount() != 0 ) {
788 final PhylogenyNode n1 = new PhylogenyNode();
789 final PhylogenyNode n2 = new PhylogenyNode( "", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
790 final PhylogenyNode n3 = new PhylogenyNode( "n3", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
791 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
792 if ( n1.isHasAssignedEvent() ) {
795 if ( PhylogenyNode.getNodeCount() != 4 ) {
798 if ( n3.getIndicator() != 0 ) {
801 if ( n3.getNumberOfExternalNodes() != 1 ) {
804 if ( !n3.isExternal() ) {
807 if ( !n3.isRoot() ) {
810 if ( !n4.getName().equals( "n4" ) ) {
814 catch ( final Exception e ) {
815 e.printStackTrace( System.out );
821 private static boolean testBasicPhyloXMLparsing() {
823 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
824 final PhyloXmlParser xml_parser = new PhyloXmlParser();
825 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
827 if ( xml_parser.getErrorCount() > 0 ) {
828 System.out.println( xml_parser.getErrorMessages().toString() );
831 if ( phylogenies_0.length != 4 ) {
834 final Phylogeny t1 = phylogenies_0[ 0 ];
835 final Phylogeny t2 = phylogenies_0[ 1 ];
836 final Phylogeny t3 = phylogenies_0[ 2 ];
837 final Phylogeny t4 = phylogenies_0[ 3 ];
838 if ( t1.getNumberOfExternalNodes() != 1 ) {
841 if ( !t1.isRooted() ) {
844 if ( t1.isRerootable() ) {
847 if ( !t1.getType().equals( "gene_tree" ) ) {
850 if ( t2.getNumberOfExternalNodes() != 2 ) {
853 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
856 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
859 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
862 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
865 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
868 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
871 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
872 .startsWith( "actgtgggggt" ) ) {
875 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
876 .startsWith( "ctgtgatgcat" ) ) {
879 if ( t3.getNumberOfExternalNodes() != 4 ) {
882 if ( !t1.getName().equals( "t1" ) ) {
885 if ( !t2.getName().equals( "t2" ) ) {
888 if ( !t3.getName().equals( "t3" ) ) {
891 if ( !t4.getName().equals( "t4" ) ) {
894 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
897 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
900 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
903 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
904 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
907 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
910 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
913 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
916 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
917 .equals( "apoptosis" ) ) {
920 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
921 .equals( "GO:0006915" ) ) {
924 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
925 .equals( "UniProtKB" ) ) {
928 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
929 .equals( "experimental" ) ) {
932 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
933 .equals( "function" ) ) {
936 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
940 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
941 .getType().equals( "ml" ) ) {
944 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
945 .equals( "apoptosis" ) ) {
948 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
949 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
952 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
953 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
956 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
957 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
960 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
961 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
964 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
965 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
968 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
969 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
972 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
973 .equals( "GO:0005829" ) ) {
976 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
977 .equals( "intracellular organelle" ) ) {
980 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
983 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
984 .equals( "UniProt link" ) ) ) {
987 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
990 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
993 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
996 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
999 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1002 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1005 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1008 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1011 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1014 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1017 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1018 // .equals( "B" ) ) {
1021 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1024 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1027 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1030 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1031 // .getConfidence() != 2144 ) {
1034 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1035 // .equals( "pfam" ) ) {
1038 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1041 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1044 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1047 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1050 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1051 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1055 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1058 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1061 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1064 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1067 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1070 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1073 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1076 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1078 // if ( xml_parser.getErrorCount() > 0 ) {
1079 // System.out.println( xml_parser.getErrorMessages().toString() );
1082 // if ( phylogenies_1.length != 2 ) {
1085 // final Phylogeny a = phylogenies_1[ 0 ];
1086 // if ( !a.getName().equals( "tree 4" ) ) {
1089 // if ( a.getNumberOfExternalNodes() != 3 ) {
1092 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1095 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1099 catch ( final Exception e ) {
1100 e.printStackTrace( System.out );
1106 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1108 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1109 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1110 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1111 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1114 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1116 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1118 if ( xml_parser.getErrorCount() > 0 ) {
1119 System.out.println( xml_parser.getErrorMessages().toString() );
1122 if ( phylogenies_0.length != 4 ) {
1125 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1126 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1127 if ( phylogenies_t1.length != 1 ) {
1130 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1131 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1134 if ( !t1_rt.isRooted() ) {
1137 if ( t1_rt.isRerootable() ) {
1140 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1143 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1144 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1145 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1146 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1149 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1152 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1155 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1158 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1159 .startsWith( "actgtgggggt" ) ) {
1162 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1163 .startsWith( "ctgtgatgcat" ) ) {
1166 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1167 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1168 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1169 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1170 if ( phylogenies_1.length != 1 ) {
1173 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1174 if ( !t3_rt.getName().equals( "t3" ) ) {
1177 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1180 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1183 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1186 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1189 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1190 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1193 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1196 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1199 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1200 .equals( "UniProtKB" ) ) {
1203 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1204 .equals( "apoptosis" ) ) {
1207 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1208 .equals( "GO:0006915" ) ) {
1211 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1212 .equals( "UniProtKB" ) ) {
1215 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1216 .equals( "experimental" ) ) {
1219 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1220 .equals( "function" ) ) {
1223 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1224 .getValue() != 1 ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1228 .getType().equals( "ml" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1232 .equals( "apoptosis" ) ) {
1235 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1236 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1240 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1243 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1244 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1248 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1252 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1255 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1256 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1259 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1260 .equals( "GO:0005829" ) ) {
1263 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1264 .equals( "intracellular organelle" ) ) {
1267 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1270 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1271 .equals( "UniProt link" ) ) ) {
1274 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1277 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1280 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1281 .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." ) ) ) {
1284 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1287 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1290 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1293 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1296 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1297 .equals( "ncbi" ) ) {
1300 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1303 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1304 .getName().equals( "B" ) ) {
1307 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1308 .getFrom() != 21 ) {
1311 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1314 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1315 .getLength() != 24 ) {
1318 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1319 .getConfidence() != 2144 ) {
1322 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1323 .equals( "pfam" ) ) {
1326 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1329 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1332 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1335 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1338 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1339 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1342 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1345 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1348 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1351 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1354 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1357 if ( taxbb.getSynonyms().size() != 2 ) {
1360 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1363 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1366 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1369 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1372 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1375 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1376 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1380 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1383 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1386 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1389 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1392 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1395 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1398 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1402 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1405 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1406 .equalsIgnoreCase( "435" ) ) {
1409 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1412 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1413 .equalsIgnoreCase( "443.7" ) ) {
1416 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1419 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1422 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1423 .equalsIgnoreCase( "433" ) ) {
1427 catch ( final Exception e ) {
1428 e.printStackTrace( System.out );
1434 private static boolean testBasicPhyloXMLparsingValidating() {
1436 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1437 PhyloXmlParser xml_parser = null;
1439 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1441 catch ( final Exception e ) {
1442 // Do nothing -- means were not running from jar.
1444 if ( xml_parser == null ) {
1445 xml_parser = new PhyloXmlParser();
1446 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1447 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1450 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1453 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1455 if ( xml_parser.getErrorCount() > 0 ) {
1456 System.out.println( xml_parser.getErrorMessages().toString() );
1459 if ( phylogenies_0.length != 4 ) {
1462 final Phylogeny t1 = phylogenies_0[ 0 ];
1463 final Phylogeny t2 = phylogenies_0[ 1 ];
1464 final Phylogeny t3 = phylogenies_0[ 2 ];
1465 final Phylogeny t4 = phylogenies_0[ 3 ];
1466 if ( !t1.getName().equals( "t1" ) ) {
1469 if ( !t2.getName().equals( "t2" ) ) {
1472 if ( !t3.getName().equals( "t3" ) ) {
1475 if ( !t4.getName().equals( "t4" ) ) {
1478 if ( t1.getNumberOfExternalNodes() != 1 ) {
1481 if ( t2.getNumberOfExternalNodes() != 2 ) {
1484 if ( t3.getNumberOfExternalNodes() != 4 ) {
1487 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1488 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1489 if ( xml_parser.getErrorCount() > 0 ) {
1490 System.out.println( "errors:" );
1491 System.out.println( xml_parser.getErrorMessages().toString() );
1494 if ( phylogenies_1.length != 4 ) {
1497 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1499 if ( xml_parser.getErrorCount() > 0 ) {
1500 System.out.println( "errors:" );
1501 System.out.println( xml_parser.getErrorMessages().toString() );
1504 if ( phylogenies_2.length != 1 ) {
1507 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1510 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1512 if ( xml_parser.getErrorCount() > 0 ) {
1513 System.out.println( xml_parser.getErrorMessages().toString() );
1516 if ( phylogenies_3.length != 2 ) {
1519 final Phylogeny a = phylogenies_3[ 0 ];
1520 if ( !a.getName().equals( "tree 4" ) ) {
1523 if ( a.getNumberOfExternalNodes() != 3 ) {
1526 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1529 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1532 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1534 if ( xml_parser.getErrorCount() > 0 ) {
1535 System.out.println( xml_parser.getErrorMessages().toString() );
1538 if ( phylogenies_4.length != 1 ) {
1541 final Phylogeny s = phylogenies_4[ 0 ];
1542 if ( s.getNumberOfExternalNodes() != 6 ) {
1545 s.getNode( "first" );
1547 s.getNode( "\"<a'b&c'd\">\"" );
1548 s.getNode( "'''\"" );
1549 s.getNode( "\"\"\"" );
1550 s.getNode( "dick & doof" );
1552 catch ( final Exception e ) {
1553 e.printStackTrace( System.out );
1559 private static boolean testBasicTable() {
1561 final BasicTable<String> t0 = new BasicTable<String>();
1562 if ( t0.getNumberOfColumns() != 0 ) {
1565 if ( t0.getNumberOfRows() != 0 ) {
1568 t0.setValue( 3, 2, "23" );
1569 t0.setValue( 10, 1, "error" );
1570 t0.setValue( 10, 1, "110" );
1571 t0.setValue( 9, 1, "19" );
1572 t0.setValue( 1, 10, "101" );
1573 t0.setValue( 10, 10, "1010" );
1574 t0.setValue( 100, 10, "10100" );
1575 t0.setValue( 0, 0, "00" );
1576 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1579 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1582 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1585 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1588 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1591 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1594 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1597 if ( t0.getNumberOfColumns() != 101 ) {
1600 if ( t0.getNumberOfRows() != 11 ) {
1603 if ( t0.getValueAsString( 49, 4 ) != null ) {
1606 final String l = ForesterUtil.getLineSeparator();
1607 final StringBuffer source = new StringBuffer();
1608 source.append( "" + l );
1609 source.append( "# 1 1 1 1 1 1 1 1" + l );
1610 source.append( " 00 01 02 03" + l );
1611 source.append( " 10 11 12 13 " + l );
1612 source.append( "20 21 22 23 " + l );
1613 source.append( " 30 31 32 33" + l );
1614 source.append( "40 41 42 43" + l );
1615 source.append( " # 1 1 1 1 1 " + l );
1616 source.append( "50 51 52 53 54" + l );
1617 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1618 if ( t1.getNumberOfColumns() != 5 ) {
1621 if ( t1.getNumberOfRows() != 6 ) {
1624 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1627 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1630 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1633 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1636 final StringBuffer source1 = new StringBuffer();
1637 source1.append( "" + l );
1638 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1639 source1.append( " 00; 01 ;02;03" + l );
1640 source1.append( " 10; 11; 12; 13 " + l );
1641 source1.append( "20; 21; 22; 23 " + l );
1642 source1.append( " 30; 31; 32; 33" + l );
1643 source1.append( "40;41;42;43" + l );
1644 source1.append( " # 1 1 1 1 1 " + l );
1645 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1646 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1647 if ( t2.getNumberOfColumns() != 5 ) {
1650 if ( t2.getNumberOfRows() != 6 ) {
1653 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1656 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1659 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1662 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1665 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1668 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1671 final StringBuffer source2 = new StringBuffer();
1672 source2.append( "" + l );
1673 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1674 source2.append( " 00; 01 ;02;03" + l );
1675 source2.append( " 10; 11; 12; 13 " + l );
1676 source2.append( "20; 21; 22; 23 " + l );
1677 source2.append( " " + l );
1678 source2.append( " 30; 31; 32; 33" + l );
1679 source2.append( "40;41;42;43" + l );
1680 source2.append( " comment: 1 1 1 1 1 " + l );
1681 source2.append( ";;;50 ; 52; 53;;54 " + l );
1682 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1687 if ( tl.size() != 2 ) {
1690 final BasicTable<String> t3 = tl.get( 0 );
1691 final BasicTable<String> t4 = tl.get( 1 );
1692 if ( t3.getNumberOfColumns() != 4 ) {
1695 if ( t3.getNumberOfRows() != 3 ) {
1698 if ( t4.getNumberOfColumns() != 4 ) {
1701 if ( t4.getNumberOfRows() != 3 ) {
1704 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1707 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1711 catch ( final Exception e ) {
1712 e.printStackTrace( System.out );
1718 private static boolean testBasicTolXMLparsing() {
1720 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1721 final TolParser parser = new TolParser();
1722 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1723 if ( parser.getErrorCount() > 0 ) {
1724 System.out.println( parser.getErrorMessages().toString() );
1727 if ( phylogenies_0.length != 1 ) {
1730 final Phylogeny t1 = phylogenies_0[ 0 ];
1731 if ( t1.getNumberOfExternalNodes() != 5 ) {
1734 if ( !t1.isRooted() ) {
1737 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1740 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1743 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1746 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1749 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1750 if ( parser.getErrorCount() > 0 ) {
1751 System.out.println( parser.getErrorMessages().toString() );
1754 if ( phylogenies_1.length != 1 ) {
1757 final Phylogeny t2 = phylogenies_1[ 0 ];
1758 if ( t2.getNumberOfExternalNodes() != 664 ) {
1761 if ( !t2.isRooted() ) {
1764 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1767 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1770 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1773 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1776 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1779 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1780 .equals( "Aquifex" ) ) {
1783 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1784 if ( parser.getErrorCount() > 0 ) {
1785 System.out.println( parser.getErrorMessages().toString() );
1788 if ( phylogenies_2.length != 1 ) {
1791 final Phylogeny t3 = phylogenies_2[ 0 ];
1792 if ( t3.getNumberOfExternalNodes() != 184 ) {
1795 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1798 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1801 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1804 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1805 if ( parser.getErrorCount() > 0 ) {
1806 System.out.println( parser.getErrorMessages().toString() );
1809 if ( phylogenies_3.length != 1 ) {
1812 final Phylogeny t4 = phylogenies_3[ 0 ];
1813 if ( t4.getNumberOfExternalNodes() != 1 ) {
1816 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1819 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1822 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1825 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1826 if ( parser.getErrorCount() > 0 ) {
1827 System.out.println( parser.getErrorMessages().toString() );
1830 if ( phylogenies_4.length != 1 ) {
1833 final Phylogeny t5 = phylogenies_4[ 0 ];
1834 if ( t5.getNumberOfExternalNodes() != 13 ) {
1837 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1840 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1843 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1847 catch ( final Exception e ) {
1848 e.printStackTrace( System.out );
1854 private static boolean testBasicTreeMethods() {
1856 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1857 final Phylogeny t1 = factory.create();
1858 if ( !t1.isEmpty() ) {
1861 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1862 if ( t2.getNumberOfExternalNodes() != 4 ) {
1865 if ( t2.getHeight() != 8.5 ) {
1868 if ( !t2.isCompletelyBinary() ) {
1871 if ( t2.isEmpty() ) {
1874 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1875 if ( t3.getNumberOfExternalNodes() != 5 ) {
1878 if ( t3.getHeight() != 11 ) {
1881 if ( t3.isCompletelyBinary() ) {
1884 final PhylogenyNode n = t3.getNode( "ABC" );
1885 PhylogenyNodeIterator it;
1886 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1889 for( it.reset(); it.hasNext(); ) {
1892 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1893 if ( !it2.next().getName().equals( "A" ) ) {
1896 if ( !it2.next().getName().equals( "B" ) ) {
1899 if ( !it2.next().getName().equals( "C" ) ) {
1902 if ( it2.hasNext() ) {
1905 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 ];
1906 if ( t4.getNumberOfExternalNodes() != 9 ) {
1909 if ( t4.getHeight() != 11 ) {
1912 if ( t4.isCompletelyBinary() ) {
1915 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)" );
1916 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1917 if ( t5.getNumberOfExternalNodes() != 8 ) {
1920 if ( t5.getHeight() != 15 ) {
1923 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)" );
1924 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1925 if ( t6.getHeight() != 15 ) {
1928 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)" );
1929 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1930 if ( t7.getHeight() != 15 ) {
1933 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)" );
1934 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1935 if ( t8.getNumberOfExternalNodes() != 10 ) {
1938 if ( t8.getHeight() != 15 ) {
1941 final char[] a9 = new char[] {};
1942 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1943 if ( t9.getHeight() != 0 ) {
1946 final char[] a10 = new char[] { 'a', ':', '6' };
1947 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1948 if ( t10.getHeight() != 6 ) {
1952 catch ( final Exception e ) {
1953 e.printStackTrace( System.out );
1959 private static boolean testConfidenceAssessor() {
1961 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1962 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1963 final Phylogeny[] ev0 = factory
1964 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1966 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1967 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1970 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1973 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1974 final Phylogeny[] ev1 = factory
1975 .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)));",
1977 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1978 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1981 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1984 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1985 final Phylogeny[] ev_b = factory
1986 .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",
1988 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1989 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
1990 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1993 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1997 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1998 final Phylogeny[] ev1x = factory
1999 .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)));",
2001 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2002 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2005 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2008 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2009 final Phylogeny[] ev_bx = factory
2010 .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",
2012 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2013 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2016 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2020 final Phylogeny[] t2 = factory
2021 .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);",
2023 final Phylogeny[] ev2 = factory
2024 .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);",
2026 for( final Phylogeny target : t2 ) {
2027 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2030 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2031 new NHXParser() )[ 0 ];
2032 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2033 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2034 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2037 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2040 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2044 catch ( final Exception e ) {
2045 e.printStackTrace();
2051 private static boolean testCopyOfNodeData() {
2053 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]" );
2054 final PhylogenyNode n2 = n1.copyNodeData();
2055 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2059 catch ( final Exception e ) {
2060 e.printStackTrace();
2066 private static boolean testDataObjects() {
2068 final Confidence s0 = new Confidence();
2069 final Confidence s1 = new Confidence();
2070 if ( !s0.isEqual( s1 ) ) {
2073 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2074 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2075 if ( s2.isEqual( s1 ) ) {
2078 if ( !s2.isEqual( s3 ) ) {
2081 final Confidence s4 = ( Confidence ) s3.copy();
2082 if ( !s4.isEqual( s3 ) ) {
2089 final Taxonomy t1 = new Taxonomy();
2090 final Taxonomy t2 = new Taxonomy();
2091 final Taxonomy t3 = new Taxonomy();
2092 final Taxonomy t4 = new Taxonomy();
2093 final Taxonomy t5 = new Taxonomy();
2094 t1.setIdentifier( new Identifier( "ecoli" ) );
2095 t1.setTaxonomyCode( "ECOLI" );
2096 t1.setScientificName( "E. coli" );
2097 t1.setCommonName( "coli" );
2098 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2099 if ( !t1.isEqual( t0 ) ) {
2102 t2.setIdentifier( new Identifier( "ecoli" ) );
2103 t2.setTaxonomyCode( "other" );
2104 t2.setScientificName( "what" );
2105 t2.setCommonName( "something" );
2106 if ( !t1.isEqual( t2 ) ) {
2109 t2.setIdentifier( new Identifier( "nemve" ) );
2110 if ( t1.isEqual( t2 ) ) {
2113 t1.setIdentifier( null );
2114 t3.setTaxonomyCode( "ECOLI" );
2115 t3.setScientificName( "what" );
2116 t3.setCommonName( "something" );
2117 if ( !t1.isEqual( t3 ) ) {
2120 t1.setIdentifier( null );
2121 t1.setTaxonomyCode( "" );
2122 t4.setScientificName( "E. ColI" );
2123 t4.setCommonName( "something" );
2124 if ( !t1.isEqual( t4 ) ) {
2127 t4.setScientificName( "B. subtilis" );
2128 t4.setCommonName( "something" );
2129 if ( t1.isEqual( t4 ) ) {
2132 t1.setIdentifier( null );
2133 t1.setTaxonomyCode( "" );
2134 t1.setScientificName( "" );
2135 t5.setCommonName( "COLI" );
2136 if ( !t1.isEqual( t5 ) ) {
2139 t5.setCommonName( "vibrio" );
2140 if ( t1.isEqual( t5 ) ) {
2145 final Identifier id0 = new Identifier( "123", "pfam" );
2146 final Identifier id1 = ( Identifier ) id0.copy();
2147 if ( !id1.isEqual( id1 ) ) {
2150 if ( !id1.isEqual( id0 ) ) {
2153 if ( !id0.isEqual( id1 ) ) {
2160 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2161 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2162 if ( !pd1.isEqual( pd1 ) ) {
2165 if ( !pd1.isEqual( pd0 ) ) {
2170 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2171 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2172 if ( !pd3.isEqual( pd3 ) ) {
2175 if ( !pd2.isEqual( pd3 ) ) {
2178 if ( !pd0.isEqual( pd3 ) ) {
2183 // DomainArchitecture
2184 // ------------------
2185 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2186 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2187 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2188 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2189 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2190 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2195 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2196 if ( ds0.getNumberOfDomains() != 4 ) {
2199 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2200 if ( !ds0.isEqual( ds0 ) ) {
2203 if ( !ds0.isEqual( ds1 ) ) {
2206 if ( ds1.getNumberOfDomains() != 4 ) {
2209 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2214 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2215 if ( ds0.isEqual( ds2 ) ) {
2221 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2222 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2223 System.out.println( ds3.toNHX() );
2226 if ( ds3.getNumberOfDomains() != 3 ) {
2231 final Event e1 = new Event( Event.EventType.fusion );
2232 if ( e1.isDuplication() ) {
2235 if ( !e1.isFusion() ) {
2238 if ( !e1.asText().toString().equals( "fusion" ) ) {
2241 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2244 final Event e11 = new Event( Event.EventType.fusion );
2245 if ( !e11.isEqual( e1 ) ) {
2248 if ( !e11.toNHX().toString().equals( "" ) ) {
2251 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2252 if ( e2.isDuplication() ) {
2255 if ( !e2.isSpeciationOrDuplication() ) {
2258 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2261 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2264 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2267 if ( e11.isEqual( e2 ) ) {
2270 final Event e2c = ( Event ) e2.copy();
2271 if ( !e2c.isEqual( e2 ) ) {
2274 Event e3 = new Event( 1, 2, 3 );
2275 if ( e3.isDuplication() ) {
2278 if ( e3.isSpeciation() ) {
2281 if ( e3.isGeneLoss() ) {
2284 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2287 final Event e3c = ( Event ) e3.copy();
2288 final Event e3cc = ( Event ) e3c.copy();
2289 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2293 if ( !e3c.isEqual( e3cc ) ) {
2296 Event e4 = new Event( 1, 2, 3 );
2297 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2300 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2303 final Event e4c = ( Event ) e4.copy();
2305 final Event e4cc = ( Event ) e4c.copy();
2306 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2309 if ( !e4c.isEqual( e4cc ) ) {
2312 final Event e5 = new Event();
2313 if ( !e5.isUnassigned() ) {
2316 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2319 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2322 final Event e6 = new Event( 1, 0, 0 );
2323 if ( !e6.asText().toString().equals( "duplication" ) ) {
2326 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2329 final Event e7 = new Event( 0, 1, 0 );
2330 if ( !e7.asText().toString().equals( "speciation" ) ) {
2333 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2336 final Event e8 = new Event( 0, 0, 1 );
2337 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2340 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2344 catch ( final Exception e ) {
2345 e.printStackTrace( System.out );
2351 private static boolean testDeletionOfExternalNodes() {
2353 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2354 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2355 final PhylogenyWriter w = new PhylogenyWriter();
2356 if ( t0.isEmpty() ) {
2359 if ( t0.getNumberOfExternalNodes() != 1 ) {
2362 t0.deleteSubtree( t0.getNode( "A" ), false );
2363 if ( t0.getNumberOfExternalNodes() != 0 ) {
2366 if ( !t0.isEmpty() ) {
2369 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2370 if ( t1.getNumberOfExternalNodes() != 2 ) {
2373 t1.deleteSubtree( t1.getNode( "A" ), false );
2374 if ( t1.getNumberOfExternalNodes() != 1 ) {
2377 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2380 t1.deleteSubtree( t1.getNode( "B" ), false );
2381 if ( t1.getNumberOfExternalNodes() != 1 ) {
2384 t1.deleteSubtree( t1.getNode( "r" ), false );
2385 if ( !t1.isEmpty() ) {
2388 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2389 if ( t2.getNumberOfExternalNodes() != 3 ) {
2392 t2.deleteSubtree( t2.getNode( "B" ), false );
2393 if ( t2.getNumberOfExternalNodes() != 2 ) {
2396 t2.toNewHampshireX();
2397 PhylogenyNode n = t2.getNode( "A" );
2398 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2401 t2.deleteSubtree( t2.getNode( "A" ), false );
2402 if ( t2.getNumberOfExternalNodes() != 2 ) {
2405 t2.deleteSubtree( t2.getNode( "C" ), true );
2406 if ( t2.getNumberOfExternalNodes() != 1 ) {
2409 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2410 if ( t3.getNumberOfExternalNodes() != 4 ) {
2413 t3.deleteSubtree( t3.getNode( "B" ), true );
2414 if ( t3.getNumberOfExternalNodes() != 3 ) {
2417 n = t3.getNode( "A" );
2418 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2421 n = n.getNextExternalNode();
2422 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2425 t3.deleteSubtree( t3.getNode( "A" ), true );
2426 if ( t3.getNumberOfExternalNodes() != 2 ) {
2429 n = t3.getNode( "C" );
2430 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2433 t3.deleteSubtree( t3.getNode( "C" ), true );
2434 if ( t3.getNumberOfExternalNodes() != 1 ) {
2437 t3.deleteSubtree( t3.getNode( "D" ), true );
2438 if ( t3.getNumberOfExternalNodes() != 0 ) {
2441 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2442 if ( t4.getNumberOfExternalNodes() != 6 ) {
2445 t4.deleteSubtree( t4.getNode( "B2" ), true );
2446 if ( t4.getNumberOfExternalNodes() != 5 ) {
2449 String s = w.toNewHampshire( t4, false, true ).toString();
2450 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2453 t4.deleteSubtree( t4.getNode( "B11" ), true );
2454 if ( t4.getNumberOfExternalNodes() != 4 ) {
2457 t4.deleteSubtree( t4.getNode( "C" ), true );
2458 if ( t4.getNumberOfExternalNodes() != 3 ) {
2461 n = t4.getNode( "A" );
2462 n = n.getNextExternalNode();
2463 if ( !n.getName().equals( "B12" ) ) {
2466 n = n.getNextExternalNode();
2467 if ( !n.getName().equals( "D" ) ) {
2470 s = w.toNewHampshire( t4, false, true ).toString();
2471 if ( !s.equals( "((A,B12),D);" ) ) {
2474 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2475 t5.deleteSubtree( t5.getNode( "A" ), true );
2476 if ( t5.getNumberOfExternalNodes() != 5 ) {
2479 s = w.toNewHampshire( t5, false, true ).toString();
2480 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2483 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2484 t6.deleteSubtree( t6.getNode( "B11" ), true );
2485 if ( t6.getNumberOfExternalNodes() != 5 ) {
2488 s = w.toNewHampshire( t6, false, false ).toString();
2489 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2492 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2493 t7.deleteSubtree( t7.getNode( "B12" ), true );
2494 if ( t7.getNumberOfExternalNodes() != 5 ) {
2497 s = w.toNewHampshire( t7, false, true ).toString();
2498 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2501 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2502 t8.deleteSubtree( t8.getNode( "B2" ), true );
2503 if ( t8.getNumberOfExternalNodes() != 5 ) {
2506 s = w.toNewHampshire( t8, false, false ).toString();
2507 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2510 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2511 t9.deleteSubtree( t9.getNode( "C" ), true );
2512 if ( t9.getNumberOfExternalNodes() != 5 ) {
2515 s = w.toNewHampshire( t9, false, true ).toString();
2516 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2519 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2520 t10.deleteSubtree( t10.getNode( "D" ), true );
2521 if ( t10.getNumberOfExternalNodes() != 5 ) {
2524 s = w.toNewHampshire( t10, false, true ).toString();
2525 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2528 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2529 t11.deleteSubtree( t11.getNode( "A" ), true );
2530 if ( t11.getNumberOfExternalNodes() != 2 ) {
2533 s = w.toNewHampshire( t11, false, true ).toString();
2534 if ( !s.equals( "(B,C);" ) ) {
2537 t11.deleteSubtree( t11.getNode( "C" ), true );
2538 if ( t11.getNumberOfExternalNodes() != 1 ) {
2541 s = w.toNewHampshire( t11, false, false ).toString();
2542 if ( !s.equals( "B;" ) ) {
2545 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2546 t12.deleteSubtree( t12.getNode( "B2" ), true );
2547 if ( t12.getNumberOfExternalNodes() != 8 ) {
2550 s = w.toNewHampshire( t12, false, true ).toString();
2551 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2554 t12.deleteSubtree( t12.getNode( "B3" ), true );
2555 if ( t12.getNumberOfExternalNodes() != 7 ) {
2558 s = w.toNewHampshire( t12, false, true ).toString();
2559 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2562 t12.deleteSubtree( t12.getNode( "C3" ), true );
2563 if ( t12.getNumberOfExternalNodes() != 6 ) {
2566 s = w.toNewHampshire( t12, false, true ).toString();
2567 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2570 t12.deleteSubtree( t12.getNode( "A1" ), true );
2571 if ( t12.getNumberOfExternalNodes() != 5 ) {
2574 s = w.toNewHampshire( t12, false, true ).toString();
2575 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2578 t12.deleteSubtree( t12.getNode( "B1" ), true );
2579 if ( t12.getNumberOfExternalNodes() != 4 ) {
2582 s = w.toNewHampshire( t12, false, true ).toString();
2583 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2586 t12.deleteSubtree( t12.getNode( "A3" ), true );
2587 if ( t12.getNumberOfExternalNodes() != 3 ) {
2590 s = w.toNewHampshire( t12, false, true ).toString();
2591 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2594 t12.deleteSubtree( t12.getNode( "A2" ), true );
2595 if ( t12.getNumberOfExternalNodes() != 2 ) {
2598 s = w.toNewHampshire( t12, false, true ).toString();
2599 if ( !s.equals( "(C1,C2);" ) ) {
2602 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2603 t13.deleteSubtree( t13.getNode( "D" ), true );
2604 if ( t13.getNumberOfExternalNodes() != 4 ) {
2607 s = w.toNewHampshire( t13, false, true ).toString();
2608 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2611 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2612 t14.deleteSubtree( t14.getNode( "E" ), true );
2613 if ( t14.getNumberOfExternalNodes() != 5 ) {
2616 s = w.toNewHampshire( t14, false, true ).toString();
2617 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2620 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2621 t15.deleteSubtree( t15.getNode( "B2" ), true );
2622 if ( t15.getNumberOfExternalNodes() != 11 ) {
2625 t15.deleteSubtree( t15.getNode( "B1" ), true );
2626 if ( t15.getNumberOfExternalNodes() != 10 ) {
2629 t15.deleteSubtree( t15.getNode( "B3" ), true );
2630 if ( t15.getNumberOfExternalNodes() != 9 ) {
2633 t15.deleteSubtree( t15.getNode( "B4" ), true );
2634 if ( t15.getNumberOfExternalNodes() != 8 ) {
2637 t15.deleteSubtree( t15.getNode( "A1" ), true );
2638 if ( t15.getNumberOfExternalNodes() != 7 ) {
2641 t15.deleteSubtree( t15.getNode( "C4" ), true );
2642 if ( t15.getNumberOfExternalNodes() != 6 ) {
2646 catch ( final Exception e ) {
2647 e.printStackTrace( System.out );
2653 private static boolean testDescriptiveStatistics() {
2655 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2656 dss1.addValue( 82 );
2657 dss1.addValue( 78 );
2658 dss1.addValue( 70 );
2659 dss1.addValue( 58 );
2660 dss1.addValue( 42 );
2661 if ( dss1.getN() != 5 ) {
2664 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2667 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2670 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2673 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2676 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2679 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2682 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2685 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2688 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2691 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2694 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2697 dss1.addValue( 123 );
2698 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2701 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2704 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2707 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2708 dss2.addValue( -1.85 );
2709 dss2.addValue( 57.5 );
2710 dss2.addValue( 92.78 );
2711 dss2.addValue( 57.78 );
2712 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2715 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2718 final double[] a = dss2.getDataAsDoubleArray();
2719 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2722 dss2.addValue( -100 );
2723 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2726 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2729 final double[] ds = new double[ 14 ];
2744 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2745 if ( bins.length != 4 ) {
2748 if ( bins[ 0 ] != 2 ) {
2751 if ( bins[ 1 ] != 3 ) {
2754 if ( bins[ 2 ] != 4 ) {
2757 if ( bins[ 3 ] != 5 ) {
2760 final double[] ds1 = new double[ 9 ];
2770 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2771 if ( bins1.length != 4 ) {
2774 if ( bins1[ 0 ] != 2 ) {
2777 if ( bins1[ 1 ] != 3 ) {
2780 if ( bins1[ 2 ] != 0 ) {
2783 if ( bins1[ 3 ] != 4 ) {
2786 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2787 if ( bins1_1.length != 3 ) {
2790 if ( bins1_1[ 0 ] != 3 ) {
2793 if ( bins1_1[ 1 ] != 2 ) {
2796 if ( bins1_1[ 2 ] != 4 ) {
2799 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2800 if ( bins1_2.length != 3 ) {
2803 if ( bins1_2[ 0 ] != 2 ) {
2806 if ( bins1_2[ 1 ] != 2 ) {
2809 if ( bins1_2[ 2 ] != 2 ) {
2812 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2826 dss3.addValue( 10 );
2827 dss3.addValue( 10 );
2828 dss3.addValue( 10 );
2829 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2830 histo.toStringBuffer( 10, '=', 40, 5 );
2831 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2833 catch ( final Exception e ) {
2834 e.printStackTrace( System.out );
2840 private static boolean testDir( final String file ) {
2842 final File f = new File( file );
2843 if ( !f.exists() ) {
2846 if ( !f.isDirectory() ) {
2849 if ( !f.canRead() ) {
2853 catch ( final Exception e ) {
2859 private static boolean testExternalNodeRelatedMethods() {
2861 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2862 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2863 PhylogenyNode n = t1.getNode( "A" );
2864 n = n.getNextExternalNode();
2865 if ( !n.getName().equals( "B" ) ) {
2868 n = n.getNextExternalNode();
2869 if ( !n.getName().equals( "C" ) ) {
2872 n = n.getNextExternalNode();
2873 if ( !n.getName().equals( "D" ) ) {
2876 n = t1.getNode( "B" );
2877 while ( !n.isLastExternalNode() ) {
2878 n = n.getNextExternalNode();
2880 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2881 n = t2.getNode( "A" );
2882 n = n.getNextExternalNode();
2883 if ( !n.getName().equals( "B" ) ) {
2886 n = n.getNextExternalNode();
2887 if ( !n.getName().equals( "C" ) ) {
2890 n = n.getNextExternalNode();
2891 if ( !n.getName().equals( "D" ) ) {
2894 n = t2.getNode( "B" );
2895 while ( !n.isLastExternalNode() ) {
2896 n = n.getNextExternalNode();
2898 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2899 n = t3.getNode( "A" );
2900 n = n.getNextExternalNode();
2901 if ( !n.getName().equals( "B" ) ) {
2904 n = n.getNextExternalNode();
2905 if ( !n.getName().equals( "C" ) ) {
2908 n = n.getNextExternalNode();
2909 if ( !n.getName().equals( "D" ) ) {
2912 n = n.getNextExternalNode();
2913 if ( !n.getName().equals( "E" ) ) {
2916 n = n.getNextExternalNode();
2917 if ( !n.getName().equals( "F" ) ) {
2920 n = n.getNextExternalNode();
2921 if ( !n.getName().equals( "G" ) ) {
2924 n = n.getNextExternalNode();
2925 if ( !n.getName().equals( "H" ) ) {
2928 n = t3.getNode( "B" );
2929 while ( !n.isLastExternalNode() ) {
2930 n = n.getNextExternalNode();
2932 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2933 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2934 final PhylogenyNode node = iter.next();
2936 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2937 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2938 final PhylogenyNode node = iter.next();
2941 catch ( final Exception e ) {
2942 e.printStackTrace( System.out );
2948 private static boolean testGeneralTable() {
2950 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2951 t0.setValue( 3, 2, "23" );
2952 t0.setValue( 10, 1, "error" );
2953 t0.setValue( 10, 1, "110" );
2954 t0.setValue( 9, 1, "19" );
2955 t0.setValue( 1, 10, "101" );
2956 t0.setValue( 10, 10, "1010" );
2957 t0.setValue( 100, 10, "10100" );
2958 t0.setValue( 0, 0, "00" );
2959 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2962 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2965 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2968 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2971 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2974 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2977 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2980 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2983 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2986 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2987 t1.setValue( "3", "2", "23" );
2988 t1.setValue( "10", "1", "error" );
2989 t1.setValue( "10", "1", "110" );
2990 t1.setValue( "9", "1", "19" );
2991 t1.setValue( "1", "10", "101" );
2992 t1.setValue( "10", "10", "1010" );
2993 t1.setValue( "100", "10", "10100" );
2994 t1.setValue( "0", "0", "00" );
2995 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2996 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2999 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3002 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3005 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3008 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3011 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3014 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3017 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3020 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3023 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3027 catch ( final Exception e ) {
3028 e.printStackTrace( System.out );
3034 private static boolean testGetDistance() {
3036 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3037 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",
3038 new NHXParser() )[ 0 ];
3039 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3040 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3043 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3046 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3049 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3052 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3055 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3058 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3061 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3064 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3067 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3070 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3073 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3076 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3079 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3082 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3085 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3088 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3091 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3094 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3097 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3100 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3103 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3106 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3109 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3112 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3115 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3118 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3121 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3124 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3127 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3130 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3133 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",
3134 new NHXParser() )[ 0 ];
3135 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3138 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3141 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3144 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3147 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3150 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3153 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3156 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3159 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3162 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3165 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3169 catch ( final Exception e ) {
3170 e.printStackTrace( System.out );
3176 private static boolean testGetLCA() {
3178 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3179 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3180 new NHXParser() )[ 0 ];
3181 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3182 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3183 if ( !A.getName().equals( "A" ) ) {
3186 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3187 if ( !gh.getName().equals( "gh" ) ) {
3190 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3191 if ( !ab.getName().equals( "ab" ) ) {
3194 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3195 if ( !ab2.getName().equals( "ab" ) ) {
3198 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3199 if ( !gh2.getName().equals( "gh" ) ) {
3202 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3203 if ( !gh3.getName().equals( "gh" ) ) {
3206 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3207 if ( !abc.getName().equals( "abc" ) ) {
3210 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3211 if ( !abc2.getName().equals( "abc" ) ) {
3214 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3215 if ( !abcd.getName().equals( "abcd" ) ) {
3218 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3219 if ( !abcd2.getName().equals( "abcd" ) ) {
3222 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3223 if ( !abcdef.getName().equals( "abcdef" ) ) {
3226 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3227 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3230 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3231 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3234 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3235 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3238 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3239 if ( !abcde.getName().equals( "abcde" ) ) {
3242 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3243 if ( !abcde2.getName().equals( "abcde" ) ) {
3246 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3247 if ( !r.getName().equals( "abcdefgh" ) ) {
3250 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3251 if ( !r2.getName().equals( "abcdefgh" ) ) {
3254 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3255 if ( !r3.getName().equals( "abcdefgh" ) ) {
3258 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3259 if ( !abcde3.getName().equals( "abcde" ) ) {
3262 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3263 if ( !abcde4.getName().equals( "abcde" ) ) {
3266 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3267 if ( !ab3.getName().equals( "ab" ) ) {
3270 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3271 if ( !ab4.getName().equals( "ab" ) ) {
3274 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3275 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3276 if ( !cd.getName().equals( "cd" ) ) {
3279 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3280 if ( !cd2.getName().equals( "cd" ) ) {
3283 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3284 if ( !cde.getName().equals( "cde" ) ) {
3287 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3288 if ( !cde2.getName().equals( "cde" ) ) {
3291 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3292 if ( !cdef.getName().equals( "cdef" ) ) {
3295 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3296 if ( !cdef2.getName().equals( "cdef" ) ) {
3299 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3300 if ( !cdef3.getName().equals( "cdef" ) ) {
3303 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3304 if ( !rt.getName().equals( "r" ) ) {
3307 final Phylogeny p3 = factory
3308 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3309 new NHXParser() )[ 0 ];
3310 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3311 if ( !bc_3.getName().equals( "bc" ) ) {
3314 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3315 if ( !ac_3.getName().equals( "abc" ) ) {
3318 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3319 if ( !ad_3.getName().equals( "abcde" ) ) {
3322 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3323 if ( !af_3.getName().equals( "abcdef" ) ) {
3326 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3327 if ( !ag_3.getName().equals( "" ) ) {
3330 if ( !ag_3.isRoot() ) {
3333 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3334 if ( !al_3.getName().equals( "" ) ) {
3337 if ( !al_3.isRoot() ) {
3340 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3341 if ( !kl_3.getName().equals( "" ) ) {
3344 if ( !kl_3.isRoot() ) {
3347 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3348 if ( !fl_3.getName().equals( "" ) ) {
3351 if ( !fl_3.isRoot() ) {
3354 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3355 if ( !gk_3.getName().equals( "ghijk" ) ) {
3358 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3359 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3360 if ( !r_4.getName().equals( "r" ) ) {
3363 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3364 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3365 if ( !r_5.getName().equals( "root" ) ) {
3368 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3369 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3370 if ( !r_6.getName().equals( "rot" ) ) {
3373 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3374 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3375 if ( !r_7.getName().equals( "rott" ) ) {
3379 catch ( final Exception e ) {
3380 e.printStackTrace( System.out );
3386 private static boolean testHmmscanOutputParser() {
3387 final String test_dir = Test.PATH_TO_TEST_DATA;
3389 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3390 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3392 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3393 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3394 final List<Protein> domain_collections = parser2.parse();
3395 if ( parser2.getProteinsEncountered() != 4 ) {
3398 if ( domain_collections.size() != 4 ) {
3401 if ( parser2.getDomainsEncountered() != 69 ) {
3404 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3407 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3410 final Protein p1 = domain_collections.get( 0 );
3411 if ( p1.getNumberOfProteinDomains() != 15 ) {
3414 final Protein p4 = domain_collections.get( 3 );
3415 if ( p4.getNumberOfProteinDomains() != 1 ) {
3418 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3421 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3424 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3427 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3430 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3433 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3436 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3439 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3442 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3446 catch ( final Exception e ) {
3447 e.printStackTrace( System.out );
3453 private static boolean testLastExternalNodeMethods() {
3455 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3456 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3457 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3458 final PhylogenyNode n1 = t0.getNode( "A" );
3459 if ( n1.isLastExternalNode() ) {
3462 final PhylogenyNode n2 = t0.getNode( "B" );
3463 if ( n2.isLastExternalNode() ) {
3466 final PhylogenyNode n3 = t0.getNode( "C" );
3467 if ( n3.isLastExternalNode() ) {
3470 final PhylogenyNode n4 = t0.getNode( "D" );
3471 if ( !n4.isLastExternalNode() ) {
3475 catch ( final Exception e ) {
3476 e.printStackTrace( System.out );
3482 private static boolean testLevelOrderIterator() {
3484 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3485 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3486 PhylogenyNodeIterator it0;
3487 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3490 for( it0.reset(); it0.hasNext(); ) {
3493 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3494 if ( !it.next().getName().equals( "r" ) ) {
3497 if ( !it.next().getName().equals( "ab" ) ) {
3500 if ( !it.next().getName().equals( "cd" ) ) {
3503 if ( !it.next().getName().equals( "A" ) ) {
3506 if ( !it.next().getName().equals( "B" ) ) {
3509 if ( !it.next().getName().equals( "C" ) ) {
3512 if ( !it.next().getName().equals( "D" ) ) {
3515 if ( it.hasNext() ) {
3518 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",
3519 new NHXParser() )[ 0 ];
3520 PhylogenyNodeIterator it2;
3521 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3524 for( it2.reset(); it2.hasNext(); ) {
3527 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3528 if ( !it3.next().getName().equals( "r" ) ) {
3531 if ( !it3.next().getName().equals( "abc" ) ) {
3534 if ( !it3.next().getName().equals( "defg" ) ) {
3537 if ( !it3.next().getName().equals( "A" ) ) {
3540 if ( !it3.next().getName().equals( "B" ) ) {
3543 if ( !it3.next().getName().equals( "C" ) ) {
3546 if ( !it3.next().getName().equals( "D" ) ) {
3549 if ( !it3.next().getName().equals( "E" ) ) {
3552 if ( !it3.next().getName().equals( "F" ) ) {
3555 if ( !it3.next().getName().equals( "G" ) ) {
3558 if ( !it3.next().getName().equals( "1" ) ) {
3561 if ( !it3.next().getName().equals( "2" ) ) {
3564 if ( !it3.next().getName().equals( "3" ) ) {
3567 if ( !it3.next().getName().equals( "4" ) ) {
3570 if ( !it3.next().getName().equals( "5" ) ) {
3573 if ( !it3.next().getName().equals( "6" ) ) {
3576 if ( !it3.next().getName().equals( "f1" ) ) {
3579 if ( !it3.next().getName().equals( "f2" ) ) {
3582 if ( !it3.next().getName().equals( "f3" ) ) {
3585 if ( !it3.next().getName().equals( "a" ) ) {
3588 if ( !it3.next().getName().equals( "b" ) ) {
3591 if ( !it3.next().getName().equals( "f21" ) ) {
3594 if ( !it3.next().getName().equals( "X" ) ) {
3597 if ( !it3.next().getName().equals( "Y" ) ) {
3600 if ( !it3.next().getName().equals( "Z" ) ) {
3603 if ( it3.hasNext() ) {
3606 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3607 PhylogenyNodeIterator it4;
3608 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3611 for( it4.reset(); it4.hasNext(); ) {
3614 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3615 if ( !it5.next().getName().equals( "r" ) ) {
3618 if ( !it5.next().getName().equals( "A" ) ) {
3621 if ( !it5.next().getName().equals( "B" ) ) {
3624 if ( !it5.next().getName().equals( "C" ) ) {
3627 if ( !it5.next().getName().equals( "D" ) ) {
3630 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3631 PhylogenyNodeIterator it6;
3632 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3635 for( it6.reset(); it6.hasNext(); ) {
3638 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3639 if ( !it7.next().getName().equals( "A" ) ) {
3642 if ( it.hasNext() ) {
3646 catch ( final Exception e ) {
3647 e.printStackTrace( System.out );
3653 private static boolean testMidpointrooting() {
3655 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3656 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",
3657 new NHXParser() )[ 0 ];
3658 if ( !t1.isRooted() ) {
3661 PhylogenyMethods.midpointRoot( t1 );
3662 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3665 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3668 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3671 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3674 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3677 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3680 t1.reRoot( t1.getNode( "A" ) );
3681 PhylogenyMethods.midpointRoot( t1 );
3682 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3685 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3688 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3691 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3694 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3697 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3701 catch ( final Exception e ) {
3702 e.printStackTrace( System.out );
3708 private static boolean testNexusCharactersParsing() {
3710 final NexusCharactersParser parser = new NexusCharactersParser();
3711 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3713 String[] labels = parser.getCharStateLabels();
3714 if ( labels.length != 7 ) {
3717 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3720 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3723 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3726 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3729 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3732 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3735 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3738 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3740 labels = parser.getCharStateLabels();
3741 if ( labels.length != 7 ) {
3744 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3747 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3750 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3753 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3756 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3759 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3762 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3766 catch ( final Exception e ) {
3767 e.printStackTrace( System.out );
3773 private static boolean testNexusMatrixParsing() {
3775 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3776 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3778 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3779 if ( m.getNumberOfCharacters() != 9 ) {
3782 if ( m.getNumberOfIdentifiers() != 5 ) {
3785 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3788 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3791 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3794 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3797 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3800 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3803 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3806 // if ( labels.length != 7 ) {
3809 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3812 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3815 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3818 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3821 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3824 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3827 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3830 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3832 // labels = parser.getCharStateLabels();
3833 // if ( labels.length != 7 ) {
3836 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3839 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3842 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3845 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3848 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3851 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3854 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3858 catch ( final Exception e ) {
3859 e.printStackTrace( System.out );
3865 private static boolean testNexusTreeParsing() {
3867 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3868 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3869 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3870 if ( phylogenies.length != 1 ) {
3873 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3876 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3880 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3881 if ( phylogenies.length != 1 ) {
3884 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3887 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3891 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3892 if ( phylogenies.length != 1 ) {
3895 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3898 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3901 if ( phylogenies[ 0 ].isRooted() ) {
3905 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3906 if ( phylogenies.length != 18 ) {
3909 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3912 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3915 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3918 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3921 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3924 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3927 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3930 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3933 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3936 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3939 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3942 if ( phylogenies[ 8 ].isRooted() ) {
3945 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3948 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3951 if ( !phylogenies[ 9 ].isRooted() ) {
3954 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3957 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3960 if ( !phylogenies[ 10 ].isRooted() ) {
3963 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3966 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3969 if ( phylogenies[ 11 ].isRooted() ) {
3972 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
3975 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
3978 if ( !phylogenies[ 12 ].isRooted() ) {
3981 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
3984 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
3987 if ( !phylogenies[ 13 ].isRooted() ) {
3990 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
3993 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
3996 if ( !phylogenies[ 14 ].isRooted() ) {
3999 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4002 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4005 if ( phylogenies[ 15 ].isRooted() ) {
4008 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4011 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4014 if ( !phylogenies[ 16 ].isRooted() ) {
4017 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4020 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4023 if ( phylogenies[ 17 ].isRooted() ) {
4026 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4030 catch ( final Exception e ) {
4031 e.printStackTrace( System.out );
4037 private static boolean testNexusTreeParsingTranslating() {
4039 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4040 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4041 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4042 if ( phylogenies.length != 1 ) {
4045 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4048 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4051 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4054 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4057 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4058 .equals( "Aranaeus" ) ) {
4062 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4063 if ( phylogenies.length != 3 ) {
4066 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4069 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4072 if ( phylogenies[ 0 ].isRooted() ) {
4075 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4078 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4081 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4082 .equals( "Aranaeus" ) ) {
4085 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4088 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4091 if ( phylogenies[ 1 ].isRooted() ) {
4094 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4097 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4100 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4101 .equals( "Aranaeus" ) ) {
4104 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4107 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4110 if ( !phylogenies[ 2 ].isRooted() ) {
4113 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4116 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4119 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4120 .equals( "Aranaeus" ) ) {
4124 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4125 if ( phylogenies.length != 3 ) {
4128 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4131 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4134 if ( phylogenies[ 0 ].isRooted() ) {
4137 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4140 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4143 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4144 .equals( "Aranaeus" ) ) {
4147 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4150 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4153 if ( phylogenies[ 1 ].isRooted() ) {
4156 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4159 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4162 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4163 .equals( "Aranaeus" ) ) {
4166 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4169 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4172 if ( !phylogenies[ 2 ].isRooted() ) {
4175 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4178 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4181 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4182 .equals( "Aranaeus" ) ) {
4186 catch ( final Exception e ) {
4187 e.printStackTrace( System.out );
4193 private static boolean testNHParsing() {
4195 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4196 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4197 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4200 final NHXParser nhxp = new NHXParser();
4201 nhxp.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
4202 nhxp.setReplaceUnderscores( true );
4203 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4204 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4207 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4210 final Phylogeny p1b = factory
4211 .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 ",
4212 new NHXParser() )[ 0 ];
4213 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4216 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4219 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4220 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4221 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4222 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4223 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4224 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4225 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4226 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4227 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4228 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4229 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4230 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4231 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4233 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4236 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4239 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4242 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4245 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4246 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4247 final String p16_S = "((A,B),C)";
4248 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4249 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4252 final String p17_S = "(C,(A,B))";
4253 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4254 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4257 final String p18_S = "((A,B),(C,D))";
4258 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4259 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4262 final String p19_S = "(((A,B),C),D)";
4263 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4264 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4267 final String p20_S = "(A,(B,(C,D)))";
4268 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4269 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4272 final String p21_S = "(A,(B,(C,(D,E))))";
4273 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4274 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4277 final String p22_S = "((((A,B),C),D),E)";
4278 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4279 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4282 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4283 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4284 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4287 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4288 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4289 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4292 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4293 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4294 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4295 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4298 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4301 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4302 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4303 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4304 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4305 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4306 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4307 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4308 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4309 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4310 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4313 final String p26_S = "(A,B)ab";
4314 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4315 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4318 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4319 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4321 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4324 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4325 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4326 final String p28_S3 = "(A,B)ab";
4327 final String p28_S4 = "((((A,B),C),D),;E;)";
4328 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4330 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4333 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4336 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4339 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4342 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";
4343 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4344 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4347 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";
4348 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4349 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4352 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4353 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4354 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4357 final String p33_S = "A";
4358 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4359 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4362 final String p34_S = "B;";
4363 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4364 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4367 final String p35_S = "B:0.2";
4368 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4369 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4372 final String p36_S = "(A)";
4373 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4374 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4377 final String p37_S = "((A))";
4378 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4379 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4382 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4383 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4384 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4387 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4388 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4389 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4392 final String p40_S = "(A,B,C)";
4393 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4394 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4397 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4398 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4399 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4402 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4403 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4404 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4407 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)";
4408 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4409 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4412 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)))";
4413 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4414 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4417 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4418 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4419 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4422 final String p46_S = "";
4423 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4424 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4428 catch ( final Exception e ) {
4429 e.printStackTrace( System.out );
4435 private static boolean testNHXconversion() {
4437 final PhylogenyNode n1 = new PhylogenyNode();
4438 final PhylogenyNode n2 = new PhylogenyNode( "" );
4439 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4440 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4441 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]" );
4442 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]" );
4443 if ( !n1.toNewHampshireX().equals( "" ) ) {
4446 if ( !n2.toNewHampshireX().equals( "" ) ) {
4449 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4452 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4455 if ( !n5.toNewHampshireX()
4456 .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]" ) ) {
4459 if ( !n6.toNewHampshireX()
4460 .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]" ) ) {
4464 catch ( final Exception e ) {
4465 e.printStackTrace( System.out );
4471 private static boolean testNHXNodeParsing() {
4473 final PhylogenyNode n1 = new PhylogenyNode();
4474 final PhylogenyNode n2 = new PhylogenyNode( "" );
4475 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4476 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4477 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]" );
4478 if ( !n3.getName().equals( "n3" ) ) {
4481 if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4484 if ( n3.isDuplication() ) {
4487 if ( n3.isHasAssignedEvent() ) {
4490 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4493 if ( !n4.getName().equals( "n4" ) ) {
4496 if ( n4.getDistanceToParent() != 0.01 ) {
4499 if ( !n5.getName().equals( "n5" ) ) {
4502 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4505 if ( n5.getDistanceToParent() != 0.1 ) {
4508 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4511 if ( !n5.isDuplication() ) {
4514 if ( !n5.isHasAssignedEvent() ) {
4517 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4520 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4523 final PhylogenyNode n8 = new PhylogenyNode( "n8_ECOLI/12:0.01",
4524 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4525 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4528 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4531 final PhylogenyNode n9 = new PhylogenyNode( "n9_ECOLI/12=12:0.01",
4532 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4533 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4536 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4539 final PhylogenyNode n10 = new PhylogenyNode( "n10.ECOLI", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4540 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4543 final PhylogenyNode n20 = new PhylogenyNode( "n20_ECOLI/1-2",
4544 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4545 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4548 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4551 final PhylogenyNode n20x = new PhylogenyNode( "n20_ECOL1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4552 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4555 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4558 final PhylogenyNode n20xx = new PhylogenyNode( "n20_eCOL1/1-2",
4559 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4560 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4563 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4566 final PhylogenyNode n20xxx = new PhylogenyNode( "n20_ecoli/1-2",
4567 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4568 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4571 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4574 final PhylogenyNode n20xxxx = new PhylogenyNode( "n20_Ecoli/1-2",
4575 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4576 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4579 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4582 final PhylogenyNode n21 = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4583 if ( !n21.getName().equals( "n21_PIG" ) ) {
4586 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4589 final PhylogenyNode n21x = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4590 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4593 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4596 final PhylogenyNode n22 = new PhylogenyNode( "n22/PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4597 if ( !n22.getName().equals( "n22/PIG" ) ) {
4600 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4603 final PhylogenyNode n23 = new PhylogenyNode( "n23/PIG_1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4604 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4607 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4610 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4611 final PhylogenyNode a = new PhylogenyNode( "n10_ECOLI/1-2",
4612 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4613 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4616 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4619 final PhylogenyNode b = new PhylogenyNode( "n10_ECOLI1/1-2",
4620 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4621 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4624 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4627 final PhylogenyNode c = new PhylogenyNode( "n10_RATAF12/1000-2000",
4628 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4629 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4632 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4635 final PhylogenyNode d = new PhylogenyNode( "n10_RAT1/1-2",
4636 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4637 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4640 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4643 final PhylogenyNode e = new PhylogenyNode( "n10_RAT1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4644 if ( !e.getName().equals( "n10_RAT1" ) ) {
4647 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4651 final PhylogenyNode n11 = new PhylogenyNode( "n111111_ECOLI/jdj:0.4",
4652 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4653 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4656 if ( n11.getDistanceToParent() != 0.4 ) {
4659 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4662 final PhylogenyNode n12 = new PhylogenyNode( "n111111-ECOLI---/jdj:0.4",
4663 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4664 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4667 if ( n12.getDistanceToParent() != 0.4 ) {
4670 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4673 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4674 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4675 if ( !tvu1.getRef().equals( "tag1" ) ) {
4678 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4681 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4684 if ( !tvu1.getValue().equals( "value1" ) ) {
4687 if ( !tvu3.getRef().equals( "tag3" ) ) {
4690 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4693 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4696 if ( !tvu3.getValue().equals( "value3" ) ) {
4699 if ( n1.getName().compareTo( "" ) != 0 ) {
4702 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4705 if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4708 if ( n2.getName().compareTo( "" ) != 0 ) {
4711 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4714 if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4717 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]" );
4718 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4721 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4724 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4727 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4730 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4733 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4736 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4739 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4742 final PhylogenyNode nx = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4743 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4746 final PhylogenyNode nx2 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4747 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4750 final PhylogenyNode n13 = new PhylogenyNode( "blah_12345/1-2",
4751 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4752 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4755 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4758 final PhylogenyNode n14 = new PhylogenyNode( "blah_12X45/1-2",
4759 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4760 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4763 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4766 final PhylogenyNode n15 = new PhylogenyNode( "something_wicked[123]",
4767 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4768 if ( !n15.getName().equals( "something_wicked" ) ) {
4771 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4774 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4777 final PhylogenyNode n16 = new PhylogenyNode( "something_wicked2[9]",
4778 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4779 if ( !n16.getName().equals( "something_wicked2" ) ) {
4782 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4785 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4788 final PhylogenyNode n17 = new PhylogenyNode( "something_wicked3[a]",
4789 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4790 if ( !n17.getName().equals( "something_wicked3" ) ) {
4793 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4796 final PhylogenyNode n18 = new PhylogenyNode( ":0.5[91]", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4797 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4800 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4803 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4807 catch ( final Exception e ) {
4808 e.printStackTrace( System.out );
4814 private static boolean testNHXParsing() {
4816 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4817 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4818 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4821 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]";
4822 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4823 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4826 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]";
4827 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4828 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4831 final Phylogeny[] p3 = factory
4832 .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]",
4834 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4837 final Phylogeny[] p4 = factory
4838 .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(]",
4840 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4843 final Phylogeny[] p5 = factory
4844 .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(((]",
4846 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4849 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)";
4850 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)";
4851 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4852 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4855 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)))";
4856 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)))";
4857 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4858 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4861 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]) ))[,,, ])))))))";
4862 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4863 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4864 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4867 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4868 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]" ) ) {
4871 final Phylogeny p10 = factory
4872 .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]",
4873 new NHXParser() )[ 0 ];
4874 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]" ) ) {
4878 catch ( final Exception e ) {
4879 e.printStackTrace( System.out );
4885 private static boolean testNHXParsingQuotes() {
4887 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4888 final NHXParser p = new NHXParser();
4889 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4890 if ( phylogenies_0.length != 5 ) {
4893 final Phylogeny phy = phylogenies_0[ 4 ];
4894 if ( phy.getNumberOfExternalNodes() != 7 ) {
4897 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4900 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4903 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4904 .getScientificName().equals( "hsapiens" ) ) {
4907 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4910 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4913 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4916 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4919 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4922 final NHXParser p1p = new NHXParser();
4923 p1p.setIgnoreQuotes( true );
4924 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4925 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4928 final NHXParser p2p = new NHXParser();
4929 p1p.setIgnoreQuotes( false );
4930 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4931 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4934 final NHXParser p3p = new NHXParser();
4935 p3p.setIgnoreQuotes( false );
4936 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4937 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4940 final NHXParser p4p = new NHXParser();
4941 p4p.setIgnoreQuotes( false );
4942 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4943 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
4946 final Phylogeny p10 = factory
4947 .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]",
4948 new NHXParser() )[ 0 ];
4949 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]";
4950 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
4953 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
4954 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
4958 final Phylogeny p12 = factory
4959 .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]",
4960 new NHXParser() )[ 0 ];
4961 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]";
4962 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
4965 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
4966 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
4969 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;";
4970 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
4973 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
4974 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
4978 catch ( final Exception e ) {
4979 e.printStackTrace( System.out );
4985 private static boolean testPhylogenyBranch() {
4987 final PhylogenyNode a1 = new PhylogenyNode( "a" );
4988 final PhylogenyNode b1 = new PhylogenyNode( "b" );
4989 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
4990 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
4991 if ( !a1b1.equals( a1b1 ) ) {
4994 if ( !a1b1.equals( b1a1 ) ) {
4997 if ( !b1a1.equals( a1b1 ) ) {
5000 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5001 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5002 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5003 if ( a1_b1.equals( b1_a1 ) ) {
5006 if ( a1_b1.equals( a1_b1_ ) ) {
5009 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5010 if ( !a1_b1.equals( b1_a1_ ) ) {
5013 if ( a1_b1_.equals( b1_a1_ ) ) {
5016 if ( !a1_b1_.equals( b1_a1 ) ) {
5020 catch ( final Exception e ) {
5021 e.printStackTrace( System.out );
5027 private static boolean testPhyloXMLparsingOfDistributionElement() {
5029 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5030 PhyloXmlParser xml_parser = null;
5032 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5034 catch ( final Exception e ) {
5035 // Do nothing -- means were not running from jar.
5037 if ( xml_parser == null ) {
5038 xml_parser = new PhyloXmlParser();
5039 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5040 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5043 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5046 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5048 if ( xml_parser.getErrorCount() > 0 ) {
5049 System.out.println( xml_parser.getErrorMessages().toString() );
5052 if ( phylogenies_0.length != 1 ) {
5055 final Phylogeny t1 = phylogenies_0[ 0 ];
5056 PhylogenyNode n = null;
5057 Distribution d = null;
5058 n = t1.getNode( "root node" );
5059 if ( !n.getNodeData().isHasDistribution() ) {
5062 if ( n.getNodeData().getDistributions().size() != 1 ) {
5065 d = n.getNodeData().getDistribution();
5066 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5069 if ( d.getPoints().size() != 1 ) {
5072 if ( d.getPolygons() != null ) {
5075 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5078 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5081 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5084 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5087 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5090 n = t1.getNode( "node a" );
5091 if ( !n.getNodeData().isHasDistribution() ) {
5094 if ( n.getNodeData().getDistributions().size() != 2 ) {
5097 d = n.getNodeData().getDistribution( 1 );
5098 if ( !d.getDesc().equals( "San Diego" ) ) {
5101 if ( d.getPoints().size() != 1 ) {
5104 if ( d.getPolygons() != null ) {
5107 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5110 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5113 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5116 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5119 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5122 n = t1.getNode( "node bb" );
5123 if ( !n.getNodeData().isHasDistribution() ) {
5126 if ( n.getNodeData().getDistributions().size() != 1 ) {
5129 d = n.getNodeData().getDistribution( 0 );
5130 if ( d.getPoints().size() != 3 ) {
5133 if ( d.getPolygons().size() != 2 ) {
5136 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5139 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5142 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5145 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5148 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5151 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5154 Polygon p = d.getPolygons().get( 0 );
5155 if ( p.getPoints().size() != 3 ) {
5158 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5161 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5164 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5167 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5170 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5173 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5176 p = d.getPolygons().get( 1 );
5177 if ( p.getPoints().size() != 3 ) {
5180 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5183 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5186 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5190 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5191 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5192 if ( rt.length != 1 ) {
5195 final Phylogeny t1_rt = rt[ 0 ];
5196 n = t1_rt.getNode( "root node" );
5197 if ( !n.getNodeData().isHasDistribution() ) {
5200 if ( n.getNodeData().getDistributions().size() != 1 ) {
5203 d = n.getNodeData().getDistribution();
5204 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5207 if ( d.getPoints().size() != 1 ) {
5210 if ( d.getPolygons() != null ) {
5213 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5216 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5219 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5222 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5225 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5228 n = t1_rt.getNode( "node a" );
5229 if ( !n.getNodeData().isHasDistribution() ) {
5232 if ( n.getNodeData().getDistributions().size() != 2 ) {
5235 d = n.getNodeData().getDistribution( 1 );
5236 if ( !d.getDesc().equals( "San Diego" ) ) {
5239 if ( d.getPoints().size() != 1 ) {
5242 if ( d.getPolygons() != null ) {
5245 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5248 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5251 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5254 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5257 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5260 n = t1_rt.getNode( "node bb" );
5261 if ( !n.getNodeData().isHasDistribution() ) {
5264 if ( n.getNodeData().getDistributions().size() != 1 ) {
5267 d = n.getNodeData().getDistribution( 0 );
5268 if ( d.getPoints().size() != 3 ) {
5271 if ( d.getPolygons().size() != 2 ) {
5274 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5277 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5280 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5283 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5286 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5289 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5292 p = d.getPolygons().get( 0 );
5293 if ( p.getPoints().size() != 3 ) {
5296 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5299 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5302 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5305 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5308 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5311 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5314 p = d.getPolygons().get( 1 );
5315 if ( p.getPoints().size() != 3 ) {
5318 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5321 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5324 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5328 catch ( final Exception e ) {
5329 e.printStackTrace( System.out );
5335 private static boolean testPostOrderIterator() {
5337 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5338 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5339 PhylogenyNodeIterator it0;
5340 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5343 for( it0.reset(); it0.hasNext(); ) {
5346 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5347 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5348 if ( !it.next().getName().equals( "A" ) ) {
5351 if ( !it.next().getName().equals( "B" ) ) {
5354 if ( !it.next().getName().equals( "ab" ) ) {
5357 if ( !it.next().getName().equals( "C" ) ) {
5360 if ( !it.next().getName().equals( "D" ) ) {
5363 if ( !it.next().getName().equals( "cd" ) ) {
5366 if ( !it.next().getName().equals( "abcd" ) ) {
5369 if ( !it.next().getName().equals( "E" ) ) {
5372 if ( !it.next().getName().equals( "F" ) ) {
5375 if ( !it.next().getName().equals( "ef" ) ) {
5378 if ( !it.next().getName().equals( "G" ) ) {
5381 if ( !it.next().getName().equals( "H" ) ) {
5384 if ( !it.next().getName().equals( "gh" ) ) {
5387 if ( !it.next().getName().equals( "efgh" ) ) {
5390 if ( !it.next().getName().equals( "r" ) ) {
5393 if ( it.hasNext() ) {
5397 catch ( final Exception e ) {
5398 e.printStackTrace( System.out );
5404 private static boolean testPreOrderIterator() {
5406 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5407 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5408 PhylogenyNodeIterator it0;
5409 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5412 for( it0.reset(); it0.hasNext(); ) {
5415 PhylogenyNodeIterator it = t0.iteratorPreorder();
5416 if ( !it.next().getName().equals( "r" ) ) {
5419 if ( !it.next().getName().equals( "ab" ) ) {
5422 if ( !it.next().getName().equals( "A" ) ) {
5425 if ( !it.next().getName().equals( "B" ) ) {
5428 if ( !it.next().getName().equals( "cd" ) ) {
5431 if ( !it.next().getName().equals( "C" ) ) {
5434 if ( !it.next().getName().equals( "D" ) ) {
5437 if ( it.hasNext() ) {
5440 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5441 it = t1.iteratorPreorder();
5442 if ( !it.next().getName().equals( "r" ) ) {
5445 if ( !it.next().getName().equals( "abcd" ) ) {
5448 if ( !it.next().getName().equals( "ab" ) ) {
5451 if ( !it.next().getName().equals( "A" ) ) {
5454 if ( !it.next().getName().equals( "B" ) ) {
5457 if ( !it.next().getName().equals( "cd" ) ) {
5460 if ( !it.next().getName().equals( "C" ) ) {
5463 if ( !it.next().getName().equals( "D" ) ) {
5466 if ( !it.next().getName().equals( "efgh" ) ) {
5469 if ( !it.next().getName().equals( "ef" ) ) {
5472 if ( !it.next().getName().equals( "E" ) ) {
5475 if ( !it.next().getName().equals( "F" ) ) {
5478 if ( !it.next().getName().equals( "gh" ) ) {
5481 if ( !it.next().getName().equals( "G" ) ) {
5484 if ( !it.next().getName().equals( "H" ) ) {
5487 if ( it.hasNext() ) {
5491 catch ( final Exception e ) {
5492 e.printStackTrace( System.out );
5498 private static boolean testPropertiesMap() {
5500 final PropertiesMap pm = new PropertiesMap();
5501 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5502 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5503 final Property p2 = new Property( "something:else",
5505 "improbable:research",
5508 pm.addProperty( p0 );
5509 pm.addProperty( p1 );
5510 pm.addProperty( p2 );
5511 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5514 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5517 if ( pm.getProperties().size() != 3 ) {
5520 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5523 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5526 if ( pm.getProperties().size() != 3 ) {
5529 pm.removeProperty( "dimensions:diameter" );
5530 if ( pm.getProperties().size() != 2 ) {
5533 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5536 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5540 catch ( final Exception e ) {
5541 e.printStackTrace( System.out );
5547 private static boolean testReIdMethods() {
5549 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5550 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5551 final int count = PhylogenyNode.getNodeCount();
5553 if ( p.getNode( "r" ).getId() != count ) {
5556 if ( p.getNode( "A" ).getId() != count + 1 ) {
5559 if ( p.getNode( "B" ).getId() != count + 1 ) {
5562 if ( p.getNode( "C" ).getId() != count + 1 ) {
5565 if ( p.getNode( "1" ).getId() != count + 2 ) {
5568 if ( p.getNode( "2" ).getId() != count + 2 ) {
5571 if ( p.getNode( "3" ).getId() != count + 2 ) {
5574 if ( p.getNode( "4" ).getId() != count + 2 ) {
5577 if ( p.getNode( "5" ).getId() != count + 2 ) {
5580 if ( p.getNode( "6" ).getId() != count + 2 ) {
5583 if ( p.getNode( "a" ).getId() != count + 3 ) {
5586 if ( p.getNode( "b" ).getId() != count + 3 ) {
5589 if ( p.getNode( "X" ).getId() != count + 4 ) {
5592 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5595 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5599 catch ( final Exception e ) {
5600 e.printStackTrace( System.out );
5606 private static boolean testRerooting() {
5608 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5609 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",
5610 new NHXParser() )[ 0 ];
5611 if ( !t1.isRooted() ) {
5614 t1.reRoot( t1.getNode( "D" ) );
5615 t1.reRoot( t1.getNode( "CD" ) );
5616 t1.reRoot( t1.getNode( "A" ) );
5617 t1.reRoot( t1.getNode( "B" ) );
5618 t1.reRoot( t1.getNode( "AB" ) );
5619 t1.reRoot( t1.getNode( "D" ) );
5620 t1.reRoot( t1.getNode( "C" ) );
5621 t1.reRoot( t1.getNode( "CD" ) );
5622 t1.reRoot( t1.getNode( "A" ) );
5623 t1.reRoot( t1.getNode( "B" ) );
5624 t1.reRoot( t1.getNode( "AB" ) );
5625 t1.reRoot( t1.getNode( "D" ) );
5626 t1.reRoot( t1.getNode( "D" ) );
5627 t1.reRoot( t1.getNode( "C" ) );
5628 t1.reRoot( t1.getNode( "A" ) );
5629 t1.reRoot( t1.getNode( "B" ) );
5630 t1.reRoot( t1.getNode( "AB" ) );
5631 t1.reRoot( t1.getNode( "C" ) );
5632 t1.reRoot( t1.getNode( "D" ) );
5633 t1.reRoot( t1.getNode( "CD" ) );
5634 t1.reRoot( t1.getNode( "D" ) );
5635 t1.reRoot( t1.getNode( "A" ) );
5636 t1.reRoot( t1.getNode( "B" ) );
5637 t1.reRoot( t1.getNode( "AB" ) );
5638 t1.reRoot( t1.getNode( "C" ) );
5639 t1.reRoot( t1.getNode( "D" ) );
5640 t1.reRoot( t1.getNode( "CD" ) );
5641 t1.reRoot( t1.getNode( "D" ) );
5642 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5645 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5648 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5651 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5654 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5657 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5660 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",
5661 new NHXParser() )[ 0 ];
5662 t2.reRoot( t2.getNode( "A" ) );
5663 t2.reRoot( t2.getNode( "D" ) );
5664 t2.reRoot( t2.getNode( "ABC" ) );
5665 t2.reRoot( t2.getNode( "A" ) );
5666 t2.reRoot( t2.getNode( "B" ) );
5667 t2.reRoot( t2.getNode( "D" ) );
5668 t2.reRoot( t2.getNode( "C" ) );
5669 t2.reRoot( t2.getNode( "ABC" ) );
5670 t2.reRoot( t2.getNode( "A" ) );
5671 t2.reRoot( t2.getNode( "B" ) );
5672 t2.reRoot( t2.getNode( "AB" ) );
5673 t2.reRoot( t2.getNode( "AB" ) );
5674 t2.reRoot( t2.getNode( "D" ) );
5675 t2.reRoot( t2.getNode( "C" ) );
5676 t2.reRoot( t2.getNode( "B" ) );
5677 t2.reRoot( t2.getNode( "AB" ) );
5678 t2.reRoot( t2.getNode( "D" ) );
5679 t2.reRoot( t2.getNode( "D" ) );
5680 t2.reRoot( t2.getNode( "ABC" ) );
5681 t2.reRoot( t2.getNode( "A" ) );
5682 t2.reRoot( t2.getNode( "B" ) );
5683 t2.reRoot( t2.getNode( "AB" ) );
5684 t2.reRoot( t2.getNode( "D" ) );
5685 t2.reRoot( t2.getNode( "C" ) );
5686 t2.reRoot( t2.getNode( "ABC" ) );
5687 t2.reRoot( t2.getNode( "A" ) );
5688 t2.reRoot( t2.getNode( "B" ) );
5689 t2.reRoot( t2.getNode( "AB" ) );
5690 t2.reRoot( t2.getNode( "D" ) );
5691 t2.reRoot( t2.getNode( "D" ) );
5692 t2.reRoot( t2.getNode( "C" ) );
5693 t2.reRoot( t2.getNode( "A" ) );
5694 t2.reRoot( t2.getNode( "B" ) );
5695 t2.reRoot( t2.getNode( "AB" ) );
5696 t2.reRoot( t2.getNode( "C" ) );
5697 t2.reRoot( t2.getNode( "D" ) );
5698 t2.reRoot( t2.getNode( "ABC" ) );
5699 t2.reRoot( t2.getNode( "D" ) );
5700 t2.reRoot( t2.getNode( "A" ) );
5701 t2.reRoot( t2.getNode( "B" ) );
5702 t2.reRoot( t2.getNode( "AB" ) );
5703 t2.reRoot( t2.getNode( "C" ) );
5704 t2.reRoot( t2.getNode( "D" ) );
5705 t2.reRoot( t2.getNode( "ABC" ) );
5706 t2.reRoot( t2.getNode( "D" ) );
5707 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5710 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5713 t2.reRoot( t2.getNode( "ABC" ) );
5714 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5717 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5720 t2.reRoot( t2.getNode( "AB" ) );
5721 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5724 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5727 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5730 t2.reRoot( t2.getNode( "AB" ) );
5731 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5734 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5737 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5740 t2.reRoot( t2.getNode( "D" ) );
5741 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5744 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5747 t2.reRoot( t2.getNode( "ABC" ) );
5748 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5751 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5754 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5755 new NHXParser() )[ 0 ];
5756 t3.reRoot( t3.getNode( "B" ) );
5757 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5760 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5763 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5766 t3.reRoot( t3.getNode( "B" ) );
5767 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5770 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5773 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5776 t3.reRoot( t3.getRoot() );
5777 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5780 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5783 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5787 catch ( final Exception e ) {
5788 e.printStackTrace( System.out );
5794 private static boolean testSDIse() {
5796 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5797 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5798 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5799 gene1.setRooted( true );
5800 species1.setRooted( true );
5801 final SDI sdi = new SDIse( gene1, species1 );
5802 if ( !gene1.getRoot().isDuplication() ) {
5805 final Phylogeny species2 = factory
5806 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5807 new NHXParser() )[ 0 ];
5808 final Phylogeny gene2 = factory
5809 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5810 new NHXParser() )[ 0 ];
5811 species2.setRooted( true );
5812 gene2.setRooted( true );
5813 final SDI sdi2 = new SDIse( gene2, species2 );
5814 if ( sdi2.getDuplicationsSum() != 0 ) {
5817 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5820 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5823 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5826 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5829 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5832 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5835 final Phylogeny species3 = factory
5836 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5837 new NHXParser() )[ 0 ];
5838 final Phylogeny gene3 = factory
5839 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5840 new NHXParser() )[ 0 ];
5841 species3.setRooted( true );
5842 gene3.setRooted( true );
5843 final SDI sdi3 = new SDIse( gene3, species3 );
5844 if ( sdi3.getDuplicationsSum() != 1 ) {
5847 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5850 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5853 final Phylogeny species4 = factory
5854 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5855 new NHXParser() )[ 0 ];
5856 final Phylogeny gene4 = factory
5857 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5858 new NHXParser() )[ 0 ];
5859 species4.setRooted( true );
5860 gene4.setRooted( true );
5861 final SDI sdi4 = new SDIse( gene4, species4 );
5862 if ( sdi4.getDuplicationsSum() != 1 ) {
5865 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5868 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5871 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5874 if ( species4.getNumberOfExternalNodes() != 6 ) {
5877 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5880 final Phylogeny species5 = factory
5881 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5882 new NHXParser() )[ 0 ];
5883 final Phylogeny gene5 = factory
5884 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5885 new NHXParser() )[ 0 ];
5886 species5.setRooted( true );
5887 gene5.setRooted( true );
5888 final SDI sdi5 = new SDIse( gene5, species5 );
5889 if ( sdi5.getDuplicationsSum() != 2 ) {
5892 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
5895 if ( !gene5.getNode( "adc" ).isDuplication() ) {
5898 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
5901 if ( species5.getNumberOfExternalNodes() != 6 ) {
5904 if ( gene5.getNumberOfExternalNodes() != 6 ) {
5907 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
5908 // Conjecture for Comparing Molecular Phylogenies"
5909 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
5910 final Phylogeny species6 = factory
5911 .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,"
5912 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
5913 new NHXParser() )[ 0 ];
5914 final Phylogeny gene6 = factory
5915 .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,"
5916 + "((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,"
5917 + "(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;",
5918 new NHXParser() )[ 0 ];
5919 species6.setRooted( true );
5920 gene6.setRooted( true );
5921 final SDI sdi6 = new SDIse( gene6, species6 );
5922 if ( sdi6.getDuplicationsSum() != 3 ) {
5925 if ( !gene6.getNode( "r" ).isDuplication() ) {
5928 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
5931 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
5934 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
5937 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
5940 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
5943 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
5946 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
5949 sdi6.computeMappingCostL();
5950 if ( sdi6.computeMappingCostL() != 17 ) {
5953 if ( species6.getNumberOfExternalNodes() != 9 ) {
5956 if ( gene6.getNumberOfExternalNodes() != 9 ) {
5959 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
5960 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
5961 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
5962 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
5963 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
5964 species7.setRooted( true );
5965 final Phylogeny gene7_1 = Test
5966 .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])" );
5967 gene7_1.setRooted( true );
5968 final SDI sdi7 = new SDIse( gene7_1, species7 );
5969 if ( sdi7.getDuplicationsSum() != 0 ) {
5972 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
5975 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
5978 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
5981 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
5984 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
5987 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
5990 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
5993 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
5996 final Phylogeny gene7_2 = Test
5997 .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])" );
5998 gene7_2.setRooted( true );
5999 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6000 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6003 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6006 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6009 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6012 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6015 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6018 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6021 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6024 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6027 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6031 catch ( final Exception e ) {
6037 private static boolean testSDIunrooted() {
6039 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6040 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6041 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6042 final Iterator<PhylogenyBranch> iter = l.iterator();
6043 PhylogenyBranch br = iter.next();
6044 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6047 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6051 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6054 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6058 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6061 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6065 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6068 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6072 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6075 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6079 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6082 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6086 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6089 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6093 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6096 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6100 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6103 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6107 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6110 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6114 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6117 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6121 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6124 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6128 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6131 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6135 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6138 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6142 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6145 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6148 if ( iter.hasNext() ) {
6151 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6152 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6153 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6155 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6158 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6162 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6165 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6169 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6172 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6175 if ( iter1.hasNext() ) {
6178 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6179 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6180 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6182 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6185 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6189 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6192 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6196 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6199 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6202 if ( iter2.hasNext() ) {
6205 final Phylogeny species0 = factory
6206 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6207 new NHXParser() )[ 0 ];
6208 final Phylogeny gene1 = factory
6209 .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])",
6210 new NHXParser() )[ 0 ];
6211 species0.setRooted( true );
6212 gene1.setRooted( true );
6213 final SDIR sdi_unrooted = new SDIR();
6214 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6215 if ( sdi_unrooted.getCount() != 1 ) {
6218 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6221 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6224 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6227 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6230 final Phylogeny gene2 = factory
6231 .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])",
6232 new NHXParser() )[ 0 ];
6233 gene2.setRooted( true );
6234 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6235 if ( sdi_unrooted.getCount() != 1 ) {
6238 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6241 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6244 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6247 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6250 final Phylogeny species6 = factory
6251 .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,"
6252 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6253 new NHXParser() )[ 0 ];
6254 final Phylogeny gene6 = factory
6255 .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],"
6256 + "(((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],"
6257 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6258 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6259 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6260 new NHXParser() )[ 0 ];
6261 species6.setRooted( true );
6262 gene6.setRooted( true );
6263 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6264 if ( sdi_unrooted.getCount() != 1 ) {
6267 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6270 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6273 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6276 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6279 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6282 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6285 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6288 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6291 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6294 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6297 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6300 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6304 final Phylogeny species7 = factory
6305 .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,"
6306 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6307 new NHXParser() )[ 0 ];
6308 final Phylogeny gene7 = factory
6309 .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],"
6310 + "(((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],"
6311 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6312 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6313 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6314 new NHXParser() )[ 0 ];
6315 species7.setRooted( true );
6316 gene7.setRooted( true );
6317 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6318 if ( sdi_unrooted.getCount() != 1 ) {
6321 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6324 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6327 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6330 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6333 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6336 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6339 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6342 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6345 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6348 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6351 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6354 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6358 final Phylogeny species8 = factory
6359 .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,"
6360 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6361 new NHXParser() )[ 0 ];
6362 final Phylogeny gene8 = factory
6363 .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],"
6364 + "(((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],"
6365 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6366 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6367 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6368 new NHXParser() )[ 0 ];
6369 species8.setRooted( true );
6370 gene8.setRooted( true );
6371 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6372 if ( sdi_unrooted.getCount() != 1 ) {
6375 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6378 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6381 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6384 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6387 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6390 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6393 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6396 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6399 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6402 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6405 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6408 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6413 catch ( final Exception e ) {
6414 e.printStackTrace( System.out );
6420 private static boolean testSplit() {
6422 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6423 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6424 //Archaeopteryx.createApplication( p0 );
6425 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6426 ex.add( new PhylogenyNode( "A" ) );
6427 ex.add( new PhylogenyNode( "B" ) );
6428 ex.add( new PhylogenyNode( "C" ) );
6429 ex.add( new PhylogenyNode( "D" ) );
6430 ex.add( new PhylogenyNode( "E" ) );
6431 ex.add( new PhylogenyNode( "F" ) );
6432 ex.add( new PhylogenyNode( "G" ) );
6433 ex.add( new PhylogenyNode( "X" ) );
6434 ex.add( new PhylogenyNode( "Y" ) );
6435 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6436 // System.out.println( s0.toString() );
6438 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6439 query_nodes.add( new PhylogenyNode( "A" ) );
6440 query_nodes.add( new PhylogenyNode( "B" ) );
6441 if ( s0.match( query_nodes ) ) {
6444 query_nodes = new HashSet<PhylogenyNode>();
6445 query_nodes.add( new PhylogenyNode( "A" ) );
6446 query_nodes.add( new PhylogenyNode( "B" ) );
6447 query_nodes.add( new PhylogenyNode( "C" ) );
6448 query_nodes.add( new PhylogenyNode( "D" ) );
6449 query_nodes.add( new PhylogenyNode( "E" ) );
6450 query_nodes.add( new PhylogenyNode( "F" ) );
6451 query_nodes.add( new PhylogenyNode( "G" ) );
6452 if ( !s0.match( query_nodes ) ) {
6456 query_nodes = new HashSet<PhylogenyNode>();
6457 query_nodes.add( new PhylogenyNode( "A" ) );
6458 query_nodes.add( new PhylogenyNode( "B" ) );
6459 query_nodes.add( new PhylogenyNode( "C" ) );
6460 if ( !s0.match( query_nodes ) ) {
6464 query_nodes = new HashSet<PhylogenyNode>();
6465 query_nodes.add( new PhylogenyNode( "D" ) );
6466 query_nodes.add( new PhylogenyNode( "E" ) );
6467 query_nodes.add( new PhylogenyNode( "F" ) );
6468 query_nodes.add( new PhylogenyNode( "G" ) );
6469 if ( !s0.match( query_nodes ) ) {
6473 query_nodes = new HashSet<PhylogenyNode>();
6474 query_nodes.add( new PhylogenyNode( "A" ) );
6475 query_nodes.add( new PhylogenyNode( "B" ) );
6476 query_nodes.add( new PhylogenyNode( "C" ) );
6477 query_nodes.add( new PhylogenyNode( "D" ) );
6478 if ( !s0.match( query_nodes ) ) {
6482 query_nodes = new HashSet<PhylogenyNode>();
6483 query_nodes.add( new PhylogenyNode( "E" ) );
6484 query_nodes.add( new PhylogenyNode( "F" ) );
6485 query_nodes.add( new PhylogenyNode( "G" ) );
6486 if ( !s0.match( query_nodes ) ) {
6490 query_nodes = new HashSet<PhylogenyNode>();
6491 query_nodes.add( new PhylogenyNode( "F" ) );
6492 query_nodes.add( new PhylogenyNode( "G" ) );
6493 if ( !s0.match( query_nodes ) ) {
6497 query_nodes = new HashSet<PhylogenyNode>();
6498 query_nodes.add( new PhylogenyNode( "E" ) );
6499 query_nodes.add( new PhylogenyNode( "D" ) );
6500 query_nodes.add( new PhylogenyNode( "C" ) );
6501 query_nodes.add( new PhylogenyNode( "B" ) );
6502 query_nodes.add( new PhylogenyNode( "A" ) );
6503 if ( !s0.match( query_nodes ) ) {
6507 query_nodes = new HashSet<PhylogenyNode>();
6508 query_nodes.add( new PhylogenyNode( "F" ) );
6509 query_nodes.add( new PhylogenyNode( "G" ) );
6510 query_nodes.add( new PhylogenyNode( "E" ) );
6511 if ( !s0.match( query_nodes ) ) {
6515 query_nodes = new HashSet<PhylogenyNode>();
6516 query_nodes.add( new PhylogenyNode( "F" ) );
6517 query_nodes.add( new PhylogenyNode( "G" ) );
6518 query_nodes.add( new PhylogenyNode( "E" ) );
6519 query_nodes.add( new PhylogenyNode( "D" ) );
6520 if ( !s0.match( query_nodes ) ) {
6524 query_nodes = new HashSet<PhylogenyNode>();
6525 query_nodes.add( new PhylogenyNode( "F" ) );
6526 query_nodes.add( new PhylogenyNode( "A" ) );
6527 if ( s0.match( query_nodes ) ) {
6531 query_nodes = new HashSet<PhylogenyNode>();
6532 query_nodes.add( new PhylogenyNode( "A" ) );
6533 query_nodes.add( new PhylogenyNode( "E" ) );
6534 query_nodes.add( new PhylogenyNode( "B" ) );
6535 query_nodes.add( new PhylogenyNode( "C" ) );
6536 if ( s0.match( query_nodes ) ) {
6540 query_nodes = new HashSet<PhylogenyNode>();
6541 query_nodes.add( new PhylogenyNode( "F" ) );
6542 query_nodes.add( new PhylogenyNode( "G" ) );
6543 query_nodes.add( new PhylogenyNode( "E" ) );
6544 query_nodes.add( new PhylogenyNode( "D" ) );
6545 query_nodes.add( new PhylogenyNode( "C" ) );
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( "B" ) );
6553 query_nodes.add( new PhylogenyNode( "D" ) );
6554 if ( s0.match( query_nodes ) ) {
6558 query_nodes = new HashSet<PhylogenyNode>();
6559 query_nodes.add( new PhylogenyNode( "A" ) );
6560 query_nodes.add( new PhylogenyNode( "D" ) );
6561 if ( s0.match( query_nodes ) ) {
6565 query_nodes = new HashSet<PhylogenyNode>();
6566 query_nodes.add( new PhylogenyNode( "A" ) );
6567 query_nodes.add( new PhylogenyNode( "B" ) );
6568 if ( s0.match( query_nodes ) ) {
6572 query_nodes = new HashSet<PhylogenyNode>();
6573 query_nodes.add( new PhylogenyNode( "A" ) );
6574 query_nodes.add( new PhylogenyNode( "C" ) );
6575 if ( s0.match( query_nodes ) ) {
6579 query_nodes = new HashSet<PhylogenyNode>();
6580 query_nodes.add( new PhylogenyNode( "A" ) );
6581 query_nodes.add( new PhylogenyNode( "E" ) );
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( "F" ) );
6589 if ( s0.match( query_nodes ) ) {
6593 query_nodes = new HashSet<PhylogenyNode>();
6594 query_nodes.add( new PhylogenyNode( "A" ) );
6595 query_nodes.add( new PhylogenyNode( "G" ) );
6596 if ( s0.match( query_nodes ) ) {
6600 query_nodes = new HashSet<PhylogenyNode>();
6601 query_nodes.add( new PhylogenyNode( "A" ) );
6602 query_nodes.add( new PhylogenyNode( "F" ) );
6603 query_nodes.add( new PhylogenyNode( "G" ) );
6604 if ( s0.match( query_nodes ) ) {
6608 query_nodes = new HashSet<PhylogenyNode>();
6609 query_nodes.add( new PhylogenyNode( "A" ) );
6610 query_nodes.add( new PhylogenyNode( "B" ) );
6611 query_nodes.add( new PhylogenyNode( "D" ) );
6612 if ( s0.match( query_nodes ) ) {
6616 query_nodes = new HashSet<PhylogenyNode>();
6617 query_nodes.add( new PhylogenyNode( "E" ) );
6618 query_nodes.add( new PhylogenyNode( "D" ) );
6619 query_nodes.add( new PhylogenyNode( "A" ) );
6620 if ( s0.match( query_nodes ) ) {
6624 query_nodes = new HashSet<PhylogenyNode>();
6625 query_nodes.add( new PhylogenyNode( "E" ) );
6626 query_nodes.add( new PhylogenyNode( "D" ) );
6627 query_nodes.add( new PhylogenyNode( "A" ) );
6628 query_nodes.add( new PhylogenyNode( "G" ) );
6629 if ( s0.match( query_nodes ) ) {
6633 // query_nodes = new HashSet<PhylogenyNode>();
6634 // query_nodes.add( new PhylogenyNode( "X" ) );
6635 // query_nodes.add( new PhylogenyNode( "Y" ) );
6636 // query_nodes.add( new PhylogenyNode( "A" ) );
6637 // query_nodes.add( new PhylogenyNode( "B" ) );
6638 // query_nodes.add( new PhylogenyNode( "C" ) );
6639 // query_nodes.add( new PhylogenyNode( "D" ) );
6640 // query_nodes.add( new PhylogenyNode( "E" ) );
6641 // query_nodes.add( new PhylogenyNode( "F" ) );
6642 // query_nodes.add( new PhylogenyNode( "G" ) );
6643 // if ( !s0.match( query_nodes ) ) {
6646 // query_nodes = new HashSet<PhylogenyNode>();
6647 // query_nodes.add( new PhylogenyNode( "X" ) );
6648 // query_nodes.add( new PhylogenyNode( "Y" ) );
6649 // query_nodes.add( new PhylogenyNode( "A" ) );
6650 // query_nodes.add( new PhylogenyNode( "B" ) );
6651 // query_nodes.add( new PhylogenyNode( "C" ) );
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( "D" ) );
6660 // query_nodes.add( new PhylogenyNode( "E" ) );
6661 // query_nodes.add( new PhylogenyNode( "F" ) );
6662 // query_nodes.add( new PhylogenyNode( "G" ) );
6663 // if ( !s0.match( query_nodes ) ) {
6667 // query_nodes = new HashSet<PhylogenyNode>();
6668 // query_nodes.add( new PhylogenyNode( "X" ) );
6669 // query_nodes.add( new PhylogenyNode( "Y" ) );
6670 // query_nodes.add( new PhylogenyNode( "A" ) );
6671 // query_nodes.add( new PhylogenyNode( "B" ) );
6672 // query_nodes.add( new PhylogenyNode( "C" ) );
6673 // query_nodes.add( new PhylogenyNode( "D" ) );
6674 // if ( !s0.match( query_nodes ) ) {
6678 // query_nodes = new HashSet<PhylogenyNode>();
6679 // query_nodes.add( new PhylogenyNode( "X" ) );
6680 // query_nodes.add( new PhylogenyNode( "Y" ) );
6681 // query_nodes.add( new PhylogenyNode( "E" ) );
6682 // query_nodes.add( new PhylogenyNode( "F" ) );
6683 // query_nodes.add( new PhylogenyNode( "G" ) );
6684 // if ( !s0.match( query_nodes ) ) {
6688 // query_nodes = new HashSet<PhylogenyNode>();
6689 // query_nodes.add( new PhylogenyNode( "X" ) );
6690 // query_nodes.add( new PhylogenyNode( "Y" ) );
6691 // query_nodes.add( new PhylogenyNode( "F" ) );
6692 // query_nodes.add( new PhylogenyNode( "G" ) );
6693 // if ( !s0.match( query_nodes ) ) {
6697 query_nodes = new HashSet<PhylogenyNode>();
6698 query_nodes.add( new PhylogenyNode( "X" ) );
6699 query_nodes.add( new PhylogenyNode( "Y" ) );
6700 query_nodes.add( new PhylogenyNode( "E" ) );
6701 query_nodes.add( new PhylogenyNode( "G" ) );
6702 if ( s0.match( query_nodes ) ) {
6706 query_nodes = new HashSet<PhylogenyNode>();
6707 query_nodes.add( new PhylogenyNode( "X" ) );
6708 query_nodes.add( new PhylogenyNode( "Y" ) );
6709 query_nodes.add( new PhylogenyNode( "A" ) );
6710 query_nodes.add( new PhylogenyNode( "B" ) );
6711 if ( s0.match( query_nodes ) ) {
6714 ///////////////////////////
6716 query_nodes = new HashSet<PhylogenyNode>();
6717 query_nodes.add( new PhylogenyNode( "X" ) );
6718 query_nodes.add( new PhylogenyNode( "Y" ) );
6719 query_nodes.add( new PhylogenyNode( "A" ) );
6720 query_nodes.add( new PhylogenyNode( "D" ) );
6721 if ( s0.match( query_nodes ) ) {
6725 query_nodes = new HashSet<PhylogenyNode>();
6726 query_nodes.add( new PhylogenyNode( "X" ) );
6727 query_nodes.add( new PhylogenyNode( "Y" ) );
6728 query_nodes.add( new PhylogenyNode( "A" ) );
6729 query_nodes.add( new PhylogenyNode( "B" ) );
6730 if ( s0.match( query_nodes ) ) {
6734 query_nodes = new HashSet<PhylogenyNode>();
6735 query_nodes.add( new PhylogenyNode( "X" ) );
6736 query_nodes.add( new PhylogenyNode( "Y" ) );
6737 query_nodes.add( new PhylogenyNode( "A" ) );
6738 query_nodes.add( new PhylogenyNode( "C" ) );
6739 if ( s0.match( query_nodes ) ) {
6743 query_nodes = new HashSet<PhylogenyNode>();
6744 query_nodes.add( new PhylogenyNode( "X" ) );
6745 query_nodes.add( new PhylogenyNode( "Y" ) );
6746 query_nodes.add( new PhylogenyNode( "A" ) );
6747 query_nodes.add( new PhylogenyNode( "E" ) );
6748 if ( s0.match( query_nodes ) ) {
6752 query_nodes = new HashSet<PhylogenyNode>();
6753 query_nodes.add( new PhylogenyNode( "X" ) );
6754 query_nodes.add( new PhylogenyNode( "Y" ) );
6755 query_nodes.add( new PhylogenyNode( "A" ) );
6756 query_nodes.add( new PhylogenyNode( "F" ) );
6757 if ( s0.match( query_nodes ) ) {
6761 query_nodes = new HashSet<PhylogenyNode>();
6762 query_nodes.add( new PhylogenyNode( "Y" ) );
6763 query_nodes.add( new PhylogenyNode( "A" ) );
6764 query_nodes.add( new PhylogenyNode( "G" ) );
6765 if ( s0.match( query_nodes ) ) {
6769 query_nodes = new HashSet<PhylogenyNode>();
6770 query_nodes.add( new PhylogenyNode( "X" ) );
6771 query_nodes.add( new PhylogenyNode( "Y" ) );
6772 query_nodes.add( new PhylogenyNode( "A" ) );
6773 query_nodes.add( new PhylogenyNode( "F" ) );
6774 query_nodes.add( new PhylogenyNode( "G" ) );
6775 if ( s0.match( query_nodes ) ) {
6779 query_nodes = new HashSet<PhylogenyNode>();
6780 query_nodes.add( new PhylogenyNode( "X" ) );
6781 query_nodes.add( new PhylogenyNode( "Y" ) );
6782 query_nodes.add( new PhylogenyNode( "A" ) );
6783 query_nodes.add( new PhylogenyNode( "B" ) );
6784 query_nodes.add( new PhylogenyNode( "D" ) );
6785 if ( s0.match( query_nodes ) ) {
6789 query_nodes = new HashSet<PhylogenyNode>();
6790 query_nodes.add( new PhylogenyNode( "X" ) );
6791 query_nodes.add( new PhylogenyNode( "Y" ) );
6792 query_nodes.add( new PhylogenyNode( "E" ) );
6793 query_nodes.add( new PhylogenyNode( "D" ) );
6794 query_nodes.add( new PhylogenyNode( "A" ) );
6795 if ( s0.match( query_nodes ) ) {
6799 query_nodes = new HashSet<PhylogenyNode>();
6800 query_nodes.add( new PhylogenyNode( "X" ) );
6801 query_nodes.add( new PhylogenyNode( "Y" ) );
6802 query_nodes.add( new PhylogenyNode( "E" ) );
6803 query_nodes.add( new PhylogenyNode( "D" ) );
6804 query_nodes.add( new PhylogenyNode( "A" ) );
6805 query_nodes.add( new PhylogenyNode( "G" ) );
6806 if ( s0.match( query_nodes ) ) {
6810 catch ( final Exception e ) {
6811 e.printStackTrace();
6817 private static boolean testSplitStrict() {
6819 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6820 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6821 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6822 ex.add( new PhylogenyNode( "A" ) );
6823 ex.add( new PhylogenyNode( "B" ) );
6824 ex.add( new PhylogenyNode( "C" ) );
6825 ex.add( new PhylogenyNode( "D" ) );
6826 ex.add( new PhylogenyNode( "E" ) );
6827 ex.add( new PhylogenyNode( "F" ) );
6828 ex.add( new PhylogenyNode( "G" ) );
6829 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6830 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6831 query_nodes.add( new PhylogenyNode( "A" ) );
6832 query_nodes.add( new PhylogenyNode( "B" ) );
6833 if ( s0.match( query_nodes ) ) {
6836 query_nodes = new HashSet<PhylogenyNode>();
6837 query_nodes.add( new PhylogenyNode( "A" ) );
6838 query_nodes.add( new PhylogenyNode( "B" ) );
6839 query_nodes.add( new PhylogenyNode( "C" ) );
6840 query_nodes.add( new PhylogenyNode( "D" ) );
6841 query_nodes.add( new PhylogenyNode( "E" ) );
6842 query_nodes.add( new PhylogenyNode( "F" ) );
6843 query_nodes.add( new PhylogenyNode( "G" ) );
6844 if ( !s0.match( query_nodes ) ) {
6848 query_nodes = new HashSet<PhylogenyNode>();
6849 query_nodes.add( new PhylogenyNode( "A" ) );
6850 query_nodes.add( new PhylogenyNode( "B" ) );
6851 query_nodes.add( new PhylogenyNode( "C" ) );
6852 if ( !s0.match( query_nodes ) ) {
6856 query_nodes = new HashSet<PhylogenyNode>();
6857 query_nodes.add( new PhylogenyNode( "D" ) );
6858 query_nodes.add( new PhylogenyNode( "E" ) );
6859 query_nodes.add( new PhylogenyNode( "F" ) );
6860 query_nodes.add( new PhylogenyNode( "G" ) );
6861 if ( !s0.match( query_nodes ) ) {
6865 query_nodes = new HashSet<PhylogenyNode>();
6866 query_nodes.add( new PhylogenyNode( "A" ) );
6867 query_nodes.add( new PhylogenyNode( "B" ) );
6868 query_nodes.add( new PhylogenyNode( "C" ) );
6869 query_nodes.add( new PhylogenyNode( "D" ) );
6870 if ( !s0.match( query_nodes ) ) {
6874 query_nodes = new HashSet<PhylogenyNode>();
6875 query_nodes.add( new PhylogenyNode( "E" ) );
6876 query_nodes.add( new PhylogenyNode( "F" ) );
6877 query_nodes.add( new PhylogenyNode( "G" ) );
6878 if ( !s0.match( query_nodes ) ) {
6882 query_nodes = new HashSet<PhylogenyNode>();
6883 query_nodes.add( new PhylogenyNode( "F" ) );
6884 query_nodes.add( new PhylogenyNode( "G" ) );
6885 if ( !s0.match( query_nodes ) ) {
6889 query_nodes = new HashSet<PhylogenyNode>();
6890 query_nodes.add( new PhylogenyNode( "E" ) );
6891 query_nodes.add( new PhylogenyNode( "D" ) );
6892 query_nodes.add( new PhylogenyNode( "C" ) );
6893 query_nodes.add( new PhylogenyNode( "B" ) );
6894 query_nodes.add( new PhylogenyNode( "A" ) );
6895 if ( !s0.match( query_nodes ) ) {
6899 query_nodes = new HashSet<PhylogenyNode>();
6900 query_nodes.add( new PhylogenyNode( "F" ) );
6901 query_nodes.add( new PhylogenyNode( "G" ) );
6902 query_nodes.add( new PhylogenyNode( "E" ) );
6903 if ( !s0.match( query_nodes ) ) {
6907 query_nodes = new HashSet<PhylogenyNode>();
6908 query_nodes.add( new PhylogenyNode( "F" ) );
6909 query_nodes.add( new PhylogenyNode( "G" ) );
6910 query_nodes.add( new PhylogenyNode( "E" ) );
6911 query_nodes.add( new PhylogenyNode( "D" ) );
6912 if ( !s0.match( query_nodes ) ) {
6916 query_nodes = new HashSet<PhylogenyNode>();
6917 query_nodes.add( new PhylogenyNode( "F" ) );
6918 query_nodes.add( new PhylogenyNode( "A" ) );
6919 if ( s0.match( query_nodes ) ) {
6923 query_nodes = new HashSet<PhylogenyNode>();
6924 query_nodes.add( new PhylogenyNode( "A" ) );
6925 query_nodes.add( new PhylogenyNode( "E" ) );
6926 query_nodes.add( new PhylogenyNode( "B" ) );
6927 query_nodes.add( new PhylogenyNode( "C" ) );
6928 if ( s0.match( query_nodes ) ) {
6932 query_nodes = new HashSet<PhylogenyNode>();
6933 query_nodes.add( new PhylogenyNode( "F" ) );
6934 query_nodes.add( new PhylogenyNode( "G" ) );
6935 query_nodes.add( new PhylogenyNode( "E" ) );
6936 query_nodes.add( new PhylogenyNode( "D" ) );
6937 query_nodes.add( new PhylogenyNode( "C" ) );
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( "B" ) );
6945 query_nodes.add( new PhylogenyNode( "D" ) );
6946 if ( s0.match( query_nodes ) ) {
6950 query_nodes = new HashSet<PhylogenyNode>();
6951 query_nodes.add( new PhylogenyNode( "A" ) );
6952 query_nodes.add( new PhylogenyNode( "D" ) );
6953 if ( s0.match( query_nodes ) ) {
6957 query_nodes = new HashSet<PhylogenyNode>();
6958 query_nodes.add( new PhylogenyNode( "A" ) );
6959 query_nodes.add( new PhylogenyNode( "B" ) );
6960 if ( s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( new PhylogenyNode( "A" ) );
6966 query_nodes.add( new PhylogenyNode( "C" ) );
6967 if ( s0.match( query_nodes ) ) {
6971 query_nodes = new HashSet<PhylogenyNode>();
6972 query_nodes.add( new PhylogenyNode( "A" ) );
6973 query_nodes.add( new PhylogenyNode( "E" ) );
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( "F" ) );
6981 if ( s0.match( query_nodes ) ) {
6985 query_nodes = new HashSet<PhylogenyNode>();
6986 query_nodes.add( new PhylogenyNode( "A" ) );
6987 query_nodes.add( new PhylogenyNode( "G" ) );
6988 if ( s0.match( query_nodes ) ) {
6992 query_nodes = new HashSet<PhylogenyNode>();
6993 query_nodes.add( new PhylogenyNode( "A" ) );
6994 query_nodes.add( new PhylogenyNode( "F" ) );
6995 query_nodes.add( new PhylogenyNode( "G" ) );
6996 if ( s0.match( query_nodes ) ) {
7000 query_nodes = new HashSet<PhylogenyNode>();
7001 query_nodes.add( new PhylogenyNode( "A" ) );
7002 query_nodes.add( new PhylogenyNode( "B" ) );
7003 query_nodes.add( new PhylogenyNode( "D" ) );
7004 if ( s0.match( query_nodes ) ) {
7008 query_nodes = new HashSet<PhylogenyNode>();
7009 query_nodes.add( new PhylogenyNode( "E" ) );
7010 query_nodes.add( new PhylogenyNode( "D" ) );
7011 query_nodes.add( new PhylogenyNode( "A" ) );
7012 if ( s0.match( query_nodes ) ) {
7016 query_nodes = new HashSet<PhylogenyNode>();
7017 query_nodes.add( new PhylogenyNode( "E" ) );
7018 query_nodes.add( new PhylogenyNode( "D" ) );
7019 query_nodes.add( new PhylogenyNode( "A" ) );
7020 query_nodes.add( new PhylogenyNode( "G" ) );
7021 if ( s0.match( query_nodes ) ) {
7025 catch ( final Exception e ) {
7026 e.printStackTrace();
7032 private static boolean testSubtreeDeletion() {
7034 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7035 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7036 t1.deleteSubtree( t1.getNode( "A" ), false );
7037 if ( t1.getNumberOfExternalNodes() != 5 ) {
7040 t1.toNewHampshireX();
7041 t1.deleteSubtree( t1.getNode( "E" ), false );
7042 if ( t1.getNumberOfExternalNodes() != 4 ) {
7045 t1.toNewHampshireX();
7046 t1.deleteSubtree( t1.getNode( "F" ), false );
7047 if ( t1.getNumberOfExternalNodes() != 3 ) {
7050 t1.toNewHampshireX();
7051 t1.deleteSubtree( t1.getNode( "D" ), false );
7052 t1.toNewHampshireX();
7053 if ( t1.getNumberOfExternalNodes() != 3 ) {
7056 t1.deleteSubtree( t1.getNode( "def" ), false );
7057 t1.toNewHampshireX();
7058 if ( t1.getNumberOfExternalNodes() != 2 ) {
7061 t1.deleteSubtree( t1.getNode( "B" ), false );
7062 t1.toNewHampshireX();
7063 if ( t1.getNumberOfExternalNodes() != 1 ) {
7066 t1.deleteSubtree( t1.getNode( "C" ), false );
7067 t1.toNewHampshireX();
7068 if ( t1.getNumberOfExternalNodes() != 1 ) {
7071 t1.deleteSubtree( t1.getNode( "abc" ), false );
7072 t1.toNewHampshireX();
7073 if ( t1.getNumberOfExternalNodes() != 1 ) {
7076 t1.deleteSubtree( t1.getNode( "r" ), false );
7077 if ( t1.getNumberOfExternalNodes() != 0 ) {
7080 if ( !t1.isEmpty() ) {
7083 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7084 t2.deleteSubtree( t2.getNode( "A" ), false );
7085 t2.toNewHampshireX();
7086 if ( t2.getNumberOfExternalNodes() != 5 ) {
7089 t2.deleteSubtree( t2.getNode( "abc" ), false );
7090 t2.toNewHampshireX();
7091 if ( t2.getNumberOfExternalNodes() != 3 ) {
7094 t2.deleteSubtree( t2.getNode( "def" ), false );
7095 t2.toNewHampshireX();
7096 if ( t2.getNumberOfExternalNodes() != 1 ) {
7100 catch ( final Exception e ) {
7101 e.printStackTrace( System.out );
7107 private static boolean testSupportCount() {
7109 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7110 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7111 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7112 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7113 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7114 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7115 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7117 SupportCount.count( t0_1, phylogenies_1, true, false );
7118 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7119 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7120 + "(((((A,B),C),D),E),((F,G),X))"
7121 + "(((((A,Y),B),C),D),((F,G),E))"
7122 + "(((((A,B),C),D),E),(F,G))"
7123 + "(((((A,B),C),D),E),(F,G))"
7124 + "(((((A,B),C),D),E),(F,G))"
7125 + "(((((A,B),C),D),E),(F,G),Z)"
7126 + "(((((A,B),C),D),E),(F,G))"
7127 + "((((((A,B),C),D),E),F),G)"
7128 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7130 SupportCount.count( t0_2, phylogenies_2, true, false );
7131 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7132 while ( it.hasNext() ) {
7133 final PhylogenyNode n = it.next();
7134 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7138 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7139 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7140 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7141 SupportCount.count( t0_3, phylogenies_3, true, false );
7142 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7143 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7146 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7149 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7152 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7155 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7158 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7161 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7164 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7167 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7170 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7173 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7174 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7175 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7176 SupportCount.count( t0_4, phylogenies_4, true, false );
7177 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7178 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7181 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7184 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7187 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7190 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7193 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7196 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7199 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7202 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7205 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7208 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7209 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7210 double d = SupportCount.compare( b1, a, true, true, true );
7211 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7214 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7215 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7216 d = SupportCount.compare( b2, a, true, true, true );
7217 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7220 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7221 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7222 d = SupportCount.compare( b3, a, true, true, true );
7223 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7226 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7227 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7228 d = SupportCount.compare( b4, a, true, true, false );
7229 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7233 catch ( final Exception e ) {
7234 e.printStackTrace( System.out );
7240 private static boolean testSupportTransfer() {
7242 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7243 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)",
7244 new NHXParser() )[ 0 ];
7245 final Phylogeny p2 = factory
7246 .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 ];
7247 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7250 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7253 support_transfer.moveBranchLengthsToBootstrap( p1 );
7254 support_transfer.transferSupportValues( p1, p2 );
7255 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7258 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7261 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7264 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7267 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7270 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7273 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7276 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7280 catch ( final Exception e ) {
7281 e.printStackTrace( System.out );
7287 private static boolean testTaxonomyAssigner() {
7289 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]";
7290 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7291 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7292 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7293 s0.setRooted( true );
7294 g0.setRooted( true );
7295 TaxonomyAssigner.execute( g0, s0 );
7296 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7299 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7302 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7305 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7306 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7307 g0.setRooted( true );
7308 TaxonomyAssigner.execute( g0, s0 );
7309 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7312 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7315 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7318 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7319 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7320 g0.setRooted( true );
7321 TaxonomyAssigner.execute( g0, s0 );
7322 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7325 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7328 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7331 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7332 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7333 g0.setRooted( true );
7334 TaxonomyAssigner.execute( g0, s0 );
7335 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7338 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7341 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7344 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7345 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7346 g0.setRooted( true );
7347 TaxonomyAssigner.execute( g0, s0 );
7348 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7351 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7354 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7357 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7358 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7359 g0.setRooted( true );
7360 TaxonomyAssigner.execute( g0, s0 );
7361 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7364 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7367 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7370 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
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( "ABCDE" ) ) {
7377 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7380 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7383 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7384 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7385 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7386 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7387 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7388 s0.setRooted( true );
7389 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7390 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7391 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7392 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])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=I])c, "
7414 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&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( "IJKL" ) ) {
7427 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7430 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7433 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7434 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7435 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7436 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])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( "ABCD" ) ) {
7443 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7446 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7449 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7452 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7455 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7456 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7457 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7458 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7459 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7460 g0.setRooted( true );
7461 TaxonomyAssigner.execute( g0, s0 );
7462 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7465 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7468 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7471 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7474 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7477 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7478 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7479 g0.setRooted( true );
7480 TaxonomyAssigner.execute( g0, s0 );
7481 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7484 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7487 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7490 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7491 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7492 g0.setRooted( true );
7493 TaxonomyAssigner.execute( g0, s0 );
7494 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7497 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7500 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7503 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7504 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7505 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7506 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7507 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7508 g0.setRooted( true );
7509 TaxonomyAssigner.execute( g0, s0 );
7510 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7513 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7516 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7519 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7522 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7525 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7528 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7531 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7532 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7533 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7534 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7535 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7536 g0.setRooted( true );
7537 TaxonomyAssigner.execute( g0, s0 );
7538 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7541 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7544 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7547 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7550 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7553 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7556 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7559 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7560 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7561 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7562 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7563 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7564 g0.setRooted( true );
7565 TaxonomyAssigner.execute( g0, s0 );
7566 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7569 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7572 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7575 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7578 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7581 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7584 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7587 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7588 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7589 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7590 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7591 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7592 g0.setRooted( true );
7593 TaxonomyAssigner.execute( g0, s0 );
7594 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7597 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7600 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7603 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7606 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7609 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7612 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7615 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7616 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7617 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7618 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7619 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7620 s0.setRooted( true );
7621 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7622 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7623 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7624 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7625 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7626 g0.setRooted( true );
7627 TaxonomyAssigner.execute( g0, s0 );
7628 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7631 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7635 catch ( final Exception e ) {
7636 e.printStackTrace( System.out );
7642 private static boolean testUniprotTaxonomySearch() {
7644 List<UniProtTaxonomy> results = UniProtWsTools
7645 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7646 if ( results.size() != 1 ) {
7649 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7652 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7655 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7658 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7661 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7665 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7666 if ( results.size() != 1 ) {
7669 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7672 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7675 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7678 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7681 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7685 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7686 if ( results.size() != 1 ) {
7689 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7692 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7695 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7698 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7701 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7705 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7706 if ( results.size() != 1 ) {
7709 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7712 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7715 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7718 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7721 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7724 if ( !results.get( 0 ).getLineage()[ 0 ].equals( "Eukaryota" ) ) {
7727 if ( !results.get( 0 ).getLineage()[ 1 ].equals( "Metazoa" ) ) {
7730 if ( !results.get( 0 ).getLineage()[ results.get( 0 ).getLineage().length - 1 ].equals( "Nematostella" ) ) {
7734 catch ( final IOException e ) {
7735 System.out.println();
7736 System.out.println( "the following might be due to absence internet connection:" );
7737 e.printStackTrace( System.out );
7740 catch ( final Exception e ) {
7746 private static boolean testEmblEntryRetrieval() {
7747 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7748 System.out.println( DatabaseTools.parseGenbankAccessor( "AY423861" ));
7754 private static boolean testUniprotEntryRetrieval() {
7755 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7758 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7761 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7764 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7767 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7770 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7773 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7777 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7778 if ( !entry.getAccession().equals( "P12345" ) ) {
7781 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7784 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7787 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7790 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7794 catch ( final IOException e ) {
7795 System.out.println();
7796 System.out.println( "the following might be due to absence internet connection:" );
7797 e.printStackTrace( System.out );
7800 catch ( final Exception e ) {
7806 private static boolean testWabiTxSearch() {
7809 result = TxSearch.searchSimple( "nematostella" );
7810 result = TxSearch.getTxId( "nematostella" );
7811 if ( !result.equals( "45350" ) ) {
7814 result = TxSearch.getTxName( "45350" );
7815 if ( !result.equals( "Nematostella" ) ) {
7818 result = TxSearch.getTxId( "nematostella vectensis" );
7819 if ( !result.equals( "45351" ) ) {
7822 result = TxSearch.getTxName( "45351" );
7823 if ( !result.equals( "Nematostella vectensis" ) ) {
7826 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7827 if ( !result.equals( "536089" ) ) {
7830 result = TxSearch.getTxName( "536089" );
7831 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7834 final List<String> queries = new ArrayList<String>();
7835 queries.add( "Campylobacter coli" );
7836 queries.add( "Escherichia coli" );
7837 queries.add( "Arabidopsis" );
7838 queries.add( "Trichoplax" );
7839 queries.add( "Samanea saman" );
7840 queries.add( "Kluyveromyces marxianus" );
7841 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7842 queries.add( "Bornavirus parrot/PDD/2008" );
7843 final List<RANKS> ranks = new ArrayList<RANKS>();
7844 ranks.add( RANKS.SUPERKINGDOM );
7845 ranks.add( RANKS.KINGDOM );
7846 ranks.add( RANKS.FAMILY );
7847 ranks.add( RANKS.GENUS );
7848 ranks.add( RANKS.TRIBE );
7849 result = TxSearch.searchLineage( queries, ranks );
7850 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7851 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7853 catch ( final Exception e ) {
7854 System.out.println();
7855 System.out.println( "the following might be due to absence internet connection:" );
7856 e.printStackTrace( System.out );
7862 private static boolean testAminoAcidSequence() {
7864 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7865 if ( aa1.getLength() != 13 ) {
7868 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7871 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7874 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7877 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7878 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7881 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7882 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7885 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7886 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7890 catch ( final Exception e ) {
7891 e.printStackTrace();
7897 private static boolean testCreateBalancedPhylogeny() {
7899 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7900 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7903 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7906 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7907 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7910 if ( p1.getNumberOfExternalNodes() != 100 ) {
7914 catch ( final Exception e ) {
7915 e.printStackTrace();
7921 private static boolean testFastaParser() {
7923 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7926 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7929 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7930 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7933 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7936 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7939 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7942 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
7945 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
7949 catch ( final Exception e ) {
7950 e.printStackTrace();
7956 private static boolean testGeneralMsaParser() {
7958 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
7959 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
7960 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
7961 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
7962 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
7963 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
7964 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
7965 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
7966 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
7967 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7970 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7973 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7976 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
7977 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
7980 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
7983 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
7986 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
7987 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7990 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7993 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7997 catch ( final Exception e ) {
7998 e.printStackTrace();
8004 private static boolean testMafft() {
8006 final List<String> opts = new ArrayList<String>();
8007 opts.add( "--maxiterate" );
8009 opts.add( "--localpair" );
8010 opts.add( "--quiet" );
8012 final MsaInferrer mafft = Mafft.createInstance();
8013 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
8014 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8018 catch ( final Exception e ) {
8019 e.printStackTrace( System.out );