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.SequenceDatabaseEntry;
103 import org.forester.ws.uniprot.UniProtTaxonomy;
104 import org.forester.ws.uniprot.UniProtWsTools;
105 import org.forester.ws.wabi.TxSearch;
106 import org.forester.ws.wabi.TxSearch.RANKS;
107 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
108 import org.forester.ws.wabi.TxSearch.TAX_RANK;
110 @SuppressWarnings( "unused")
111 public final class Test {
113 private final static double ZERO_DIFF = 1.0E-9;
114 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
115 + ForesterUtil.getFileSeparator() + "test_data"
116 + ForesterUtil.getFileSeparator();
117 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
118 + ForesterUtil.getFileSeparator() + "resources"
119 + ForesterUtil.getFileSeparator();
120 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
121 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
122 + ForesterConstants.PHYLO_XML_VERSION + "/"
123 + ForesterConstants.PHYLO_XML_XSD;
124 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
125 + ForesterConstants.PHYLO_XML_VERSION + "/"
126 + ForesterConstants.PHYLO_XML_XSD;
128 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
129 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
133 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
134 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
135 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
138 public static boolean isEqual( final double a, final double b ) {
139 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
142 public static void main( final String[] args ) {
143 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
144 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
146 Locale.setDefault( Locale.US );
147 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
150 System.out.print( "[Test if directory with files for testing exists/is readable: " );
151 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
152 System.out.println( "OK.]" );
155 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
156 System.out.println( "Testing aborted." );
159 System.out.print( "[Test if resources directory exists/is readable: " );
160 if ( testDir( PATH_TO_RESOURCES ) ) {
161 System.out.println( "OK.]" );
164 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
165 System.out.println( "Testing aborted." );
168 final long start_time = new Date().getTime();
169 System.out.print( "Hmmscan output parser: " );
170 if ( testHmmscanOutputParser() ) {
171 System.out.println( "OK." );
175 System.out.println( "failed." );
178 System.out.print( "Basic node methods: " );
179 if ( Test.testBasicNodeMethods() ) {
180 System.out.println( "OK." );
184 System.out.println( "failed." );
187 System.out.print( "Basic node construction and parsing of NHX (node level): " );
188 if ( Test.testNHXNodeParsing() ) {
189 System.out.println( "OK." );
193 System.out.println( "failed." );
196 System.out.print( "NH parsing: " );
197 if ( Test.testNHParsing() ) {
198 System.out.println( "OK." );
202 System.out.println( "failed." );
205 System.out.print( "Conversion to NHX (node level): " );
206 if ( Test.testNHXconversion() ) {
207 System.out.println( "OK." );
211 System.out.println( "failed." );
214 System.out.print( "NHX parsing: " );
215 if ( Test.testNHXParsing() ) {
216 System.out.println( "OK." );
220 System.out.println( "failed." );
223 System.out.print( "NHX parsing with quotes: " );
224 if ( Test.testNHXParsingQuotes() ) {
225 System.out.println( "OK." );
229 System.out.println( "failed." );
232 System.out.print( "Nexus characters parsing: " );
233 if ( Test.testNexusCharactersParsing() ) {
234 System.out.println( "OK." );
238 System.out.println( "failed." );
241 System.out.print( "Nexus tree parsing: " );
242 if ( Test.testNexusTreeParsing() ) {
243 System.out.println( "OK." );
247 System.out.println( "failed." );
250 System.out.print( "Nexus tree parsing (translating): " );
251 if ( Test.testNexusTreeParsingTranslating() ) {
252 System.out.println( "OK." );
256 System.out.println( "failed." );
259 System.out.print( "Nexus matrix parsing: " );
260 if ( Test.testNexusMatrixParsing() ) {
261 System.out.println( "OK." );
265 System.out.println( "failed." );
268 System.out.print( "Basic phyloXML parsing: " );
269 if ( Test.testBasicPhyloXMLparsing() ) {
270 System.out.println( "OK." );
274 System.out.println( "failed." );
277 System.out.print( "Basic phyloXML parsing (validating against schema): " );
278 if ( testBasicPhyloXMLparsingValidating() ) {
279 System.out.println( "OK." );
283 System.out.println( "failed." );
286 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
287 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
288 System.out.println( "OK." );
292 System.out.println( "failed." );
295 System.out.print( "phyloXML Distribution Element: " );
296 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
297 System.out.println( "OK." );
301 System.out.println( "failed." );
304 System.out.print( "Tol XML parsing: " );
305 if ( Test.testBasicTolXMLparsing() ) {
306 System.out.println( "OK." );
310 System.out.println( "failed." );
313 System.out.print( "Copying of node data: " );
314 if ( Test.testCopyOfNodeData() ) {
315 System.out.println( "OK." );
319 System.out.println( "failed." );
322 System.out.print( "Basic tree methods: " );
323 if ( Test.testBasicTreeMethods() ) {
324 System.out.println( "OK." );
328 System.out.println( "failed." );
331 System.out.print( "Postorder Iterator: " );
332 if ( Test.testPostOrderIterator() ) {
333 System.out.println( "OK." );
337 System.out.println( "failed." );
340 System.out.print( "Preorder Iterator: " );
341 if ( Test.testPreOrderIterator() ) {
342 System.out.println( "OK." );
346 System.out.println( "failed." );
349 System.out.print( "Levelorder Iterator: " );
350 if ( Test.testLevelOrderIterator() ) {
351 System.out.println( "OK." );
355 System.out.println( "failed." );
358 System.out.print( "Re-id methods: " );
359 if ( Test.testReIdMethods() ) {
360 System.out.println( "OK." );
364 System.out.println( "failed." );
367 System.out.print( "Methods on last external nodes: " );
368 if ( Test.testLastExternalNodeMethods() ) {
369 System.out.println( "OK." );
373 System.out.println( "failed." );
376 System.out.print( "Methods on external nodes: " );
377 if ( Test.testExternalNodeRelatedMethods() ) {
378 System.out.println( "OK." );
382 System.out.println( "failed." );
385 System.out.print( "Deletion of external nodes: " );
386 if ( Test.testDeletionOfExternalNodes() ) {
387 System.out.println( "OK." );
391 System.out.println( "failed." );
394 System.out.print( "Subtree deletion: " );
395 if ( Test.testSubtreeDeletion() ) {
396 System.out.println( "OK." );
400 System.out.println( "failed." );
403 System.out.print( "Phylogeny branch: " );
404 if ( Test.testPhylogenyBranch() ) {
405 System.out.println( "OK." );
409 System.out.println( "failed." );
412 System.out.print( "Rerooting: " );
413 if ( Test.testRerooting() ) {
414 System.out.println( "OK." );
418 System.out.println( "failed." );
421 System.out.print( "Mipoint rooting: " );
422 if ( Test.testMidpointrooting() ) {
423 System.out.println( "OK." );
427 System.out.println( "failed." );
430 System.out.print( "Support count: " );
431 if ( Test.testSupportCount() ) {
432 System.out.println( "OK." );
436 System.out.println( "failed." );
439 System.out.print( "Support transfer: " );
440 if ( Test.testSupportTransfer() ) {
441 System.out.println( "OK." );
445 System.out.println( "failed." );
448 System.out.print( "Finding of LCA: " );
449 if ( Test.testGetLCA() ) {
450 System.out.println( "OK." );
454 System.out.println( "failed." );
457 System.out.print( "Calculation of distance between nodes: " );
458 if ( Test.testGetDistance() ) {
459 System.out.println( "OK." );
463 System.out.println( "failed." );
466 System.out.print( "SDIse: " );
467 if ( Test.testSDIse() ) {
468 System.out.println( "OK." );
472 System.out.println( "failed." );
475 System.out.print( "Taxonomy assigner: " );
476 if ( Test.testTaxonomyAssigner() ) {
477 System.out.println( "OK." );
481 System.out.println( "failed." );
484 System.out.print( "SDIunrooted: " );
485 if ( Test.testSDIunrooted() ) {
486 System.out.println( "OK." );
490 System.out.println( "failed." );
493 System.out.print( "GSDI: " );
494 if ( TestGSDI.test() ) {
495 System.out.println( "OK." );
499 System.out.println( "failed." );
502 System.out.print( "Descriptive statistics: " );
503 if ( Test.testDescriptiveStatistics() ) {
504 System.out.println( "OK." );
508 System.out.println( "failed." );
511 System.out.print( "Data objects and methods: " );
512 if ( Test.testDataObjects() ) {
513 System.out.println( "OK." );
517 System.out.println( "failed." );
520 System.out.print( "Properties map: " );
521 if ( Test.testPropertiesMap() ) {
522 System.out.println( "OK." );
526 System.out.println( "failed." );
529 System.out.print( "Phylogeny reconstruction:" );
530 System.out.println();
531 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
532 System.out.println( "OK." );
536 System.out.println( "failed." );
539 System.out.print( "Analysis of domain architectures: " );
540 System.out.println();
541 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
542 System.out.println( "OK." );
546 System.out.println( "failed." );
549 System.out.print( "GO: " );
550 System.out.println();
551 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
552 System.out.println( "OK." );
556 System.out.println( "failed." );
559 System.out.print( "Modeling tools: " );
560 if ( TestPccx.test() ) {
561 System.out.println( "OK." );
565 System.out.println( "failed." );
568 System.out.print( "Split Matrix strict: " );
569 if ( Test.testSplitStrict() ) {
570 System.out.println( "OK." );
574 System.out.println( "failed." );
577 System.out.print( "Split Matrix: " );
578 if ( Test.testSplit() ) {
579 System.out.println( "OK." );
583 System.out.println( "failed." );
586 System.out.print( "Confidence Assessor: " );
587 if ( Test.testConfidenceAssessor() ) {
588 System.out.println( "OK." );
592 System.out.println( "failed." );
595 System.out.print( "Basic table: " );
596 if ( Test.testBasicTable() ) {
597 System.out.println( "OK." );
601 System.out.println( "failed." );
604 System.out.print( "General table: " );
605 if ( Test.testGeneralTable() ) {
606 System.out.println( "OK." );
610 System.out.println( "failed." );
613 System.out.print( "Amino acid sequence: " );
614 if ( Test.testAminoAcidSequence() ) {
615 System.out.println( "OK." );
619 System.out.println( "failed." );
622 System.out.print( "General MSA parser: " );
623 if ( Test.testGeneralMsaParser() ) {
624 System.out.println( "OK." );
628 System.out.println( "failed." );
631 System.out.print( "Fasta parser for msa: " );
632 if ( Test.testFastaParser() ) {
633 System.out.println( "OK." );
637 System.out.println( "failed." );
640 System.out.print( "Creation of balanced phylogeny: " );
641 if ( Test.testCreateBalancedPhylogeny() ) {
642 System.out.println( "OK." );
646 System.out.println( "failed." );
649 System.out.print( "Uniprot Entry Retrieval: " );
650 if ( Test.testUniprotEntryRetrieval() ) {
651 System.out.println( "OK." );
655 System.out.println( "failed." );
658 System.out.print( "Uniprot Taxonomy Search: " );
659 if ( Test.testUniprotTaxonomySearch() ) {
660 System.out.println( "OK." );
664 System.out.println( "failed." );
667 if ( Mafft.isInstalled() ) {
668 System.out.print( "MAFFT (external program): " );
669 if ( Test.testMafft() ) {
670 System.out.println( "OK." );
674 System.out.println( "failed [will not count towards failed tests]" );
677 // System.out.print( "WABI TxSearch: " );
678 // if ( Test.testWabiTxSearch() ) {
679 // System.out.println( "OK." );
684 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
686 System.out.println();
687 final Runtime rt = java.lang.Runtime.getRuntime();
688 final long free_memory = rt.freeMemory() / 1000000;
689 final long total_memory = rt.totalMemory() / 1000000;
690 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
691 + free_memory + "MB, total memory: " + total_memory + "MB)" );
692 System.out.println();
693 System.out.println( "Successful tests: " + succeeded );
694 System.out.println( "Failed tests: " + failed );
695 System.out.println();
697 System.out.println( "OK." );
700 System.out.println( "Not OK." );
702 // System.out.println();
703 // Development.setTime( true );
705 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
706 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
707 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
708 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
709 // "multifurcations_ex_1.nhx";
710 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
711 // final Phylogeny t1 = factory.create( new File( domains ), new
712 // NHXParser() )[ 0 ];
713 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
715 // catch ( final Exception e ) {
716 // e.printStackTrace();
718 // t1.getRoot().preorderPrint();
719 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
723 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
724 // + "\\AtNBSpos.nhx" ) );
726 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
727 // new NHXParser() );
728 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
729 // + "\\AtNBSpos.nhx" ) );
731 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
732 // new NHXParser() );
735 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
736 // + "\\big_tree.nhx" ) );
737 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
738 // + "\\big_tree.nhx" ) );
740 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
741 // new NHXParser() );
743 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
744 // new NHXParser() );
746 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
747 // + "\\big_tree.nhx" ) );
748 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
749 // + "\\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 // + "\\AtNBSpos.nhx" ) );
761 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
762 // new NHXParser() );
765 // catch ( IOException e ) {
766 // // TODO Auto-generated catch block
767 // e.printStackTrace();
771 private static boolean testBasicNodeMethods() {
773 if ( PhylogenyNode.getNodeCount() != 0 ) {
776 final PhylogenyNode n1 = new PhylogenyNode();
777 final PhylogenyNode n2 = new PhylogenyNode( "", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
778 final PhylogenyNode n3 = new PhylogenyNode( "n3", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
779 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
780 if ( n1.isHasAssignedEvent() ) {
783 if ( PhylogenyNode.getNodeCount() != 4 ) {
786 if ( n3.getIndicator() != 0 ) {
789 if ( n3.getNumberOfExternalNodes() != 1 ) {
792 if ( !n3.isExternal() ) {
795 if ( !n3.isRoot() ) {
798 if ( !n4.getName().equals( "n4" ) ) {
802 catch ( final Exception e ) {
803 e.printStackTrace( System.out );
809 private static boolean testBasicPhyloXMLparsing() {
811 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
812 final PhyloXmlParser xml_parser = new PhyloXmlParser();
813 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
815 if ( xml_parser.getErrorCount() > 0 ) {
816 System.out.println( xml_parser.getErrorMessages().toString() );
819 if ( phylogenies_0.length != 4 ) {
822 final Phylogeny t1 = phylogenies_0[ 0 ];
823 final Phylogeny t2 = phylogenies_0[ 1 ];
824 final Phylogeny t3 = phylogenies_0[ 2 ];
825 final Phylogeny t4 = phylogenies_0[ 3 ];
826 if ( t1.getNumberOfExternalNodes() != 1 ) {
829 if ( !t1.isRooted() ) {
832 if ( t1.isRerootable() ) {
835 if ( !t1.getType().equals( "gene_tree" ) ) {
838 if ( t2.getNumberOfExternalNodes() != 2 ) {
841 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
844 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
847 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
850 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
853 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
856 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
859 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
860 .startsWith( "actgtgggggt" ) ) {
863 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
864 .startsWith( "ctgtgatgcat" ) ) {
867 if ( t3.getNumberOfExternalNodes() != 4 ) {
870 if ( !t1.getName().equals( "t1" ) ) {
873 if ( !t2.getName().equals( "t2" ) ) {
876 if ( !t3.getName().equals( "t3" ) ) {
879 if ( !t4.getName().equals( "t4" ) ) {
882 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
885 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
888 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
891 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
892 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
895 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
898 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
901 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
904 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
905 .equals( "apoptosis" ) ) {
908 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
909 .equals( "GO:0006915" ) ) {
912 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
913 .equals( "UniProtKB" ) ) {
916 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
917 .equals( "experimental" ) ) {
920 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
921 .equals( "function" ) ) {
924 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
928 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
929 .getType().equals( "ml" ) ) {
932 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
933 .equals( "apoptosis" ) ) {
936 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
937 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
940 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
941 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
944 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
945 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
948 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
949 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
952 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
953 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
956 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
957 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
960 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
961 .equals( "GO:0005829" ) ) {
964 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
965 .equals( "intracellular organelle" ) ) {
968 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
971 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
972 .equals( "UniProt link" ) ) ) {
975 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
978 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
981 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
984 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
987 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
990 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
993 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
996 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
999 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1002 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1005 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1006 // .equals( "B" ) ) {
1009 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1012 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1015 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1018 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1019 // .getConfidence() != 2144 ) {
1022 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1023 // .equals( "pfam" ) ) {
1026 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1029 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1032 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1035 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1038 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1039 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1043 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1046 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1049 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1052 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1055 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1058 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1061 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1064 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1066 // if ( xml_parser.getErrorCount() > 0 ) {
1067 // System.out.println( xml_parser.getErrorMessages().toString() );
1070 // if ( phylogenies_1.length != 2 ) {
1073 // final Phylogeny a = phylogenies_1[ 0 ];
1074 // if ( !a.getName().equals( "tree 4" ) ) {
1077 // if ( a.getNumberOfExternalNodes() != 3 ) {
1080 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1083 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1087 catch ( final Exception e ) {
1088 e.printStackTrace( System.out );
1094 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1096 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1097 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1098 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1099 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1102 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1104 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1106 if ( xml_parser.getErrorCount() > 0 ) {
1107 System.out.println( xml_parser.getErrorMessages().toString() );
1110 if ( phylogenies_0.length != 4 ) {
1113 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1114 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1115 if ( phylogenies_t1.length != 1 ) {
1118 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1119 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1122 if ( !t1_rt.isRooted() ) {
1125 if ( t1_rt.isRerootable() ) {
1128 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1131 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1132 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1133 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1134 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1137 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1140 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1143 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1146 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1147 .startsWith( "actgtgggggt" ) ) {
1150 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1151 .startsWith( "ctgtgatgcat" ) ) {
1154 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1155 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1156 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1157 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1158 if ( phylogenies_1.length != 1 ) {
1161 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1162 if ( !t3_rt.getName().equals( "t3" ) ) {
1165 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1168 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1171 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1174 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1177 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1178 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1181 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1184 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1187 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1188 .equals( "UniProtKB" ) ) {
1191 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1192 .equals( "apoptosis" ) ) {
1195 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1196 .equals( "GO:0006915" ) ) {
1199 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1200 .equals( "UniProtKB" ) ) {
1203 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1204 .equals( "experimental" ) ) {
1207 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1208 .equals( "function" ) ) {
1211 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1212 .getValue() != 1 ) {
1215 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1216 .getType().equals( "ml" ) ) {
1219 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1220 .equals( "apoptosis" ) ) {
1223 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1224 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1227 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1228 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1231 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1232 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1235 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1236 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1239 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1240 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1243 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1244 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1247 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1248 .equals( "GO:0005829" ) ) {
1251 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1252 .equals( "intracellular organelle" ) ) {
1255 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1258 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1259 .equals( "UniProt link" ) ) ) {
1262 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1265 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1268 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1269 .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." ) ) ) {
1272 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1275 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1278 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1281 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1284 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1285 .equals( "ncbi" ) ) {
1288 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1291 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1292 .getName().equals( "B" ) ) {
1295 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1296 .getFrom() != 21 ) {
1299 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1302 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1303 .getLength() != 24 ) {
1306 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1307 .getConfidence() != 2144 ) {
1310 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1311 .equals( "pfam" ) ) {
1314 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1317 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1320 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1323 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1326 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1327 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1330 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1333 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1336 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1339 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1342 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1345 if ( taxbb.getSynonyms().size() != 2 ) {
1348 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1351 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1354 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1357 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1360 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1363 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1364 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1368 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1371 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1374 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1377 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1380 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1383 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1386 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1390 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1393 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1394 .equalsIgnoreCase( "435" ) ) {
1397 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1400 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1401 .equalsIgnoreCase( "443.7" ) ) {
1404 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1407 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1410 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1411 .equalsIgnoreCase( "433" ) ) {
1415 catch ( final Exception e ) {
1416 e.printStackTrace( System.out );
1422 private static boolean testBasicPhyloXMLparsingValidating() {
1424 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1425 PhyloXmlParser xml_parser = null;
1427 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1429 catch ( final Exception e ) {
1430 // Do nothing -- means were not running from jar.
1432 if ( xml_parser == null ) {
1433 xml_parser = new PhyloXmlParser();
1434 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1435 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1438 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1441 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1443 if ( xml_parser.getErrorCount() > 0 ) {
1444 System.out.println( xml_parser.getErrorMessages().toString() );
1447 if ( phylogenies_0.length != 4 ) {
1450 final Phylogeny t1 = phylogenies_0[ 0 ];
1451 final Phylogeny t2 = phylogenies_0[ 1 ];
1452 final Phylogeny t3 = phylogenies_0[ 2 ];
1453 final Phylogeny t4 = phylogenies_0[ 3 ];
1454 if ( !t1.getName().equals( "t1" ) ) {
1457 if ( !t2.getName().equals( "t2" ) ) {
1460 if ( !t3.getName().equals( "t3" ) ) {
1463 if ( !t4.getName().equals( "t4" ) ) {
1466 if ( t1.getNumberOfExternalNodes() != 1 ) {
1469 if ( t2.getNumberOfExternalNodes() != 2 ) {
1472 if ( t3.getNumberOfExternalNodes() != 4 ) {
1475 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1476 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1477 if ( xml_parser.getErrorCount() > 0 ) {
1478 System.out.println( "errors:" );
1479 System.out.println( xml_parser.getErrorMessages().toString() );
1482 if ( phylogenies_1.length != 4 ) {
1485 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1487 if ( xml_parser.getErrorCount() > 0 ) {
1488 System.out.println( "errors:" );
1489 System.out.println( xml_parser.getErrorMessages().toString() );
1492 if ( phylogenies_2.length != 1 ) {
1495 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1498 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1500 if ( xml_parser.getErrorCount() > 0 ) {
1501 System.out.println( xml_parser.getErrorMessages().toString() );
1504 if ( phylogenies_3.length != 2 ) {
1507 final Phylogeny a = phylogenies_3[ 0 ];
1508 if ( !a.getName().equals( "tree 4" ) ) {
1511 if ( a.getNumberOfExternalNodes() != 3 ) {
1514 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1517 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1520 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1522 if ( xml_parser.getErrorCount() > 0 ) {
1523 System.out.println( xml_parser.getErrorMessages().toString() );
1526 if ( phylogenies_4.length != 1 ) {
1529 final Phylogeny s = phylogenies_4[ 0 ];
1530 if ( s.getNumberOfExternalNodes() != 6 ) {
1533 s.getNode( "first" );
1535 s.getNode( "\"<a'b&c'd\">\"" );
1536 s.getNode( "'''\"" );
1537 s.getNode( "\"\"\"" );
1538 s.getNode( "dick & doof" );
1540 catch ( final Exception e ) {
1541 e.printStackTrace( System.out );
1547 private static boolean testBasicTable() {
1549 final BasicTable<String> t0 = new BasicTable<String>();
1550 if ( t0.getNumberOfColumns() != 0 ) {
1553 if ( t0.getNumberOfRows() != 0 ) {
1556 t0.setValue( 3, 2, "23" );
1557 t0.setValue( 10, 1, "error" );
1558 t0.setValue( 10, 1, "110" );
1559 t0.setValue( 9, 1, "19" );
1560 t0.setValue( 1, 10, "101" );
1561 t0.setValue( 10, 10, "1010" );
1562 t0.setValue( 100, 10, "10100" );
1563 t0.setValue( 0, 0, "00" );
1564 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1567 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1570 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1573 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1576 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1579 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1582 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1585 if ( t0.getNumberOfColumns() != 101 ) {
1588 if ( t0.getNumberOfRows() != 11 ) {
1591 if ( t0.getValueAsString( 49, 4 ) != null ) {
1594 final String l = ForesterUtil.getLineSeparator();
1595 final StringBuffer source = new StringBuffer();
1596 source.append( "" + l );
1597 source.append( "# 1 1 1 1 1 1 1 1" + l );
1598 source.append( " 00 01 02 03" + l );
1599 source.append( " 10 11 12 13 " + l );
1600 source.append( "20 21 22 23 " + l );
1601 source.append( " 30 31 32 33" + l );
1602 source.append( "40 41 42 43" + l );
1603 source.append( " # 1 1 1 1 1 " + l );
1604 source.append( "50 51 52 53 54" + l );
1605 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1606 if ( t1.getNumberOfColumns() != 5 ) {
1609 if ( t1.getNumberOfRows() != 6 ) {
1612 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1615 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1618 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1621 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1624 final StringBuffer source1 = new StringBuffer();
1625 source1.append( "" + l );
1626 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1627 source1.append( " 00; 01 ;02;03" + l );
1628 source1.append( " 10; 11; 12; 13 " + l );
1629 source1.append( "20; 21; 22; 23 " + l );
1630 source1.append( " 30; 31; 32; 33" + l );
1631 source1.append( "40;41;42;43" + l );
1632 source1.append( " # 1 1 1 1 1 " + l );
1633 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1634 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1635 if ( t2.getNumberOfColumns() != 5 ) {
1638 if ( t2.getNumberOfRows() != 6 ) {
1641 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1644 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1647 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1650 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1653 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1656 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1659 final StringBuffer source2 = new StringBuffer();
1660 source2.append( "" + l );
1661 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1662 source2.append( " 00; 01 ;02;03" + l );
1663 source2.append( " 10; 11; 12; 13 " + l );
1664 source2.append( "20; 21; 22; 23 " + l );
1665 source2.append( " " + l );
1666 source2.append( " 30; 31; 32; 33" + l );
1667 source2.append( "40;41;42;43" + l );
1668 source2.append( " comment: 1 1 1 1 1 " + l );
1669 source2.append( ";;;50 ; 52; 53;;54 " + l );
1670 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1675 if ( tl.size() != 2 ) {
1678 final BasicTable<String> t3 = tl.get( 0 );
1679 final BasicTable<String> t4 = tl.get( 1 );
1680 if ( t3.getNumberOfColumns() != 4 ) {
1683 if ( t3.getNumberOfRows() != 3 ) {
1686 if ( t4.getNumberOfColumns() != 4 ) {
1689 if ( t4.getNumberOfRows() != 3 ) {
1692 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1695 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1699 catch ( final Exception e ) {
1700 e.printStackTrace( System.out );
1706 private static boolean testBasicTolXMLparsing() {
1708 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1709 final TolParser parser = new TolParser();
1710 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1711 if ( parser.getErrorCount() > 0 ) {
1712 System.out.println( parser.getErrorMessages().toString() );
1715 if ( phylogenies_0.length != 1 ) {
1718 final Phylogeny t1 = phylogenies_0[ 0 ];
1719 if ( t1.getNumberOfExternalNodes() != 5 ) {
1722 if ( !t1.isRooted() ) {
1725 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1728 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1731 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1734 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1737 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1738 if ( parser.getErrorCount() > 0 ) {
1739 System.out.println( parser.getErrorMessages().toString() );
1742 if ( phylogenies_1.length != 1 ) {
1745 final Phylogeny t2 = phylogenies_1[ 0 ];
1746 if ( t2.getNumberOfExternalNodes() != 664 ) {
1749 if ( !t2.isRooted() ) {
1752 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1755 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1758 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1761 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1764 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1767 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1768 .equals( "Aquifex" ) ) {
1771 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1772 if ( parser.getErrorCount() > 0 ) {
1773 System.out.println( parser.getErrorMessages().toString() );
1776 if ( phylogenies_2.length != 1 ) {
1779 final Phylogeny t3 = phylogenies_2[ 0 ];
1780 if ( t3.getNumberOfExternalNodes() != 184 ) {
1783 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1786 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1789 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1792 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1793 if ( parser.getErrorCount() > 0 ) {
1794 System.out.println( parser.getErrorMessages().toString() );
1797 if ( phylogenies_3.length != 1 ) {
1800 final Phylogeny t4 = phylogenies_3[ 0 ];
1801 if ( t4.getNumberOfExternalNodes() != 1 ) {
1804 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1807 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1810 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1813 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1814 if ( parser.getErrorCount() > 0 ) {
1815 System.out.println( parser.getErrorMessages().toString() );
1818 if ( phylogenies_4.length != 1 ) {
1821 final Phylogeny t5 = phylogenies_4[ 0 ];
1822 if ( t5.getNumberOfExternalNodes() != 13 ) {
1825 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1828 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1831 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1835 catch ( final Exception e ) {
1836 e.printStackTrace( System.out );
1842 private static boolean testBasicTreeMethods() {
1844 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1845 final Phylogeny t1 = factory.create();
1846 if ( !t1.isEmpty() ) {
1849 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1850 if ( t2.getNumberOfExternalNodes() != 4 ) {
1853 if ( t2.getHeight() != 8.5 ) {
1856 if ( !t2.isCompletelyBinary() ) {
1859 if ( t2.isEmpty() ) {
1862 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1863 if ( t3.getNumberOfExternalNodes() != 5 ) {
1866 if ( t3.getHeight() != 11 ) {
1869 if ( t3.isCompletelyBinary() ) {
1872 final PhylogenyNode n = t3.getNode( "ABC" );
1873 PhylogenyNodeIterator it;
1874 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1877 for( it.reset(); it.hasNext(); ) {
1880 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1881 if ( !it2.next().getName().equals( "A" ) ) {
1884 if ( !it2.next().getName().equals( "B" ) ) {
1887 if ( !it2.next().getName().equals( "C" ) ) {
1890 if ( it2.hasNext() ) {
1893 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 ];
1894 if ( t4.getNumberOfExternalNodes() != 9 ) {
1897 if ( t4.getHeight() != 11 ) {
1900 if ( t4.isCompletelyBinary() ) {
1903 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)" );
1904 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1905 if ( t5.getNumberOfExternalNodes() != 8 ) {
1908 if ( t5.getHeight() != 15 ) {
1911 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)" );
1912 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1913 if ( t6.getHeight() != 15 ) {
1916 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)" );
1917 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1918 if ( t7.getHeight() != 15 ) {
1921 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)" );
1922 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1923 if ( t8.getNumberOfExternalNodes() != 10 ) {
1926 if ( t8.getHeight() != 15 ) {
1929 final char[] a9 = new char[] {};
1930 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1931 if ( t9.getHeight() != 0 ) {
1934 final char[] a10 = new char[] { 'a', ':', '6' };
1935 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1936 if ( t10.getHeight() != 6 ) {
1940 catch ( final Exception e ) {
1941 e.printStackTrace( System.out );
1947 private static boolean testConfidenceAssessor() {
1949 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1950 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1951 final Phylogeny[] ev0 = factory
1952 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1954 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1955 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1958 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1961 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1962 final Phylogeny[] ev1 = factory
1963 .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)));",
1965 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1966 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
1969 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1972 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1973 final Phylogeny[] ev_b = factory
1974 .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",
1976 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
1977 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
1978 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
1981 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
1985 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1986 final Phylogeny[] ev1x = factory
1987 .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)));",
1989 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
1990 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1993 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
1996 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
1997 final Phylogeny[] ev_bx = factory
1998 .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",
2000 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2001 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2004 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2008 final Phylogeny[] t2 = factory
2009 .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);",
2011 final Phylogeny[] ev2 = factory
2012 .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);",
2014 for( final Phylogeny target : t2 ) {
2015 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2018 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2019 new NHXParser() )[ 0 ];
2020 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2021 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2022 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2025 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2028 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2032 catch ( final Exception e ) {
2033 e.printStackTrace();
2039 private static boolean testCopyOfNodeData() {
2041 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]" );
2042 final PhylogenyNode n2 = n1.copyNodeData();
2043 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2047 catch ( final Exception e ) {
2048 e.printStackTrace();
2054 private static boolean testDataObjects() {
2056 final Confidence s0 = new Confidence();
2057 final Confidence s1 = new Confidence();
2058 if ( !s0.isEqual( s1 ) ) {
2061 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2062 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2063 if ( s2.isEqual( s1 ) ) {
2066 if ( !s2.isEqual( s3 ) ) {
2069 final Confidence s4 = ( Confidence ) s3.copy();
2070 if ( !s4.isEqual( s3 ) ) {
2077 final Taxonomy t1 = new Taxonomy();
2078 final Taxonomy t2 = new Taxonomy();
2079 final Taxonomy t3 = new Taxonomy();
2080 final Taxonomy t4 = new Taxonomy();
2081 final Taxonomy t5 = new Taxonomy();
2082 t1.setIdentifier( new Identifier( "ecoli" ) );
2083 t1.setTaxonomyCode( "ECOLI" );
2084 t1.setScientificName( "E. coli" );
2085 t1.setCommonName( "coli" );
2086 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2087 if ( !t1.isEqual( t0 ) ) {
2090 t2.setIdentifier( new Identifier( "ecoli" ) );
2091 t2.setTaxonomyCode( "other" );
2092 t2.setScientificName( "what" );
2093 t2.setCommonName( "something" );
2094 if ( !t1.isEqual( t2 ) ) {
2097 t2.setIdentifier( new Identifier( "nemve" ) );
2098 if ( t1.isEqual( t2 ) ) {
2101 t1.setIdentifier( null );
2102 t3.setTaxonomyCode( "ECOLI" );
2103 t3.setScientificName( "what" );
2104 t3.setCommonName( "something" );
2105 if ( !t1.isEqual( t3 ) ) {
2108 t1.setIdentifier( null );
2109 t1.setTaxonomyCode( "" );
2110 t4.setScientificName( "E. ColI" );
2111 t4.setCommonName( "something" );
2112 if ( !t1.isEqual( t4 ) ) {
2115 t4.setScientificName( "B. subtilis" );
2116 t4.setCommonName( "something" );
2117 if ( t1.isEqual( t4 ) ) {
2120 t1.setIdentifier( null );
2121 t1.setTaxonomyCode( "" );
2122 t1.setScientificName( "" );
2123 t5.setCommonName( "COLI" );
2124 if ( !t1.isEqual( t5 ) ) {
2127 t5.setCommonName( "vibrio" );
2128 if ( t1.isEqual( t5 ) ) {
2133 final Identifier id0 = new Identifier( "123", "pfam" );
2134 final Identifier id1 = ( Identifier ) id0.copy();
2135 if ( !id1.isEqual( id1 ) ) {
2138 if ( !id1.isEqual( id0 ) ) {
2141 if ( !id0.isEqual( id1 ) ) {
2148 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2149 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2150 if ( !pd1.isEqual( pd1 ) ) {
2153 if ( !pd1.isEqual( pd0 ) ) {
2158 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2159 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2160 if ( !pd3.isEqual( pd3 ) ) {
2163 if ( !pd2.isEqual( pd3 ) ) {
2166 if ( !pd0.isEqual( pd3 ) ) {
2171 // DomainArchitecture
2172 // ------------------
2173 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2174 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2175 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2176 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2177 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2178 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2183 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2184 if ( ds0.getNumberOfDomains() != 4 ) {
2187 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2188 if ( !ds0.isEqual( ds0 ) ) {
2191 if ( !ds0.isEqual( ds1 ) ) {
2194 if ( ds1.getNumberOfDomains() != 4 ) {
2197 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2202 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2203 if ( ds0.isEqual( ds2 ) ) {
2209 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2210 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2211 System.out.println( ds3.toNHX() );
2214 if ( ds3.getNumberOfDomains() != 3 ) {
2219 final Event e1 = new Event( Event.EventType.fusion );
2220 if ( e1.isDuplication() ) {
2223 if ( !e1.isFusion() ) {
2226 if ( !e1.asText().toString().equals( "fusion" ) ) {
2229 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2232 final Event e11 = new Event( Event.EventType.fusion );
2233 if ( !e11.isEqual( e1 ) ) {
2236 if ( !e11.toNHX().toString().equals( "" ) ) {
2239 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2240 if ( e2.isDuplication() ) {
2243 if ( !e2.isSpeciationOrDuplication() ) {
2246 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2249 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2252 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2255 if ( e11.isEqual( e2 ) ) {
2258 final Event e2c = ( Event ) e2.copy();
2259 if ( !e2c.isEqual( e2 ) ) {
2262 Event e3 = new Event( 1, 2, 3 );
2263 if ( e3.isDuplication() ) {
2266 if ( e3.isSpeciation() ) {
2269 if ( e3.isGeneLoss() ) {
2272 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2275 final Event e3c = ( Event ) e3.copy();
2276 final Event e3cc = ( Event ) e3c.copy();
2277 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2281 if ( !e3c.isEqual( e3cc ) ) {
2284 Event e4 = new Event( 1, 2, 3 );
2285 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2288 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2291 final Event e4c = ( Event ) e4.copy();
2293 final Event e4cc = ( Event ) e4c.copy();
2294 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2297 if ( !e4c.isEqual( e4cc ) ) {
2300 final Event e5 = new Event();
2301 if ( !e5.isUnassigned() ) {
2304 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2307 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2310 final Event e6 = new Event( 1, 0, 0 );
2311 if ( !e6.asText().toString().equals( "duplication" ) ) {
2314 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2317 final Event e7 = new Event( 0, 1, 0 );
2318 if ( !e7.asText().toString().equals( "speciation" ) ) {
2321 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2324 final Event e8 = new Event( 0, 0, 1 );
2325 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2328 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2332 catch ( final Exception e ) {
2333 e.printStackTrace( System.out );
2339 private static boolean testDeletionOfExternalNodes() {
2341 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2342 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2343 final PhylogenyWriter w = new PhylogenyWriter();
2344 if ( t0.isEmpty() ) {
2347 if ( t0.getNumberOfExternalNodes() != 1 ) {
2350 t0.deleteSubtree( t0.getNode( "A" ), false );
2351 if ( t0.getNumberOfExternalNodes() != 0 ) {
2354 if ( !t0.isEmpty() ) {
2357 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2358 if ( t1.getNumberOfExternalNodes() != 2 ) {
2361 t1.deleteSubtree( t1.getNode( "A" ), false );
2362 if ( t1.getNumberOfExternalNodes() != 1 ) {
2365 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2368 t1.deleteSubtree( t1.getNode( "B" ), false );
2369 if ( t1.getNumberOfExternalNodes() != 1 ) {
2372 t1.deleteSubtree( t1.getNode( "r" ), false );
2373 if ( !t1.isEmpty() ) {
2376 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2377 if ( t2.getNumberOfExternalNodes() != 3 ) {
2380 t2.deleteSubtree( t2.getNode( "B" ), false );
2381 if ( t2.getNumberOfExternalNodes() != 2 ) {
2384 t2.toNewHampshireX();
2385 PhylogenyNode n = t2.getNode( "A" );
2386 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2389 t2.deleteSubtree( t2.getNode( "A" ), false );
2390 if ( t2.getNumberOfExternalNodes() != 2 ) {
2393 t2.deleteSubtree( t2.getNode( "C" ), true );
2394 if ( t2.getNumberOfExternalNodes() != 1 ) {
2397 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2398 if ( t3.getNumberOfExternalNodes() != 4 ) {
2401 t3.deleteSubtree( t3.getNode( "B" ), true );
2402 if ( t3.getNumberOfExternalNodes() != 3 ) {
2405 n = t3.getNode( "A" );
2406 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2409 n = n.getNextExternalNode();
2410 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2413 t3.deleteSubtree( t3.getNode( "A" ), true );
2414 if ( t3.getNumberOfExternalNodes() != 2 ) {
2417 n = t3.getNode( "C" );
2418 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2421 t3.deleteSubtree( t3.getNode( "C" ), true );
2422 if ( t3.getNumberOfExternalNodes() != 1 ) {
2425 t3.deleteSubtree( t3.getNode( "D" ), true );
2426 if ( t3.getNumberOfExternalNodes() != 0 ) {
2429 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2430 if ( t4.getNumberOfExternalNodes() != 6 ) {
2433 t4.deleteSubtree( t4.getNode( "B2" ), true );
2434 if ( t4.getNumberOfExternalNodes() != 5 ) {
2437 String s = w.toNewHampshire( t4, false, true ).toString();
2438 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2441 t4.deleteSubtree( t4.getNode( "B11" ), true );
2442 if ( t4.getNumberOfExternalNodes() != 4 ) {
2445 t4.deleteSubtree( t4.getNode( "C" ), true );
2446 if ( t4.getNumberOfExternalNodes() != 3 ) {
2449 n = t4.getNode( "A" );
2450 n = n.getNextExternalNode();
2451 if ( !n.getName().equals( "B12" ) ) {
2454 n = n.getNextExternalNode();
2455 if ( !n.getName().equals( "D" ) ) {
2458 s = w.toNewHampshire( t4, false, true ).toString();
2459 if ( !s.equals( "((A,B12),D);" ) ) {
2462 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2463 t5.deleteSubtree( t5.getNode( "A" ), true );
2464 if ( t5.getNumberOfExternalNodes() != 5 ) {
2467 s = w.toNewHampshire( t5, false, true ).toString();
2468 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2471 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2472 t6.deleteSubtree( t6.getNode( "B11" ), true );
2473 if ( t6.getNumberOfExternalNodes() != 5 ) {
2476 s = w.toNewHampshire( t6, false, false ).toString();
2477 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2480 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2481 t7.deleteSubtree( t7.getNode( "B12" ), true );
2482 if ( t7.getNumberOfExternalNodes() != 5 ) {
2485 s = w.toNewHampshire( t7, false, true ).toString();
2486 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2489 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2490 t8.deleteSubtree( t8.getNode( "B2" ), true );
2491 if ( t8.getNumberOfExternalNodes() != 5 ) {
2494 s = w.toNewHampshire( t8, false, false ).toString();
2495 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2498 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2499 t9.deleteSubtree( t9.getNode( "C" ), true );
2500 if ( t9.getNumberOfExternalNodes() != 5 ) {
2503 s = w.toNewHampshire( t9, false, true ).toString();
2504 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2507 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2508 t10.deleteSubtree( t10.getNode( "D" ), true );
2509 if ( t10.getNumberOfExternalNodes() != 5 ) {
2512 s = w.toNewHampshire( t10, false, true ).toString();
2513 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2516 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2517 t11.deleteSubtree( t11.getNode( "A" ), true );
2518 if ( t11.getNumberOfExternalNodes() != 2 ) {
2521 s = w.toNewHampshire( t11, false, true ).toString();
2522 if ( !s.equals( "(B,C);" ) ) {
2525 t11.deleteSubtree( t11.getNode( "C" ), true );
2526 if ( t11.getNumberOfExternalNodes() != 1 ) {
2529 s = w.toNewHampshire( t11, false, false ).toString();
2530 if ( !s.equals( "B;" ) ) {
2533 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2534 t12.deleteSubtree( t12.getNode( "B2" ), true );
2535 if ( t12.getNumberOfExternalNodes() != 8 ) {
2538 s = w.toNewHampshire( t12, false, true ).toString();
2539 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2542 t12.deleteSubtree( t12.getNode( "B3" ), true );
2543 if ( t12.getNumberOfExternalNodes() != 7 ) {
2546 s = w.toNewHampshire( t12, false, true ).toString();
2547 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2550 t12.deleteSubtree( t12.getNode( "C3" ), true );
2551 if ( t12.getNumberOfExternalNodes() != 6 ) {
2554 s = w.toNewHampshire( t12, false, true ).toString();
2555 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2558 t12.deleteSubtree( t12.getNode( "A1" ), true );
2559 if ( t12.getNumberOfExternalNodes() != 5 ) {
2562 s = w.toNewHampshire( t12, false, true ).toString();
2563 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2566 t12.deleteSubtree( t12.getNode( "B1" ), true );
2567 if ( t12.getNumberOfExternalNodes() != 4 ) {
2570 s = w.toNewHampshire( t12, false, true ).toString();
2571 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2574 t12.deleteSubtree( t12.getNode( "A3" ), true );
2575 if ( t12.getNumberOfExternalNodes() != 3 ) {
2578 s = w.toNewHampshire( t12, false, true ).toString();
2579 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2582 t12.deleteSubtree( t12.getNode( "A2" ), true );
2583 if ( t12.getNumberOfExternalNodes() != 2 ) {
2586 s = w.toNewHampshire( t12, false, true ).toString();
2587 if ( !s.equals( "(C1,C2);" ) ) {
2590 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2591 t13.deleteSubtree( t13.getNode( "D" ), true );
2592 if ( t13.getNumberOfExternalNodes() != 4 ) {
2595 s = w.toNewHampshire( t13, false, true ).toString();
2596 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2599 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2600 t14.deleteSubtree( t14.getNode( "E" ), true );
2601 if ( t14.getNumberOfExternalNodes() != 5 ) {
2604 s = w.toNewHampshire( t14, false, true ).toString();
2605 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2608 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2609 t15.deleteSubtree( t15.getNode( "B2" ), true );
2610 if ( t15.getNumberOfExternalNodes() != 11 ) {
2613 t15.deleteSubtree( t15.getNode( "B1" ), true );
2614 if ( t15.getNumberOfExternalNodes() != 10 ) {
2617 t15.deleteSubtree( t15.getNode( "B3" ), true );
2618 if ( t15.getNumberOfExternalNodes() != 9 ) {
2621 t15.deleteSubtree( t15.getNode( "B4" ), true );
2622 if ( t15.getNumberOfExternalNodes() != 8 ) {
2625 t15.deleteSubtree( t15.getNode( "A1" ), true );
2626 if ( t15.getNumberOfExternalNodes() != 7 ) {
2629 t15.deleteSubtree( t15.getNode( "C4" ), true );
2630 if ( t15.getNumberOfExternalNodes() != 6 ) {
2634 catch ( final Exception e ) {
2635 e.printStackTrace( System.out );
2641 private static boolean testDescriptiveStatistics() {
2643 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2644 dss1.addValue( 82 );
2645 dss1.addValue( 78 );
2646 dss1.addValue( 70 );
2647 dss1.addValue( 58 );
2648 dss1.addValue( 42 );
2649 if ( dss1.getN() != 5 ) {
2652 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2655 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2658 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2661 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2664 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2667 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2670 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2673 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2676 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2679 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2682 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2685 dss1.addValue( 123 );
2686 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2689 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2692 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2695 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2696 dss2.addValue( -1.85 );
2697 dss2.addValue( 57.5 );
2698 dss2.addValue( 92.78 );
2699 dss2.addValue( 57.78 );
2700 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2703 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2706 final double[] a = dss2.getDataAsDoubleArray();
2707 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2710 dss2.addValue( -100 );
2711 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2714 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2717 final double[] ds = new double[ 14 ];
2732 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2733 if ( bins.length != 4 ) {
2736 if ( bins[ 0 ] != 2 ) {
2739 if ( bins[ 1 ] != 3 ) {
2742 if ( bins[ 2 ] != 4 ) {
2745 if ( bins[ 3 ] != 5 ) {
2748 final double[] ds1 = new double[ 9 ];
2758 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2759 if ( bins1.length != 4 ) {
2762 if ( bins1[ 0 ] != 2 ) {
2765 if ( bins1[ 1 ] != 3 ) {
2768 if ( bins1[ 2 ] != 0 ) {
2771 if ( bins1[ 3 ] != 4 ) {
2774 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2775 if ( bins1_1.length != 3 ) {
2778 if ( bins1_1[ 0 ] != 3 ) {
2781 if ( bins1_1[ 1 ] != 2 ) {
2784 if ( bins1_1[ 2 ] != 4 ) {
2787 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2788 if ( bins1_2.length != 3 ) {
2791 if ( bins1_2[ 0 ] != 2 ) {
2794 if ( bins1_2[ 1 ] != 2 ) {
2797 if ( bins1_2[ 2 ] != 2 ) {
2800 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2814 dss3.addValue( 10 );
2815 dss3.addValue( 10 );
2816 dss3.addValue( 10 );
2817 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2818 histo.toStringBuffer( 10, '=', 40, 5 );
2819 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2821 catch ( final Exception e ) {
2822 e.printStackTrace( System.out );
2828 private static boolean testDir( final String file ) {
2830 final File f = new File( file );
2831 if ( !f.exists() ) {
2834 if ( !f.isDirectory() ) {
2837 if ( !f.canRead() ) {
2841 catch ( final Exception e ) {
2847 private static boolean testExternalNodeRelatedMethods() {
2849 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2850 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2851 PhylogenyNode n = t1.getNode( "A" );
2852 n = n.getNextExternalNode();
2853 if ( !n.getName().equals( "B" ) ) {
2856 n = n.getNextExternalNode();
2857 if ( !n.getName().equals( "C" ) ) {
2860 n = n.getNextExternalNode();
2861 if ( !n.getName().equals( "D" ) ) {
2864 n = t1.getNode( "B" );
2865 while ( !n.isLastExternalNode() ) {
2866 n = n.getNextExternalNode();
2868 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2869 n = t2.getNode( "A" );
2870 n = n.getNextExternalNode();
2871 if ( !n.getName().equals( "B" ) ) {
2874 n = n.getNextExternalNode();
2875 if ( !n.getName().equals( "C" ) ) {
2878 n = n.getNextExternalNode();
2879 if ( !n.getName().equals( "D" ) ) {
2882 n = t2.getNode( "B" );
2883 while ( !n.isLastExternalNode() ) {
2884 n = n.getNextExternalNode();
2886 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2887 n = t3.getNode( "A" );
2888 n = n.getNextExternalNode();
2889 if ( !n.getName().equals( "B" ) ) {
2892 n = n.getNextExternalNode();
2893 if ( !n.getName().equals( "C" ) ) {
2896 n = n.getNextExternalNode();
2897 if ( !n.getName().equals( "D" ) ) {
2900 n = n.getNextExternalNode();
2901 if ( !n.getName().equals( "E" ) ) {
2904 n = n.getNextExternalNode();
2905 if ( !n.getName().equals( "F" ) ) {
2908 n = n.getNextExternalNode();
2909 if ( !n.getName().equals( "G" ) ) {
2912 n = n.getNextExternalNode();
2913 if ( !n.getName().equals( "H" ) ) {
2916 n = t3.getNode( "B" );
2917 while ( !n.isLastExternalNode() ) {
2918 n = n.getNextExternalNode();
2920 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2921 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2922 final PhylogenyNode node = iter.next();
2924 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2925 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2926 final PhylogenyNode node = iter.next();
2929 catch ( final Exception e ) {
2930 e.printStackTrace( System.out );
2936 private static boolean testGeneralTable() {
2938 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2939 t0.setValue( 3, 2, "23" );
2940 t0.setValue( 10, 1, "error" );
2941 t0.setValue( 10, 1, "110" );
2942 t0.setValue( 9, 1, "19" );
2943 t0.setValue( 1, 10, "101" );
2944 t0.setValue( 10, 10, "1010" );
2945 t0.setValue( 100, 10, "10100" );
2946 t0.setValue( 0, 0, "00" );
2947 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2950 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2953 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2956 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2959 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2962 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2965 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
2968 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
2971 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
2974 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
2975 t1.setValue( "3", "2", "23" );
2976 t1.setValue( "10", "1", "error" );
2977 t1.setValue( "10", "1", "110" );
2978 t1.setValue( "9", "1", "19" );
2979 t1.setValue( "1", "10", "101" );
2980 t1.setValue( "10", "10", "1010" );
2981 t1.setValue( "100", "10", "10100" );
2982 t1.setValue( "0", "0", "00" );
2983 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
2984 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
2987 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
2990 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
2993 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
2996 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
2999 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3002 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3005 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3008 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3011 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3015 catch ( final Exception e ) {
3016 e.printStackTrace( System.out );
3022 private static boolean testGetDistance() {
3024 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3025 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",
3026 new NHXParser() )[ 0 ];
3027 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3028 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3031 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3034 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3037 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3040 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3043 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3046 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3049 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3052 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3055 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3058 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3061 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3064 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3067 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3070 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3073 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3076 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3079 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3082 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3085 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3088 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3091 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3094 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3097 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3100 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3103 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3106 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3109 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3112 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3115 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3118 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3121 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",
3122 new NHXParser() )[ 0 ];
3123 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3126 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3129 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3132 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3135 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3138 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3141 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3144 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3147 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3150 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3153 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3157 catch ( final Exception e ) {
3158 e.printStackTrace( System.out );
3164 private static boolean testGetLCA() {
3166 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3167 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3168 new NHXParser() )[ 0 ];
3169 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3170 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3171 if ( !A.getName().equals( "A" ) ) {
3174 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3175 if ( !gh.getName().equals( "gh" ) ) {
3178 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3179 if ( !ab.getName().equals( "ab" ) ) {
3182 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3183 if ( !ab2.getName().equals( "ab" ) ) {
3186 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3187 if ( !gh2.getName().equals( "gh" ) ) {
3190 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3191 if ( !gh3.getName().equals( "gh" ) ) {
3194 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3195 if ( !abc.getName().equals( "abc" ) ) {
3198 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3199 if ( !abc2.getName().equals( "abc" ) ) {
3202 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3203 if ( !abcd.getName().equals( "abcd" ) ) {
3206 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3207 if ( !abcd2.getName().equals( "abcd" ) ) {
3210 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3211 if ( !abcdef.getName().equals( "abcdef" ) ) {
3214 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3215 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3218 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3219 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3222 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3223 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3226 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3227 if ( !abcde.getName().equals( "abcde" ) ) {
3230 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3231 if ( !abcde2.getName().equals( "abcde" ) ) {
3234 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3235 if ( !r.getName().equals( "abcdefgh" ) ) {
3238 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3239 if ( !r2.getName().equals( "abcdefgh" ) ) {
3242 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3243 if ( !r3.getName().equals( "abcdefgh" ) ) {
3246 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3247 if ( !abcde3.getName().equals( "abcde" ) ) {
3250 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3251 if ( !abcde4.getName().equals( "abcde" ) ) {
3254 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3255 if ( !ab3.getName().equals( "ab" ) ) {
3258 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3259 if ( !ab4.getName().equals( "ab" ) ) {
3262 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3263 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3264 if ( !cd.getName().equals( "cd" ) ) {
3267 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3268 if ( !cd2.getName().equals( "cd" ) ) {
3271 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3272 if ( !cde.getName().equals( "cde" ) ) {
3275 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3276 if ( !cde2.getName().equals( "cde" ) ) {
3279 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3280 if ( !cdef.getName().equals( "cdef" ) ) {
3283 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3284 if ( !cdef2.getName().equals( "cdef" ) ) {
3287 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3288 if ( !cdef3.getName().equals( "cdef" ) ) {
3291 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3292 if ( !rt.getName().equals( "r" ) ) {
3295 final Phylogeny p3 = factory
3296 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3297 new NHXParser() )[ 0 ];
3298 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3299 if ( !bc_3.getName().equals( "bc" ) ) {
3302 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3303 if ( !ac_3.getName().equals( "abc" ) ) {
3306 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3307 if ( !ad_3.getName().equals( "abcde" ) ) {
3310 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3311 if ( !af_3.getName().equals( "abcdef" ) ) {
3314 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3315 if ( !ag_3.getName().equals( "" ) ) {
3318 if ( !ag_3.isRoot() ) {
3321 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3322 if ( !al_3.getName().equals( "" ) ) {
3325 if ( !al_3.isRoot() ) {
3328 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3329 if ( !kl_3.getName().equals( "" ) ) {
3332 if ( !kl_3.isRoot() ) {
3335 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3336 if ( !fl_3.getName().equals( "" ) ) {
3339 if ( !fl_3.isRoot() ) {
3342 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3343 if ( !gk_3.getName().equals( "ghijk" ) ) {
3346 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3347 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3348 if ( !r_4.getName().equals( "r" ) ) {
3351 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3352 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3353 if ( !r_5.getName().equals( "root" ) ) {
3356 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3357 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3358 if ( !r_6.getName().equals( "rot" ) ) {
3361 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3362 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3363 if ( !r_7.getName().equals( "rott" ) ) {
3367 catch ( final Exception e ) {
3368 e.printStackTrace( System.out );
3374 private static boolean testHmmscanOutputParser() {
3375 final String test_dir = Test.PATH_TO_TEST_DATA;
3377 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3378 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3380 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3381 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3382 final List<Protein> domain_collections = parser2.parse();
3383 if ( parser2.getProteinsEncountered() != 4 ) {
3386 if ( domain_collections.size() != 4 ) {
3389 if ( parser2.getDomainsEncountered() != 69 ) {
3392 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3395 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3398 final Protein p1 = domain_collections.get( 0 );
3399 if ( p1.getNumberOfProteinDomains() != 15 ) {
3402 final Protein p4 = domain_collections.get( 3 );
3403 if ( p4.getNumberOfProteinDomains() != 1 ) {
3406 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3409 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3412 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3415 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3418 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3421 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3424 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3427 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3430 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3434 catch ( final Exception e ) {
3435 e.printStackTrace( System.out );
3441 private static boolean testLastExternalNodeMethods() {
3443 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3444 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3445 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3446 final PhylogenyNode n1 = t0.getNode( "A" );
3447 if ( n1.isLastExternalNode() ) {
3450 final PhylogenyNode n2 = t0.getNode( "B" );
3451 if ( n2.isLastExternalNode() ) {
3454 final PhylogenyNode n3 = t0.getNode( "C" );
3455 if ( n3.isLastExternalNode() ) {
3458 final PhylogenyNode n4 = t0.getNode( "D" );
3459 if ( !n4.isLastExternalNode() ) {
3463 catch ( final Exception e ) {
3464 e.printStackTrace( System.out );
3470 private static boolean testLevelOrderIterator() {
3472 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3473 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3474 PhylogenyNodeIterator it0;
3475 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3478 for( it0.reset(); it0.hasNext(); ) {
3481 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3482 if ( !it.next().getName().equals( "r" ) ) {
3485 if ( !it.next().getName().equals( "ab" ) ) {
3488 if ( !it.next().getName().equals( "cd" ) ) {
3491 if ( !it.next().getName().equals( "A" ) ) {
3494 if ( !it.next().getName().equals( "B" ) ) {
3497 if ( !it.next().getName().equals( "C" ) ) {
3500 if ( !it.next().getName().equals( "D" ) ) {
3503 if ( it.hasNext() ) {
3506 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",
3507 new NHXParser() )[ 0 ];
3508 PhylogenyNodeIterator it2;
3509 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3512 for( it2.reset(); it2.hasNext(); ) {
3515 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3516 if ( !it3.next().getName().equals( "r" ) ) {
3519 if ( !it3.next().getName().equals( "abc" ) ) {
3522 if ( !it3.next().getName().equals( "defg" ) ) {
3525 if ( !it3.next().getName().equals( "A" ) ) {
3528 if ( !it3.next().getName().equals( "B" ) ) {
3531 if ( !it3.next().getName().equals( "C" ) ) {
3534 if ( !it3.next().getName().equals( "D" ) ) {
3537 if ( !it3.next().getName().equals( "E" ) ) {
3540 if ( !it3.next().getName().equals( "F" ) ) {
3543 if ( !it3.next().getName().equals( "G" ) ) {
3546 if ( !it3.next().getName().equals( "1" ) ) {
3549 if ( !it3.next().getName().equals( "2" ) ) {
3552 if ( !it3.next().getName().equals( "3" ) ) {
3555 if ( !it3.next().getName().equals( "4" ) ) {
3558 if ( !it3.next().getName().equals( "5" ) ) {
3561 if ( !it3.next().getName().equals( "6" ) ) {
3564 if ( !it3.next().getName().equals( "f1" ) ) {
3567 if ( !it3.next().getName().equals( "f2" ) ) {
3570 if ( !it3.next().getName().equals( "f3" ) ) {
3573 if ( !it3.next().getName().equals( "a" ) ) {
3576 if ( !it3.next().getName().equals( "b" ) ) {
3579 if ( !it3.next().getName().equals( "f21" ) ) {
3582 if ( !it3.next().getName().equals( "X" ) ) {
3585 if ( !it3.next().getName().equals( "Y" ) ) {
3588 if ( !it3.next().getName().equals( "Z" ) ) {
3591 if ( it3.hasNext() ) {
3594 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3595 PhylogenyNodeIterator it4;
3596 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3599 for( it4.reset(); it4.hasNext(); ) {
3602 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3603 if ( !it5.next().getName().equals( "r" ) ) {
3606 if ( !it5.next().getName().equals( "A" ) ) {
3609 if ( !it5.next().getName().equals( "B" ) ) {
3612 if ( !it5.next().getName().equals( "C" ) ) {
3615 if ( !it5.next().getName().equals( "D" ) ) {
3618 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3619 PhylogenyNodeIterator it6;
3620 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3623 for( it6.reset(); it6.hasNext(); ) {
3626 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3627 if ( !it7.next().getName().equals( "A" ) ) {
3630 if ( it.hasNext() ) {
3634 catch ( final Exception e ) {
3635 e.printStackTrace( System.out );
3641 private static boolean testMidpointrooting() {
3643 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3644 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",
3645 new NHXParser() )[ 0 ];
3646 if ( !t1.isRooted() ) {
3649 PhylogenyMethods.midpointRoot( t1 );
3650 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3653 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3656 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3659 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3662 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3665 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3668 t1.reRoot( t1.getNode( "A" ) );
3669 PhylogenyMethods.midpointRoot( t1 );
3670 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3673 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3676 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3679 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3682 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3685 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3689 catch ( final Exception e ) {
3690 e.printStackTrace( System.out );
3696 private static boolean testNexusCharactersParsing() {
3698 final NexusCharactersParser parser = new NexusCharactersParser();
3699 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3701 String[] labels = parser.getCharStateLabels();
3702 if ( labels.length != 7 ) {
3705 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3708 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3711 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3714 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3717 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3720 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3723 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3726 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3728 labels = parser.getCharStateLabels();
3729 if ( labels.length != 7 ) {
3732 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3735 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3738 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3741 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3744 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3747 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3750 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3754 catch ( final Exception e ) {
3755 e.printStackTrace( System.out );
3761 private static boolean testNexusMatrixParsing() {
3763 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3764 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3766 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3767 if ( m.getNumberOfCharacters() != 9 ) {
3770 if ( m.getNumberOfIdentifiers() != 5 ) {
3773 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3776 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3779 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3782 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3785 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3788 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3791 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3794 // if ( labels.length != 7 ) {
3797 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3800 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3803 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3806 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3809 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3812 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3815 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3818 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3820 // labels = parser.getCharStateLabels();
3821 // if ( labels.length != 7 ) {
3824 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3827 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3830 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3833 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3836 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3839 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3842 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3846 catch ( final Exception e ) {
3847 e.printStackTrace( System.out );
3853 private static boolean testNexusTreeParsing() {
3855 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3856 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3857 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3858 if ( phylogenies.length != 1 ) {
3861 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3864 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3868 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3869 if ( phylogenies.length != 1 ) {
3872 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3875 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3879 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3880 if ( phylogenies.length != 1 ) {
3883 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3886 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3889 if ( phylogenies[ 0 ].isRooted() ) {
3893 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3894 if ( phylogenies.length != 18 ) {
3897 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3900 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3903 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3906 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3909 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3912 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3915 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3918 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3921 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3924 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3927 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3930 if ( phylogenies[ 8 ].isRooted() ) {
3933 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3936 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3939 if ( !phylogenies[ 9 ].isRooted() ) {
3942 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3945 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3948 if ( !phylogenies[ 10 ].isRooted() ) {
3951 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3954 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3957 if ( phylogenies[ 11 ].isRooted() ) {
3960 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
3963 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
3966 if ( !phylogenies[ 12 ].isRooted() ) {
3969 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
3972 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
3975 if ( !phylogenies[ 13 ].isRooted() ) {
3978 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
3981 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
3984 if ( !phylogenies[ 14 ].isRooted() ) {
3987 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
3990 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
3993 if ( phylogenies[ 15 ].isRooted() ) {
3996 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
3999 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4002 if ( !phylogenies[ 16 ].isRooted() ) {
4005 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4008 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4011 if ( phylogenies[ 17 ].isRooted() ) {
4014 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4018 catch ( final Exception e ) {
4019 e.printStackTrace( System.out );
4025 private static boolean testNexusTreeParsingTranslating() {
4027 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4028 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4029 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4030 if ( phylogenies.length != 1 ) {
4033 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4036 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4039 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4042 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4045 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4046 .equals( "Aranaeus" ) ) {
4050 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4051 if ( phylogenies.length != 3 ) {
4054 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4057 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4060 if ( phylogenies[ 0 ].isRooted() ) {
4063 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4066 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4069 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4070 .equals( "Aranaeus" ) ) {
4073 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4076 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4079 if ( phylogenies[ 1 ].isRooted() ) {
4082 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4085 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4088 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4089 .equals( "Aranaeus" ) ) {
4092 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4095 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4098 if ( !phylogenies[ 2 ].isRooted() ) {
4101 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4104 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4107 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4108 .equals( "Aranaeus" ) ) {
4112 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4113 if ( phylogenies.length != 3 ) {
4116 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4119 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4122 if ( phylogenies[ 0 ].isRooted() ) {
4125 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4128 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4131 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4132 .equals( "Aranaeus" ) ) {
4135 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4138 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4141 if ( phylogenies[ 1 ].isRooted() ) {
4144 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4147 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4150 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4151 .equals( "Aranaeus" ) ) {
4154 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4157 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4160 if ( !phylogenies[ 2 ].isRooted() ) {
4163 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4166 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4169 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4170 .equals( "Aranaeus" ) ) {
4174 catch ( final Exception e ) {
4175 e.printStackTrace( System.out );
4181 private static boolean testNHParsing() {
4183 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4184 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4185 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4188 final NHXParser nhxp = new NHXParser();
4189 nhxp.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
4190 nhxp.setReplaceUnderscores( true );
4191 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4192 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4195 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4198 final Phylogeny p1b = factory
4199 .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 ",
4200 new NHXParser() )[ 0 ];
4201 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4204 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4207 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4208 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4209 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4210 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4211 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4212 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4213 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4214 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4215 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4216 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4217 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4218 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4219 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4221 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4224 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4227 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4230 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4233 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4234 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4235 final String p16_S = "((A,B),C)";
4236 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4237 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4240 final String p17_S = "(C,(A,B))";
4241 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4242 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4245 final String p18_S = "((A,B),(C,D))";
4246 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4247 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4250 final String p19_S = "(((A,B),C),D)";
4251 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4252 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4255 final String p20_S = "(A,(B,(C,D)))";
4256 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4257 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4260 final String p21_S = "(A,(B,(C,(D,E))))";
4261 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4262 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4265 final String p22_S = "((((A,B),C),D),E)";
4266 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4267 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4270 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4271 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4272 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4275 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4276 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4277 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4280 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4281 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4282 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4283 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4286 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4289 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4290 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4291 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4292 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4293 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4294 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4295 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4296 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4297 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4298 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4301 final String p26_S = "(A,B)ab";
4302 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4303 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4306 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4307 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4309 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4312 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4313 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4314 final String p28_S3 = "(A,B)ab";
4315 final String p28_S4 = "((((A,B),C),D),;E;)";
4316 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4318 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4321 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4324 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4327 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4330 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";
4331 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4332 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4335 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";
4336 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4337 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4340 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4341 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4342 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4345 final String p33_S = "A";
4346 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4347 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4350 final String p34_S = "B;";
4351 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4352 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4355 final String p35_S = "B:0.2";
4356 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4357 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4360 final String p36_S = "(A)";
4361 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4362 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4365 final String p37_S = "((A))";
4366 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4367 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4370 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4371 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4372 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4375 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4376 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4377 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4380 final String p40_S = "(A,B,C)";
4381 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4382 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4385 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4386 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4387 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4390 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4391 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4392 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4395 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)";
4396 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4397 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4400 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)))";
4401 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4402 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4405 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4406 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4407 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4410 final String p46_S = "";
4411 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4412 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4416 catch ( final Exception e ) {
4417 e.printStackTrace( System.out );
4423 private static boolean testNHXconversion() {
4425 final PhylogenyNode n1 = new PhylogenyNode();
4426 final PhylogenyNode n2 = new PhylogenyNode( "" );
4427 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4428 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4429 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]" );
4430 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]" );
4431 if ( !n1.toNewHampshireX().equals( "" ) ) {
4434 if ( !n2.toNewHampshireX().equals( "" ) ) {
4437 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4440 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4443 if ( !n5.toNewHampshireX()
4444 .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]" ) ) {
4447 if ( !n6.toNewHampshireX()
4448 .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]" ) ) {
4452 catch ( final Exception e ) {
4453 e.printStackTrace( System.out );
4459 private static boolean testNHXNodeParsing() {
4461 final PhylogenyNode n1 = new PhylogenyNode();
4462 final PhylogenyNode n2 = new PhylogenyNode( "" );
4463 final PhylogenyNode n3 = new PhylogenyNode( "n3" );
4464 final PhylogenyNode n4 = new PhylogenyNode( "n4:0.01" );
4465 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]" );
4466 if ( !n3.getName().equals( "n3" ) ) {
4469 if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4472 if ( n3.isDuplication() ) {
4475 if ( n3.isHasAssignedEvent() ) {
4478 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4481 if ( !n4.getName().equals( "n4" ) ) {
4484 if ( n4.getDistanceToParent() != 0.01 ) {
4487 if ( !n5.getName().equals( "n5" ) ) {
4490 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4493 if ( n5.getDistanceToParent() != 0.1 ) {
4496 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4499 if ( !n5.isDuplication() ) {
4502 if ( !n5.isHasAssignedEvent() ) {
4505 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4508 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4511 final PhylogenyNode n8 = new PhylogenyNode( "n8_ECOLI/12:0.01",
4512 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4513 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4516 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4519 final PhylogenyNode n9 = new PhylogenyNode( "n9_ECOLI/12=12:0.01",
4520 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4521 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4524 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4527 final PhylogenyNode n10 = new PhylogenyNode( "n10.ECOLI", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4528 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4531 final PhylogenyNode n20 = new PhylogenyNode( "n20_ECOLI/1-2",
4532 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4533 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4536 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4539 final PhylogenyNode n20x = new PhylogenyNode( "n20_ECOL1/1-2", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4540 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4543 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4546 final PhylogenyNode n20xx = new PhylogenyNode( "n20_eCOL1/1-2",
4547 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4548 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4551 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4554 final PhylogenyNode n20xxx = new PhylogenyNode( "n20_ecoli/1-2",
4555 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4556 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4559 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4562 final PhylogenyNode n20xxxx = new PhylogenyNode( "n20_Ecoli/1-2",
4563 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4564 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4567 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4570 final PhylogenyNode n21 = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.YES );
4571 if ( !n21.getName().equals( "n21_PIG" ) ) {
4574 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4577 final PhylogenyNode n21x = new PhylogenyNode( "n21_PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4578 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4581 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4584 final PhylogenyNode n22 = new PhylogenyNode( "n22/PIG", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4585 if ( !n22.getName().equals( "n22/PIG" ) ) {
4588 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4591 final PhylogenyNode n23 = new PhylogenyNode( "n23/PIG_1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4592 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4595 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4598 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4599 final PhylogenyNode a = new PhylogenyNode( "n10_ECOLI/1-2",
4600 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4601 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4604 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4607 final PhylogenyNode b = new PhylogenyNode( "n10_ECOLI1/1-2",
4608 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4609 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4612 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4615 final PhylogenyNode c = new PhylogenyNode( "n10_RATAF12/1000-2000",
4616 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4617 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4620 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4623 final PhylogenyNode d = new PhylogenyNode( "n10_RAT1/1-2",
4624 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4625 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4628 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4631 final PhylogenyNode e = new PhylogenyNode( "n10_RAT1", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4632 if ( !e.getName().equals( "n10_RAT1" ) ) {
4635 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4639 final PhylogenyNode n11 = new PhylogenyNode( "n111111_ECOLI/jdj:0.4",
4640 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4641 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4644 if ( n11.getDistanceToParent() != 0.4 ) {
4647 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4650 final PhylogenyNode n12 = new PhylogenyNode( "n111111-ECOLI---/jdj:0.4",
4651 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4652 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4655 if ( n12.getDistanceToParent() != 0.4 ) {
4658 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4661 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4662 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4663 if ( !tvu1.getRef().equals( "tag1" ) ) {
4666 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4669 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4672 if ( !tvu1.getValue().equals( "value1" ) ) {
4675 if ( !tvu3.getRef().equals( "tag3" ) ) {
4678 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4681 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4684 if ( !tvu3.getValue().equals( "value3" ) ) {
4687 if ( n1.getName().compareTo( "" ) != 0 ) {
4690 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4693 if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4696 if ( n2.getName().compareTo( "" ) != 0 ) {
4699 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4702 if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4705 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]" );
4706 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4709 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4712 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4715 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4718 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4721 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4724 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4727 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4730 final PhylogenyNode nx = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4731 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4734 final PhylogenyNode nx2 = new PhylogenyNode( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4735 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4738 final PhylogenyNode n13 = new PhylogenyNode( "blah_12345/1-2",
4739 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4740 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4743 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4746 final PhylogenyNode n14 = new PhylogenyNode( "blah_12X45/1-2",
4747 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4748 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4751 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4754 final PhylogenyNode n15 = new PhylogenyNode( "something_wicked[123]",
4755 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4756 if ( !n15.getName().equals( "something_wicked" ) ) {
4759 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4762 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4765 final PhylogenyNode n16 = new PhylogenyNode( "something_wicked2[9]",
4766 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4767 if ( !n16.getName().equals( "something_wicked2" ) ) {
4770 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4773 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4776 final PhylogenyNode n17 = new PhylogenyNode( "something_wicked3[a]",
4777 ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4778 if ( !n17.getName().equals( "something_wicked3" ) ) {
4781 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4784 final PhylogenyNode n18 = new PhylogenyNode( ":0.5[91]", ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4785 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4788 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4791 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4795 catch ( final Exception e ) {
4796 e.printStackTrace( System.out );
4802 private static boolean testNHXParsing() {
4804 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4805 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4806 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4809 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]";
4810 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4811 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4814 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]";
4815 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4816 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4819 final Phylogeny[] p3 = factory
4820 .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]",
4822 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4825 final Phylogeny[] p4 = factory
4826 .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(]",
4828 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4831 final Phylogeny[] p5 = factory
4832 .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(((]",
4834 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4837 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)";
4838 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)";
4839 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4840 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4843 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)))";
4844 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)))";
4845 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4846 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4849 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]) ))[,,, ])))))))";
4850 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4851 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4852 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4855 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4856 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]" ) ) {
4859 final Phylogeny p10 = factory
4860 .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]",
4861 new NHXParser() )[ 0 ];
4862 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]" ) ) {
4866 catch ( final Exception e ) {
4867 e.printStackTrace( System.out );
4873 private static boolean testNHXParsingQuotes() {
4875 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4876 final NHXParser p = new NHXParser();
4877 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4878 if ( phylogenies_0.length != 5 ) {
4881 final Phylogeny phy = phylogenies_0[ 4 ];
4882 if ( phy.getNumberOfExternalNodes() != 7 ) {
4885 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4888 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4891 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4892 .getScientificName().equals( "hsapiens" ) ) {
4895 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4898 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4901 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4904 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4907 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4910 final NHXParser p1p = new NHXParser();
4911 p1p.setIgnoreQuotes( true );
4912 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4913 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4916 final NHXParser p2p = new NHXParser();
4917 p1p.setIgnoreQuotes( false );
4918 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4919 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4922 final NHXParser p3p = new NHXParser();
4923 p3p.setIgnoreQuotes( false );
4924 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4925 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4928 final NHXParser p4p = new NHXParser();
4929 p4p.setIgnoreQuotes( false );
4930 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4931 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
4934 final Phylogeny p10 = factory
4935 .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]",
4936 new NHXParser() )[ 0 ];
4937 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]";
4938 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
4941 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
4942 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
4946 final Phylogeny p12 = factory
4947 .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]",
4948 new NHXParser() )[ 0 ];
4949 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]";
4950 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
4953 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
4954 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
4957 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;";
4958 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
4961 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
4962 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
4966 catch ( final Exception e ) {
4967 e.printStackTrace( System.out );
4973 private static boolean testPhylogenyBranch() {
4975 final PhylogenyNode a1 = new PhylogenyNode( "a" );
4976 final PhylogenyNode b1 = new PhylogenyNode( "b" );
4977 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
4978 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
4979 if ( !a1b1.equals( a1b1 ) ) {
4982 if ( !a1b1.equals( b1a1 ) ) {
4985 if ( !b1a1.equals( a1b1 ) ) {
4988 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
4989 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
4990 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
4991 if ( a1_b1.equals( b1_a1 ) ) {
4994 if ( a1_b1.equals( a1_b1_ ) ) {
4997 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
4998 if ( !a1_b1.equals( b1_a1_ ) ) {
5001 if ( a1_b1_.equals( b1_a1_ ) ) {
5004 if ( !a1_b1_.equals( b1_a1 ) ) {
5008 catch ( final Exception e ) {
5009 e.printStackTrace( System.out );
5015 private static boolean testPhyloXMLparsingOfDistributionElement() {
5017 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5018 PhyloXmlParser xml_parser = null;
5020 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5022 catch ( final Exception e ) {
5023 // Do nothing -- means were not running from jar.
5025 if ( xml_parser == null ) {
5026 xml_parser = new PhyloXmlParser();
5027 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5028 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5031 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5034 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5036 if ( xml_parser.getErrorCount() > 0 ) {
5037 System.out.println( xml_parser.getErrorMessages().toString() );
5040 if ( phylogenies_0.length != 1 ) {
5043 final Phylogeny t1 = phylogenies_0[ 0 ];
5044 PhylogenyNode n = null;
5045 Distribution d = null;
5046 n = t1.getNode( "root node" );
5047 if ( !n.getNodeData().isHasDistribution() ) {
5050 if ( n.getNodeData().getDistributions().size() != 1 ) {
5053 d = n.getNodeData().getDistribution();
5054 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5057 if ( d.getPoints().size() != 1 ) {
5060 if ( d.getPolygons() != null ) {
5063 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5066 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5069 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5072 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5075 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5078 n = t1.getNode( "node a" );
5079 if ( !n.getNodeData().isHasDistribution() ) {
5082 if ( n.getNodeData().getDistributions().size() != 2 ) {
5085 d = n.getNodeData().getDistribution( 1 );
5086 if ( !d.getDesc().equals( "San Diego" ) ) {
5089 if ( d.getPoints().size() != 1 ) {
5092 if ( d.getPolygons() != null ) {
5095 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5098 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5101 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5104 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5107 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5110 n = t1.getNode( "node bb" );
5111 if ( !n.getNodeData().isHasDistribution() ) {
5114 if ( n.getNodeData().getDistributions().size() != 1 ) {
5117 d = n.getNodeData().getDistribution( 0 );
5118 if ( d.getPoints().size() != 3 ) {
5121 if ( d.getPolygons().size() != 2 ) {
5124 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5127 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5130 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5133 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5136 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5139 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5142 Polygon p = d.getPolygons().get( 0 );
5143 if ( p.getPoints().size() != 3 ) {
5146 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5149 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5152 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5155 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5158 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5161 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5164 p = d.getPolygons().get( 1 );
5165 if ( p.getPoints().size() != 3 ) {
5168 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5171 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5174 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5178 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5179 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5180 if ( rt.length != 1 ) {
5183 final Phylogeny t1_rt = rt[ 0 ];
5184 n = t1_rt.getNode( "root node" );
5185 if ( !n.getNodeData().isHasDistribution() ) {
5188 if ( n.getNodeData().getDistributions().size() != 1 ) {
5191 d = n.getNodeData().getDistribution();
5192 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5195 if ( d.getPoints().size() != 1 ) {
5198 if ( d.getPolygons() != null ) {
5201 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5204 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5207 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5210 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5213 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5216 n = t1_rt.getNode( "node a" );
5217 if ( !n.getNodeData().isHasDistribution() ) {
5220 if ( n.getNodeData().getDistributions().size() != 2 ) {
5223 d = n.getNodeData().getDistribution( 1 );
5224 if ( !d.getDesc().equals( "San Diego" ) ) {
5227 if ( d.getPoints().size() != 1 ) {
5230 if ( d.getPolygons() != null ) {
5233 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5236 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5239 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5242 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5245 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5248 n = t1_rt.getNode( "node bb" );
5249 if ( !n.getNodeData().isHasDistribution() ) {
5252 if ( n.getNodeData().getDistributions().size() != 1 ) {
5255 d = n.getNodeData().getDistribution( 0 );
5256 if ( d.getPoints().size() != 3 ) {
5259 if ( d.getPolygons().size() != 2 ) {
5262 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5265 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5268 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5271 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5274 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5277 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5280 p = d.getPolygons().get( 0 );
5281 if ( p.getPoints().size() != 3 ) {
5284 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5287 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5290 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5293 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5296 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5299 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5302 p = d.getPolygons().get( 1 );
5303 if ( p.getPoints().size() != 3 ) {
5306 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5309 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5312 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5316 catch ( final Exception e ) {
5317 e.printStackTrace( System.out );
5323 private static boolean testPostOrderIterator() {
5325 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5326 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5327 PhylogenyNodeIterator it0;
5328 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5331 for( it0.reset(); it0.hasNext(); ) {
5334 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5335 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5336 if ( !it.next().getName().equals( "A" ) ) {
5339 if ( !it.next().getName().equals( "B" ) ) {
5342 if ( !it.next().getName().equals( "ab" ) ) {
5345 if ( !it.next().getName().equals( "C" ) ) {
5348 if ( !it.next().getName().equals( "D" ) ) {
5351 if ( !it.next().getName().equals( "cd" ) ) {
5354 if ( !it.next().getName().equals( "abcd" ) ) {
5357 if ( !it.next().getName().equals( "E" ) ) {
5360 if ( !it.next().getName().equals( "F" ) ) {
5363 if ( !it.next().getName().equals( "ef" ) ) {
5366 if ( !it.next().getName().equals( "G" ) ) {
5369 if ( !it.next().getName().equals( "H" ) ) {
5372 if ( !it.next().getName().equals( "gh" ) ) {
5375 if ( !it.next().getName().equals( "efgh" ) ) {
5378 if ( !it.next().getName().equals( "r" ) ) {
5381 if ( it.hasNext() ) {
5385 catch ( final Exception e ) {
5386 e.printStackTrace( System.out );
5392 private static boolean testPreOrderIterator() {
5394 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5395 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5396 PhylogenyNodeIterator it0;
5397 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5400 for( it0.reset(); it0.hasNext(); ) {
5403 PhylogenyNodeIterator it = t0.iteratorPreorder();
5404 if ( !it.next().getName().equals( "r" ) ) {
5407 if ( !it.next().getName().equals( "ab" ) ) {
5410 if ( !it.next().getName().equals( "A" ) ) {
5413 if ( !it.next().getName().equals( "B" ) ) {
5416 if ( !it.next().getName().equals( "cd" ) ) {
5419 if ( !it.next().getName().equals( "C" ) ) {
5422 if ( !it.next().getName().equals( "D" ) ) {
5425 if ( it.hasNext() ) {
5428 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5429 it = t1.iteratorPreorder();
5430 if ( !it.next().getName().equals( "r" ) ) {
5433 if ( !it.next().getName().equals( "abcd" ) ) {
5436 if ( !it.next().getName().equals( "ab" ) ) {
5439 if ( !it.next().getName().equals( "A" ) ) {
5442 if ( !it.next().getName().equals( "B" ) ) {
5445 if ( !it.next().getName().equals( "cd" ) ) {
5448 if ( !it.next().getName().equals( "C" ) ) {
5451 if ( !it.next().getName().equals( "D" ) ) {
5454 if ( !it.next().getName().equals( "efgh" ) ) {
5457 if ( !it.next().getName().equals( "ef" ) ) {
5460 if ( !it.next().getName().equals( "E" ) ) {
5463 if ( !it.next().getName().equals( "F" ) ) {
5466 if ( !it.next().getName().equals( "gh" ) ) {
5469 if ( !it.next().getName().equals( "G" ) ) {
5472 if ( !it.next().getName().equals( "H" ) ) {
5475 if ( it.hasNext() ) {
5479 catch ( final Exception e ) {
5480 e.printStackTrace( System.out );
5486 private static boolean testPropertiesMap() {
5488 final PropertiesMap pm = new PropertiesMap();
5489 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5490 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5491 final Property p2 = new Property( "something:else",
5493 "improbable:research",
5496 pm.addProperty( p0 );
5497 pm.addProperty( p1 );
5498 pm.addProperty( p2 );
5499 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5502 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5505 if ( pm.getProperties().size() != 3 ) {
5508 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5511 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5514 if ( pm.getProperties().size() != 3 ) {
5517 pm.removeProperty( "dimensions:diameter" );
5518 if ( pm.getProperties().size() != 2 ) {
5521 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5524 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5528 catch ( final Exception e ) {
5529 e.printStackTrace( System.out );
5535 private static boolean testReIdMethods() {
5537 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5538 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5539 final int count = PhylogenyNode.getNodeCount();
5541 if ( p.getNode( "r" ).getId() != count ) {
5544 if ( p.getNode( "A" ).getId() != count + 1 ) {
5547 if ( p.getNode( "B" ).getId() != count + 1 ) {
5550 if ( p.getNode( "C" ).getId() != count + 1 ) {
5553 if ( p.getNode( "1" ).getId() != count + 2 ) {
5556 if ( p.getNode( "2" ).getId() != count + 2 ) {
5559 if ( p.getNode( "3" ).getId() != count + 2 ) {
5562 if ( p.getNode( "4" ).getId() != count + 2 ) {
5565 if ( p.getNode( "5" ).getId() != count + 2 ) {
5568 if ( p.getNode( "6" ).getId() != count + 2 ) {
5571 if ( p.getNode( "a" ).getId() != count + 3 ) {
5574 if ( p.getNode( "b" ).getId() != count + 3 ) {
5577 if ( p.getNode( "X" ).getId() != count + 4 ) {
5580 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5583 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5587 catch ( final Exception e ) {
5588 e.printStackTrace( System.out );
5594 private static boolean testRerooting() {
5596 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5597 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",
5598 new NHXParser() )[ 0 ];
5599 if ( !t1.isRooted() ) {
5602 t1.reRoot( t1.getNode( "D" ) );
5603 t1.reRoot( t1.getNode( "CD" ) );
5604 t1.reRoot( t1.getNode( "A" ) );
5605 t1.reRoot( t1.getNode( "B" ) );
5606 t1.reRoot( t1.getNode( "AB" ) );
5607 t1.reRoot( t1.getNode( "D" ) );
5608 t1.reRoot( t1.getNode( "C" ) );
5609 t1.reRoot( t1.getNode( "CD" ) );
5610 t1.reRoot( t1.getNode( "A" ) );
5611 t1.reRoot( t1.getNode( "B" ) );
5612 t1.reRoot( t1.getNode( "AB" ) );
5613 t1.reRoot( t1.getNode( "D" ) );
5614 t1.reRoot( t1.getNode( "D" ) );
5615 t1.reRoot( t1.getNode( "C" ) );
5616 t1.reRoot( t1.getNode( "A" ) );
5617 t1.reRoot( t1.getNode( "B" ) );
5618 t1.reRoot( t1.getNode( "AB" ) );
5619 t1.reRoot( t1.getNode( "C" ) );
5620 t1.reRoot( t1.getNode( "D" ) );
5621 t1.reRoot( t1.getNode( "CD" ) );
5622 t1.reRoot( t1.getNode( "D" ) );
5623 t1.reRoot( t1.getNode( "A" ) );
5624 t1.reRoot( t1.getNode( "B" ) );
5625 t1.reRoot( t1.getNode( "AB" ) );
5626 t1.reRoot( t1.getNode( "C" ) );
5627 t1.reRoot( t1.getNode( "D" ) );
5628 t1.reRoot( t1.getNode( "CD" ) );
5629 t1.reRoot( t1.getNode( "D" ) );
5630 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5633 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5636 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5639 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5642 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5645 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5648 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",
5649 new NHXParser() )[ 0 ];
5650 t2.reRoot( t2.getNode( "A" ) );
5651 t2.reRoot( t2.getNode( "D" ) );
5652 t2.reRoot( t2.getNode( "ABC" ) );
5653 t2.reRoot( t2.getNode( "A" ) );
5654 t2.reRoot( t2.getNode( "B" ) );
5655 t2.reRoot( t2.getNode( "D" ) );
5656 t2.reRoot( t2.getNode( "C" ) );
5657 t2.reRoot( t2.getNode( "ABC" ) );
5658 t2.reRoot( t2.getNode( "A" ) );
5659 t2.reRoot( t2.getNode( "B" ) );
5660 t2.reRoot( t2.getNode( "AB" ) );
5661 t2.reRoot( t2.getNode( "AB" ) );
5662 t2.reRoot( t2.getNode( "D" ) );
5663 t2.reRoot( t2.getNode( "C" ) );
5664 t2.reRoot( t2.getNode( "B" ) );
5665 t2.reRoot( t2.getNode( "AB" ) );
5666 t2.reRoot( t2.getNode( "D" ) );
5667 t2.reRoot( t2.getNode( "D" ) );
5668 t2.reRoot( t2.getNode( "ABC" ) );
5669 t2.reRoot( t2.getNode( "A" ) );
5670 t2.reRoot( t2.getNode( "B" ) );
5671 t2.reRoot( t2.getNode( "AB" ) );
5672 t2.reRoot( t2.getNode( "D" ) );
5673 t2.reRoot( t2.getNode( "C" ) );
5674 t2.reRoot( t2.getNode( "ABC" ) );
5675 t2.reRoot( t2.getNode( "A" ) );
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( "C" ) );
5681 t2.reRoot( t2.getNode( "A" ) );
5682 t2.reRoot( t2.getNode( "B" ) );
5683 t2.reRoot( t2.getNode( "AB" ) );
5684 t2.reRoot( t2.getNode( "C" ) );
5685 t2.reRoot( t2.getNode( "D" ) );
5686 t2.reRoot( t2.getNode( "ABC" ) );
5687 t2.reRoot( t2.getNode( "D" ) );
5688 t2.reRoot( t2.getNode( "A" ) );
5689 t2.reRoot( t2.getNode( "B" ) );
5690 t2.reRoot( t2.getNode( "AB" ) );
5691 t2.reRoot( t2.getNode( "C" ) );
5692 t2.reRoot( t2.getNode( "D" ) );
5693 t2.reRoot( t2.getNode( "ABC" ) );
5694 t2.reRoot( t2.getNode( "D" ) );
5695 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5698 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5701 t2.reRoot( t2.getNode( "ABC" ) );
5702 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5705 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5708 t2.reRoot( t2.getNode( "AB" ) );
5709 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5712 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5715 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5718 t2.reRoot( t2.getNode( "AB" ) );
5719 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5722 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5725 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5728 t2.reRoot( t2.getNode( "D" ) );
5729 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5732 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5735 t2.reRoot( t2.getNode( "ABC" ) );
5736 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5739 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5742 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5743 new NHXParser() )[ 0 ];
5744 t3.reRoot( t3.getNode( "B" ) );
5745 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5748 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5751 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5754 t3.reRoot( t3.getNode( "B" ) );
5755 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5758 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5761 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5764 t3.reRoot( t3.getRoot() );
5765 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5768 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5771 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5775 catch ( final Exception e ) {
5776 e.printStackTrace( System.out );
5782 private static boolean testSDIse() {
5784 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5785 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5786 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5787 gene1.setRooted( true );
5788 species1.setRooted( true );
5789 final SDI sdi = new SDIse( gene1, species1 );
5790 if ( !gene1.getRoot().isDuplication() ) {
5793 final Phylogeny species2 = factory
5794 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5795 new NHXParser() )[ 0 ];
5796 final Phylogeny gene2 = factory
5797 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5798 new NHXParser() )[ 0 ];
5799 species2.setRooted( true );
5800 gene2.setRooted( true );
5801 final SDI sdi2 = new SDIse( gene2, species2 );
5802 if ( sdi2.getDuplicationsSum() != 0 ) {
5805 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5808 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5811 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5814 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5817 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5820 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5823 final Phylogeny species3 = factory
5824 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5825 new NHXParser() )[ 0 ];
5826 final Phylogeny gene3 = factory
5827 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5828 new NHXParser() )[ 0 ];
5829 species3.setRooted( true );
5830 gene3.setRooted( true );
5831 final SDI sdi3 = new SDIse( gene3, species3 );
5832 if ( sdi3.getDuplicationsSum() != 1 ) {
5835 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5838 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5841 final Phylogeny species4 = factory
5842 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5843 new NHXParser() )[ 0 ];
5844 final Phylogeny gene4 = factory
5845 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5846 new NHXParser() )[ 0 ];
5847 species4.setRooted( true );
5848 gene4.setRooted( true );
5849 final SDI sdi4 = new SDIse( gene4, species4 );
5850 if ( sdi4.getDuplicationsSum() != 1 ) {
5853 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5856 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5859 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5862 if ( species4.getNumberOfExternalNodes() != 6 ) {
5865 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5868 final Phylogeny species5 = factory
5869 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5870 new NHXParser() )[ 0 ];
5871 final Phylogeny gene5 = factory
5872 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5873 new NHXParser() )[ 0 ];
5874 species5.setRooted( true );
5875 gene5.setRooted( true );
5876 final SDI sdi5 = new SDIse( gene5, species5 );
5877 if ( sdi5.getDuplicationsSum() != 2 ) {
5880 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
5883 if ( !gene5.getNode( "adc" ).isDuplication() ) {
5886 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
5889 if ( species5.getNumberOfExternalNodes() != 6 ) {
5892 if ( gene5.getNumberOfExternalNodes() != 6 ) {
5895 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
5896 // Conjecture for Comparing Molecular Phylogenies"
5897 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
5898 final Phylogeny species6 = factory
5899 .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,"
5900 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
5901 new NHXParser() )[ 0 ];
5902 final Phylogeny gene6 = factory
5903 .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,"
5904 + "((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,"
5905 + "(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;",
5906 new NHXParser() )[ 0 ];
5907 species6.setRooted( true );
5908 gene6.setRooted( true );
5909 final SDI sdi6 = new SDIse( gene6, species6 );
5910 if ( sdi6.getDuplicationsSum() != 3 ) {
5913 if ( !gene6.getNode( "r" ).isDuplication() ) {
5916 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
5919 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
5922 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
5925 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
5928 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
5931 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
5934 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
5937 sdi6.computeMappingCostL();
5938 if ( sdi6.computeMappingCostL() != 17 ) {
5941 if ( species6.getNumberOfExternalNodes() != 9 ) {
5944 if ( gene6.getNumberOfExternalNodes() != 9 ) {
5947 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
5948 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
5949 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
5950 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
5951 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
5952 species7.setRooted( true );
5953 final Phylogeny gene7_1 = Test
5954 .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])" );
5955 gene7_1.setRooted( true );
5956 final SDI sdi7 = new SDIse( gene7_1, species7 );
5957 if ( sdi7.getDuplicationsSum() != 0 ) {
5960 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
5963 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
5966 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
5969 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
5972 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
5975 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
5978 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
5981 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
5984 final Phylogeny gene7_2 = Test
5985 .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])" );
5986 gene7_2.setRooted( true );
5987 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
5988 if ( sdi7_2.getDuplicationsSum() != 1 ) {
5991 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
5994 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
5997 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6000 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6003 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6006 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6009 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6012 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6015 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6019 catch ( final Exception e ) {
6025 private static boolean testSDIunrooted() {
6027 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6028 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6029 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6030 final Iterator<PhylogenyBranch> iter = l.iterator();
6031 PhylogenyBranch br = iter.next();
6032 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6035 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6039 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6042 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6046 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6049 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6053 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6056 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6060 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6063 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6067 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6070 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6074 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6077 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6081 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6084 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6088 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6091 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6095 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6098 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6102 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6105 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6109 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6112 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6116 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6119 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6123 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6126 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6130 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6133 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6136 if ( iter.hasNext() ) {
6139 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6140 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6141 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6143 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6146 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6150 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6153 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6157 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6160 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6163 if ( iter1.hasNext() ) {
6166 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6167 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6168 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6170 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6173 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6177 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6180 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6184 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6187 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6190 if ( iter2.hasNext() ) {
6193 final Phylogeny species0 = factory
6194 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6195 new NHXParser() )[ 0 ];
6196 final Phylogeny gene1 = factory
6197 .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])",
6198 new NHXParser() )[ 0 ];
6199 species0.setRooted( true );
6200 gene1.setRooted( true );
6201 final SDIR sdi_unrooted = new SDIR();
6202 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6203 if ( sdi_unrooted.getCount() != 1 ) {
6206 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6209 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6212 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6215 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6218 final Phylogeny gene2 = factory
6219 .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])",
6220 new NHXParser() )[ 0 ];
6221 gene2.setRooted( true );
6222 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6223 if ( sdi_unrooted.getCount() != 1 ) {
6226 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6229 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6232 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6235 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6238 final Phylogeny species6 = factory
6239 .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,"
6240 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6241 new NHXParser() )[ 0 ];
6242 final Phylogeny gene6 = factory
6243 .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],"
6244 + "(((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],"
6245 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6246 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6247 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6248 new NHXParser() )[ 0 ];
6249 species6.setRooted( true );
6250 gene6.setRooted( true );
6251 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6252 if ( sdi_unrooted.getCount() != 1 ) {
6255 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6258 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6261 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6264 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6267 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6270 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6273 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6276 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6279 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6282 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6285 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6288 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6292 final Phylogeny species7 = factory
6293 .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,"
6294 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6295 new NHXParser() )[ 0 ];
6296 final Phylogeny gene7 = factory
6297 .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],"
6298 + "(((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],"
6299 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6300 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6301 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6302 new NHXParser() )[ 0 ];
6303 species7.setRooted( true );
6304 gene7.setRooted( true );
6305 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6306 if ( sdi_unrooted.getCount() != 1 ) {
6309 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6312 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6315 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6318 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6321 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6324 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6327 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6330 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6333 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6336 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6339 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6342 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6346 final Phylogeny species8 = factory
6347 .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,"
6348 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6349 new NHXParser() )[ 0 ];
6350 final Phylogeny gene8 = factory
6351 .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],"
6352 + "(((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],"
6353 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6354 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6355 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6356 new NHXParser() )[ 0 ];
6357 species8.setRooted( true );
6358 gene8.setRooted( true );
6359 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6360 if ( sdi_unrooted.getCount() != 1 ) {
6363 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6366 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6369 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6372 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6375 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6378 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6381 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6384 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6387 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6390 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6393 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6396 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6401 catch ( final Exception e ) {
6402 e.printStackTrace( System.out );
6408 private static boolean testSplit() {
6410 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6411 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6412 //Archaeopteryx.createApplication( p0 );
6413 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6414 ex.add( new PhylogenyNode( "A" ) );
6415 ex.add( new PhylogenyNode( "B" ) );
6416 ex.add( new PhylogenyNode( "C" ) );
6417 ex.add( new PhylogenyNode( "D" ) );
6418 ex.add( new PhylogenyNode( "E" ) );
6419 ex.add( new PhylogenyNode( "F" ) );
6420 ex.add( new PhylogenyNode( "G" ) );
6421 ex.add( new PhylogenyNode( "X" ) );
6422 ex.add( new PhylogenyNode( "Y" ) );
6423 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6424 // System.out.println( s0.toString() );
6426 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6427 query_nodes.add( new PhylogenyNode( "A" ) );
6428 query_nodes.add( new PhylogenyNode( "B" ) );
6429 if ( s0.match( query_nodes ) ) {
6432 query_nodes = new HashSet<PhylogenyNode>();
6433 query_nodes.add( new PhylogenyNode( "A" ) );
6434 query_nodes.add( new PhylogenyNode( "B" ) );
6435 query_nodes.add( new PhylogenyNode( "C" ) );
6436 query_nodes.add( new PhylogenyNode( "D" ) );
6437 query_nodes.add( new PhylogenyNode( "E" ) );
6438 query_nodes.add( new PhylogenyNode( "F" ) );
6439 query_nodes.add( new PhylogenyNode( "G" ) );
6440 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 if ( !s0.match( query_nodes ) ) {
6452 query_nodes = new HashSet<PhylogenyNode>();
6453 query_nodes.add( new PhylogenyNode( "D" ) );
6454 query_nodes.add( new PhylogenyNode( "E" ) );
6455 query_nodes.add( new PhylogenyNode( "F" ) );
6456 query_nodes.add( new PhylogenyNode( "G" ) );
6457 if ( !s0.match( query_nodes ) ) {
6461 query_nodes = new HashSet<PhylogenyNode>();
6462 query_nodes.add( new PhylogenyNode( "A" ) );
6463 query_nodes.add( new PhylogenyNode( "B" ) );
6464 query_nodes.add( new PhylogenyNode( "C" ) );
6465 query_nodes.add( new PhylogenyNode( "D" ) );
6466 if ( !s0.match( query_nodes ) ) {
6470 query_nodes = new HashSet<PhylogenyNode>();
6471 query_nodes.add( new PhylogenyNode( "E" ) );
6472 query_nodes.add( new PhylogenyNode( "F" ) );
6473 query_nodes.add( new PhylogenyNode( "G" ) );
6474 if ( !s0.match( query_nodes ) ) {
6478 query_nodes = new HashSet<PhylogenyNode>();
6479 query_nodes.add( new PhylogenyNode( "F" ) );
6480 query_nodes.add( new PhylogenyNode( "G" ) );
6481 if ( !s0.match( query_nodes ) ) {
6485 query_nodes = new HashSet<PhylogenyNode>();
6486 query_nodes.add( new PhylogenyNode( "E" ) );
6487 query_nodes.add( new PhylogenyNode( "D" ) );
6488 query_nodes.add( new PhylogenyNode( "C" ) );
6489 query_nodes.add( new PhylogenyNode( "B" ) );
6490 query_nodes.add( new PhylogenyNode( "A" ) );
6491 if ( !s0.match( query_nodes ) ) {
6495 query_nodes = new HashSet<PhylogenyNode>();
6496 query_nodes.add( new PhylogenyNode( "F" ) );
6497 query_nodes.add( new PhylogenyNode( "G" ) );
6498 query_nodes.add( new PhylogenyNode( "E" ) );
6499 if ( !s0.match( query_nodes ) ) {
6503 query_nodes = new HashSet<PhylogenyNode>();
6504 query_nodes.add( new PhylogenyNode( "F" ) );
6505 query_nodes.add( new PhylogenyNode( "G" ) );
6506 query_nodes.add( new PhylogenyNode( "E" ) );
6507 query_nodes.add( new PhylogenyNode( "D" ) );
6508 if ( !s0.match( query_nodes ) ) {
6512 query_nodes = new HashSet<PhylogenyNode>();
6513 query_nodes.add( new PhylogenyNode( "F" ) );
6514 query_nodes.add( new PhylogenyNode( "A" ) );
6515 if ( s0.match( query_nodes ) ) {
6519 query_nodes = new HashSet<PhylogenyNode>();
6520 query_nodes.add( new PhylogenyNode( "A" ) );
6521 query_nodes.add( new PhylogenyNode( "E" ) );
6522 query_nodes.add( new PhylogenyNode( "B" ) );
6523 query_nodes.add( new PhylogenyNode( "C" ) );
6524 if ( s0.match( query_nodes ) ) {
6528 query_nodes = new HashSet<PhylogenyNode>();
6529 query_nodes.add( new PhylogenyNode( "F" ) );
6530 query_nodes.add( new PhylogenyNode( "G" ) );
6531 query_nodes.add( new PhylogenyNode( "E" ) );
6532 query_nodes.add( new PhylogenyNode( "D" ) );
6533 query_nodes.add( new PhylogenyNode( "C" ) );
6534 if ( s0.match( query_nodes ) ) {
6538 query_nodes = new HashSet<PhylogenyNode>();
6539 query_nodes.add( new PhylogenyNode( "A" ) );
6540 query_nodes.add( new PhylogenyNode( "B" ) );
6541 query_nodes.add( new PhylogenyNode( "D" ) );
6542 if ( s0.match( query_nodes ) ) {
6546 query_nodes = new HashSet<PhylogenyNode>();
6547 query_nodes.add( new PhylogenyNode( "A" ) );
6548 query_nodes.add( new PhylogenyNode( "D" ) );
6549 if ( s0.match( query_nodes ) ) {
6553 query_nodes = new HashSet<PhylogenyNode>();
6554 query_nodes.add( new PhylogenyNode( "A" ) );
6555 query_nodes.add( new PhylogenyNode( "B" ) );
6556 if ( s0.match( query_nodes ) ) {
6560 query_nodes = new HashSet<PhylogenyNode>();
6561 query_nodes.add( new PhylogenyNode( "A" ) );
6562 query_nodes.add( new PhylogenyNode( "C" ) );
6563 if ( s0.match( query_nodes ) ) {
6567 query_nodes = new HashSet<PhylogenyNode>();
6568 query_nodes.add( new PhylogenyNode( "A" ) );
6569 query_nodes.add( new PhylogenyNode( "E" ) );
6570 if ( s0.match( query_nodes ) ) {
6574 query_nodes = new HashSet<PhylogenyNode>();
6575 query_nodes.add( new PhylogenyNode( "A" ) );
6576 query_nodes.add( new PhylogenyNode( "F" ) );
6577 if ( s0.match( query_nodes ) ) {
6581 query_nodes = new HashSet<PhylogenyNode>();
6582 query_nodes.add( new PhylogenyNode( "A" ) );
6583 query_nodes.add( new PhylogenyNode( "G" ) );
6584 if ( s0.match( query_nodes ) ) {
6588 query_nodes = new HashSet<PhylogenyNode>();
6589 query_nodes.add( new PhylogenyNode( "A" ) );
6590 query_nodes.add( new PhylogenyNode( "F" ) );
6591 query_nodes.add( new PhylogenyNode( "G" ) );
6592 if ( s0.match( query_nodes ) ) {
6596 query_nodes = new HashSet<PhylogenyNode>();
6597 query_nodes.add( new PhylogenyNode( "A" ) );
6598 query_nodes.add( new PhylogenyNode( "B" ) );
6599 query_nodes.add( new PhylogenyNode( "D" ) );
6600 if ( s0.match( query_nodes ) ) {
6604 query_nodes = new HashSet<PhylogenyNode>();
6605 query_nodes.add( new PhylogenyNode( "E" ) );
6606 query_nodes.add( new PhylogenyNode( "D" ) );
6607 query_nodes.add( new PhylogenyNode( "A" ) );
6608 if ( s0.match( query_nodes ) ) {
6612 query_nodes = new HashSet<PhylogenyNode>();
6613 query_nodes.add( new PhylogenyNode( "E" ) );
6614 query_nodes.add( new PhylogenyNode( "D" ) );
6615 query_nodes.add( new PhylogenyNode( "A" ) );
6616 query_nodes.add( new PhylogenyNode( "G" ) );
6617 if ( s0.match( query_nodes ) ) {
6621 // query_nodes = new HashSet<PhylogenyNode>();
6622 // query_nodes.add( new PhylogenyNode( "X" ) );
6623 // query_nodes.add( new PhylogenyNode( "Y" ) );
6624 // query_nodes.add( new PhylogenyNode( "A" ) );
6625 // query_nodes.add( new PhylogenyNode( "B" ) );
6626 // query_nodes.add( new PhylogenyNode( "C" ) );
6627 // query_nodes.add( new PhylogenyNode( "D" ) );
6628 // query_nodes.add( new PhylogenyNode( "E" ) );
6629 // query_nodes.add( new PhylogenyNode( "F" ) );
6630 // query_nodes.add( new PhylogenyNode( "G" ) );
6631 // if ( !s0.match( query_nodes ) ) {
6634 // query_nodes = new HashSet<PhylogenyNode>();
6635 // query_nodes.add( new PhylogenyNode( "X" ) );
6636 // query_nodes.add( new PhylogenyNode( "Y" ) );
6637 // query_nodes.add( new PhylogenyNode( "A" ) );
6638 // query_nodes.add( new PhylogenyNode( "B" ) );
6639 // query_nodes.add( new PhylogenyNode( "C" ) );
6640 // if ( !s0.match( query_nodes ) ) {
6644 // query_nodes = new HashSet<PhylogenyNode>();
6645 // query_nodes.add( new PhylogenyNode( "X" ) );
6646 // query_nodes.add( new PhylogenyNode( "Y" ) );
6647 // query_nodes.add( new PhylogenyNode( "D" ) );
6648 // query_nodes.add( new PhylogenyNode( "E" ) );
6649 // query_nodes.add( new PhylogenyNode( "F" ) );
6650 // query_nodes.add( new PhylogenyNode( "G" ) );
6651 // if ( !s0.match( query_nodes ) ) {
6655 // query_nodes = new HashSet<PhylogenyNode>();
6656 // query_nodes.add( new PhylogenyNode( "X" ) );
6657 // query_nodes.add( new PhylogenyNode( "Y" ) );
6658 // query_nodes.add( new PhylogenyNode( "A" ) );
6659 // query_nodes.add( new PhylogenyNode( "B" ) );
6660 // query_nodes.add( new PhylogenyNode( "C" ) );
6661 // query_nodes.add( new PhylogenyNode( "D" ) );
6662 // if ( !s0.match( query_nodes ) ) {
6666 // query_nodes = new HashSet<PhylogenyNode>();
6667 // query_nodes.add( new PhylogenyNode( "X" ) );
6668 // query_nodes.add( new PhylogenyNode( "Y" ) );
6669 // query_nodes.add( new PhylogenyNode( "E" ) );
6670 // query_nodes.add( new PhylogenyNode( "F" ) );
6671 // query_nodes.add( new PhylogenyNode( "G" ) );
6672 // if ( !s0.match( query_nodes ) ) {
6676 // query_nodes = new HashSet<PhylogenyNode>();
6677 // query_nodes.add( new PhylogenyNode( "X" ) );
6678 // query_nodes.add( new PhylogenyNode( "Y" ) );
6679 // query_nodes.add( new PhylogenyNode( "F" ) );
6680 // query_nodes.add( new PhylogenyNode( "G" ) );
6681 // if ( !s0.match( query_nodes ) ) {
6685 query_nodes = new HashSet<PhylogenyNode>();
6686 query_nodes.add( new PhylogenyNode( "X" ) );
6687 query_nodes.add( new PhylogenyNode( "Y" ) );
6688 query_nodes.add( new PhylogenyNode( "E" ) );
6689 query_nodes.add( new PhylogenyNode( "G" ) );
6690 if ( s0.match( query_nodes ) ) {
6694 query_nodes = new HashSet<PhylogenyNode>();
6695 query_nodes.add( new PhylogenyNode( "X" ) );
6696 query_nodes.add( new PhylogenyNode( "Y" ) );
6697 query_nodes.add( new PhylogenyNode( "A" ) );
6698 query_nodes.add( new PhylogenyNode( "B" ) );
6699 if ( s0.match( query_nodes ) ) {
6702 ///////////////////////////
6704 query_nodes = new HashSet<PhylogenyNode>();
6705 query_nodes.add( new PhylogenyNode( "X" ) );
6706 query_nodes.add( new PhylogenyNode( "Y" ) );
6707 query_nodes.add( new PhylogenyNode( "A" ) );
6708 query_nodes.add( new PhylogenyNode( "D" ) );
6709 if ( s0.match( query_nodes ) ) {
6713 query_nodes = new HashSet<PhylogenyNode>();
6714 query_nodes.add( new PhylogenyNode( "X" ) );
6715 query_nodes.add( new PhylogenyNode( "Y" ) );
6716 query_nodes.add( new PhylogenyNode( "A" ) );
6717 query_nodes.add( new PhylogenyNode( "B" ) );
6718 if ( s0.match( query_nodes ) ) {
6722 query_nodes = new HashSet<PhylogenyNode>();
6723 query_nodes.add( new PhylogenyNode( "X" ) );
6724 query_nodes.add( new PhylogenyNode( "Y" ) );
6725 query_nodes.add( new PhylogenyNode( "A" ) );
6726 query_nodes.add( new PhylogenyNode( "C" ) );
6727 if ( s0.match( query_nodes ) ) {
6731 query_nodes = new HashSet<PhylogenyNode>();
6732 query_nodes.add( new PhylogenyNode( "X" ) );
6733 query_nodes.add( new PhylogenyNode( "Y" ) );
6734 query_nodes.add( new PhylogenyNode( "A" ) );
6735 query_nodes.add( new PhylogenyNode( "E" ) );
6736 if ( s0.match( query_nodes ) ) {
6740 query_nodes = new HashSet<PhylogenyNode>();
6741 query_nodes.add( new PhylogenyNode( "X" ) );
6742 query_nodes.add( new PhylogenyNode( "Y" ) );
6743 query_nodes.add( new PhylogenyNode( "A" ) );
6744 query_nodes.add( new PhylogenyNode( "F" ) );
6745 if ( s0.match( query_nodes ) ) {
6749 query_nodes = new HashSet<PhylogenyNode>();
6750 query_nodes.add( new PhylogenyNode( "Y" ) );
6751 query_nodes.add( new PhylogenyNode( "A" ) );
6752 query_nodes.add( new PhylogenyNode( "G" ) );
6753 if ( s0.match( query_nodes ) ) {
6757 query_nodes = new HashSet<PhylogenyNode>();
6758 query_nodes.add( new PhylogenyNode( "X" ) );
6759 query_nodes.add( new PhylogenyNode( "Y" ) );
6760 query_nodes.add( new PhylogenyNode( "A" ) );
6761 query_nodes.add( new PhylogenyNode( "F" ) );
6762 query_nodes.add( new PhylogenyNode( "G" ) );
6763 if ( s0.match( query_nodes ) ) {
6767 query_nodes = new HashSet<PhylogenyNode>();
6768 query_nodes.add( new PhylogenyNode( "X" ) );
6769 query_nodes.add( new PhylogenyNode( "Y" ) );
6770 query_nodes.add( new PhylogenyNode( "A" ) );
6771 query_nodes.add( new PhylogenyNode( "B" ) );
6772 query_nodes.add( new PhylogenyNode( "D" ) );
6773 if ( s0.match( query_nodes ) ) {
6777 query_nodes = new HashSet<PhylogenyNode>();
6778 query_nodes.add( new PhylogenyNode( "X" ) );
6779 query_nodes.add( new PhylogenyNode( "Y" ) );
6780 query_nodes.add( new PhylogenyNode( "E" ) );
6781 query_nodes.add( new PhylogenyNode( "D" ) );
6782 query_nodes.add( new PhylogenyNode( "A" ) );
6783 if ( s0.match( query_nodes ) ) {
6787 query_nodes = new HashSet<PhylogenyNode>();
6788 query_nodes.add( new PhylogenyNode( "X" ) );
6789 query_nodes.add( new PhylogenyNode( "Y" ) );
6790 query_nodes.add( new PhylogenyNode( "E" ) );
6791 query_nodes.add( new PhylogenyNode( "D" ) );
6792 query_nodes.add( new PhylogenyNode( "A" ) );
6793 query_nodes.add( new PhylogenyNode( "G" ) );
6794 if ( s0.match( query_nodes ) ) {
6798 catch ( final Exception e ) {
6799 e.printStackTrace();
6805 private static boolean testSplitStrict() {
6807 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6808 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6809 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6810 ex.add( new PhylogenyNode( "A" ) );
6811 ex.add( new PhylogenyNode( "B" ) );
6812 ex.add( new PhylogenyNode( "C" ) );
6813 ex.add( new PhylogenyNode( "D" ) );
6814 ex.add( new PhylogenyNode( "E" ) );
6815 ex.add( new PhylogenyNode( "F" ) );
6816 ex.add( new PhylogenyNode( "G" ) );
6817 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6818 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6819 query_nodes.add( new PhylogenyNode( "A" ) );
6820 query_nodes.add( new PhylogenyNode( "B" ) );
6821 if ( s0.match( query_nodes ) ) {
6824 query_nodes = new HashSet<PhylogenyNode>();
6825 query_nodes.add( new PhylogenyNode( "A" ) );
6826 query_nodes.add( new PhylogenyNode( "B" ) );
6827 query_nodes.add( new PhylogenyNode( "C" ) );
6828 query_nodes.add( new PhylogenyNode( "D" ) );
6829 query_nodes.add( new PhylogenyNode( "E" ) );
6830 query_nodes.add( new PhylogenyNode( "F" ) );
6831 query_nodes.add( new PhylogenyNode( "G" ) );
6832 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 if ( !s0.match( query_nodes ) ) {
6844 query_nodes = new HashSet<PhylogenyNode>();
6845 query_nodes.add( new PhylogenyNode( "D" ) );
6846 query_nodes.add( new PhylogenyNode( "E" ) );
6847 query_nodes.add( new PhylogenyNode( "F" ) );
6848 query_nodes.add( new PhylogenyNode( "G" ) );
6849 if ( !s0.match( query_nodes ) ) {
6853 query_nodes = new HashSet<PhylogenyNode>();
6854 query_nodes.add( new PhylogenyNode( "A" ) );
6855 query_nodes.add( new PhylogenyNode( "B" ) );
6856 query_nodes.add( new PhylogenyNode( "C" ) );
6857 query_nodes.add( new PhylogenyNode( "D" ) );
6858 if ( !s0.match( query_nodes ) ) {
6862 query_nodes = new HashSet<PhylogenyNode>();
6863 query_nodes.add( new PhylogenyNode( "E" ) );
6864 query_nodes.add( new PhylogenyNode( "F" ) );
6865 query_nodes.add( new PhylogenyNode( "G" ) );
6866 if ( !s0.match( query_nodes ) ) {
6870 query_nodes = new HashSet<PhylogenyNode>();
6871 query_nodes.add( new PhylogenyNode( "F" ) );
6872 query_nodes.add( new PhylogenyNode( "G" ) );
6873 if ( !s0.match( query_nodes ) ) {
6877 query_nodes = new HashSet<PhylogenyNode>();
6878 query_nodes.add( new PhylogenyNode( "E" ) );
6879 query_nodes.add( new PhylogenyNode( "D" ) );
6880 query_nodes.add( new PhylogenyNode( "C" ) );
6881 query_nodes.add( new PhylogenyNode( "B" ) );
6882 query_nodes.add( new PhylogenyNode( "A" ) );
6883 if ( !s0.match( query_nodes ) ) {
6887 query_nodes = new HashSet<PhylogenyNode>();
6888 query_nodes.add( new PhylogenyNode( "F" ) );
6889 query_nodes.add( new PhylogenyNode( "G" ) );
6890 query_nodes.add( new PhylogenyNode( "E" ) );
6891 if ( !s0.match( query_nodes ) ) {
6895 query_nodes = new HashSet<PhylogenyNode>();
6896 query_nodes.add( new PhylogenyNode( "F" ) );
6897 query_nodes.add( new PhylogenyNode( "G" ) );
6898 query_nodes.add( new PhylogenyNode( "E" ) );
6899 query_nodes.add( new PhylogenyNode( "D" ) );
6900 if ( !s0.match( query_nodes ) ) {
6904 query_nodes = new HashSet<PhylogenyNode>();
6905 query_nodes.add( new PhylogenyNode( "F" ) );
6906 query_nodes.add( new PhylogenyNode( "A" ) );
6907 if ( s0.match( query_nodes ) ) {
6911 query_nodes = new HashSet<PhylogenyNode>();
6912 query_nodes.add( new PhylogenyNode( "A" ) );
6913 query_nodes.add( new PhylogenyNode( "E" ) );
6914 query_nodes.add( new PhylogenyNode( "B" ) );
6915 query_nodes.add( new PhylogenyNode( "C" ) );
6916 if ( s0.match( query_nodes ) ) {
6920 query_nodes = new HashSet<PhylogenyNode>();
6921 query_nodes.add( new PhylogenyNode( "F" ) );
6922 query_nodes.add( new PhylogenyNode( "G" ) );
6923 query_nodes.add( new PhylogenyNode( "E" ) );
6924 query_nodes.add( new PhylogenyNode( "D" ) );
6925 query_nodes.add( new PhylogenyNode( "C" ) );
6926 if ( s0.match( query_nodes ) ) {
6930 query_nodes = new HashSet<PhylogenyNode>();
6931 query_nodes.add( new PhylogenyNode( "A" ) );
6932 query_nodes.add( new PhylogenyNode( "B" ) );
6933 query_nodes.add( new PhylogenyNode( "D" ) );
6934 if ( s0.match( query_nodes ) ) {
6938 query_nodes = new HashSet<PhylogenyNode>();
6939 query_nodes.add( new PhylogenyNode( "A" ) );
6940 query_nodes.add( new PhylogenyNode( "D" ) );
6941 if ( s0.match( query_nodes ) ) {
6945 query_nodes = new HashSet<PhylogenyNode>();
6946 query_nodes.add( new PhylogenyNode( "A" ) );
6947 query_nodes.add( new PhylogenyNode( "B" ) );
6948 if ( s0.match( query_nodes ) ) {
6952 query_nodes = new HashSet<PhylogenyNode>();
6953 query_nodes.add( new PhylogenyNode( "A" ) );
6954 query_nodes.add( new PhylogenyNode( "C" ) );
6955 if ( s0.match( query_nodes ) ) {
6959 query_nodes = new HashSet<PhylogenyNode>();
6960 query_nodes.add( new PhylogenyNode( "A" ) );
6961 query_nodes.add( new PhylogenyNode( "E" ) );
6962 if ( s0.match( query_nodes ) ) {
6966 query_nodes = new HashSet<PhylogenyNode>();
6967 query_nodes.add( new PhylogenyNode( "A" ) );
6968 query_nodes.add( new PhylogenyNode( "F" ) );
6969 if ( s0.match( query_nodes ) ) {
6973 query_nodes = new HashSet<PhylogenyNode>();
6974 query_nodes.add( new PhylogenyNode( "A" ) );
6975 query_nodes.add( new PhylogenyNode( "G" ) );
6976 if ( s0.match( query_nodes ) ) {
6980 query_nodes = new HashSet<PhylogenyNode>();
6981 query_nodes.add( new PhylogenyNode( "A" ) );
6982 query_nodes.add( new PhylogenyNode( "F" ) );
6983 query_nodes.add( new PhylogenyNode( "G" ) );
6984 if ( s0.match( query_nodes ) ) {
6988 query_nodes = new HashSet<PhylogenyNode>();
6989 query_nodes.add( new PhylogenyNode( "A" ) );
6990 query_nodes.add( new PhylogenyNode( "B" ) );
6991 query_nodes.add( new PhylogenyNode( "D" ) );
6992 if ( s0.match( query_nodes ) ) {
6996 query_nodes = new HashSet<PhylogenyNode>();
6997 query_nodes.add( new PhylogenyNode( "E" ) );
6998 query_nodes.add( new PhylogenyNode( "D" ) );
6999 query_nodes.add( new PhylogenyNode( "A" ) );
7000 if ( s0.match( query_nodes ) ) {
7004 query_nodes = new HashSet<PhylogenyNode>();
7005 query_nodes.add( new PhylogenyNode( "E" ) );
7006 query_nodes.add( new PhylogenyNode( "D" ) );
7007 query_nodes.add( new PhylogenyNode( "A" ) );
7008 query_nodes.add( new PhylogenyNode( "G" ) );
7009 if ( s0.match( query_nodes ) ) {
7013 catch ( final Exception e ) {
7014 e.printStackTrace();
7020 private static boolean testSubtreeDeletion() {
7022 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7023 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7024 t1.deleteSubtree( t1.getNode( "A" ), false );
7025 if ( t1.getNumberOfExternalNodes() != 5 ) {
7028 t1.toNewHampshireX();
7029 t1.deleteSubtree( t1.getNode( "E" ), false );
7030 if ( t1.getNumberOfExternalNodes() != 4 ) {
7033 t1.toNewHampshireX();
7034 t1.deleteSubtree( t1.getNode( "F" ), false );
7035 if ( t1.getNumberOfExternalNodes() != 3 ) {
7038 t1.toNewHampshireX();
7039 t1.deleteSubtree( t1.getNode( "D" ), false );
7040 t1.toNewHampshireX();
7041 if ( t1.getNumberOfExternalNodes() != 3 ) {
7044 t1.deleteSubtree( t1.getNode( "def" ), false );
7045 t1.toNewHampshireX();
7046 if ( t1.getNumberOfExternalNodes() != 2 ) {
7049 t1.deleteSubtree( t1.getNode( "B" ), false );
7050 t1.toNewHampshireX();
7051 if ( t1.getNumberOfExternalNodes() != 1 ) {
7054 t1.deleteSubtree( t1.getNode( "C" ), false );
7055 t1.toNewHampshireX();
7056 if ( t1.getNumberOfExternalNodes() != 1 ) {
7059 t1.deleteSubtree( t1.getNode( "abc" ), false );
7060 t1.toNewHampshireX();
7061 if ( t1.getNumberOfExternalNodes() != 1 ) {
7064 t1.deleteSubtree( t1.getNode( "r" ), false );
7065 if ( t1.getNumberOfExternalNodes() != 0 ) {
7068 if ( !t1.isEmpty() ) {
7071 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7072 t2.deleteSubtree( t2.getNode( "A" ), false );
7073 t2.toNewHampshireX();
7074 if ( t2.getNumberOfExternalNodes() != 5 ) {
7077 t2.deleteSubtree( t2.getNode( "abc" ), false );
7078 t2.toNewHampshireX();
7079 if ( t2.getNumberOfExternalNodes() != 3 ) {
7082 t2.deleteSubtree( t2.getNode( "def" ), false );
7083 t2.toNewHampshireX();
7084 if ( t2.getNumberOfExternalNodes() != 1 ) {
7088 catch ( final Exception e ) {
7089 e.printStackTrace( System.out );
7095 private static boolean testSupportCount() {
7097 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7098 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7099 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7100 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7101 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7102 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7103 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7105 SupportCount.count( t0_1, phylogenies_1, true, false );
7106 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7107 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7108 + "(((((A,B),C),D),E),((F,G),X))"
7109 + "(((((A,Y),B),C),D),((F,G),E))"
7110 + "(((((A,B),C),D),E),(F,G))"
7111 + "(((((A,B),C),D),E),(F,G))"
7112 + "(((((A,B),C),D),E),(F,G))"
7113 + "(((((A,B),C),D),E),(F,G),Z)"
7114 + "(((((A,B),C),D),E),(F,G))"
7115 + "((((((A,B),C),D),E),F),G)"
7116 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7118 SupportCount.count( t0_2, phylogenies_2, true, false );
7119 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7120 while ( it.hasNext() ) {
7121 final PhylogenyNode n = it.next();
7122 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7126 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7127 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7128 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7129 SupportCount.count( t0_3, phylogenies_3, true, false );
7130 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7131 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7134 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7137 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7140 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7143 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7146 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7149 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7152 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7155 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7158 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7161 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7162 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7163 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7164 SupportCount.count( t0_4, phylogenies_4, true, false );
7165 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7166 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7169 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7172 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7175 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7178 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7181 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7184 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7187 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7190 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7193 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7196 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7197 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7198 double d = SupportCount.compare( b1, a, true, true, true );
7199 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7202 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7203 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7204 d = SupportCount.compare( b2, a, true, true, true );
7205 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7208 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7209 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7210 d = SupportCount.compare( b3, a, true, true, true );
7211 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7214 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7215 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7216 d = SupportCount.compare( b4, a, true, true, false );
7217 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7221 catch ( final Exception e ) {
7222 e.printStackTrace( System.out );
7228 private static boolean testSupportTransfer() {
7230 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7231 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)",
7232 new NHXParser() )[ 0 ];
7233 final Phylogeny p2 = factory
7234 .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 ];
7235 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7238 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7241 support_transfer.moveBranchLengthsToBootstrap( p1 );
7242 support_transfer.transferSupportValues( p1, p2 );
7243 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7246 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7249 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7252 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7255 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7258 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7261 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7264 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7268 catch ( final Exception e ) {
7269 e.printStackTrace( System.out );
7275 private static boolean testTaxonomyAssigner() {
7277 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]";
7278 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7279 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7280 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7281 s0.setRooted( true );
7282 g0.setRooted( true );
7283 TaxonomyAssigner.execute( g0, s0 );
7284 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7287 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7290 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7293 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7294 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7295 g0.setRooted( true );
7296 TaxonomyAssigner.execute( g0, s0 );
7297 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7300 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7303 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7306 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7307 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7308 g0.setRooted( true );
7309 TaxonomyAssigner.execute( g0, s0 );
7310 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7313 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7316 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7319 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7320 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7321 g0.setRooted( true );
7322 TaxonomyAssigner.execute( g0, s0 );
7323 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7326 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7329 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7332 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7333 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7334 g0.setRooted( true );
7335 TaxonomyAssigner.execute( g0, s0 );
7336 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7339 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7342 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7345 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7346 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7347 g0.setRooted( true );
7348 TaxonomyAssigner.execute( g0, s0 );
7349 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7352 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7355 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7358 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7359 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7360 g0.setRooted( true );
7361 TaxonomyAssigner.execute( g0, s0 );
7362 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7365 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7368 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7371 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7372 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7373 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7374 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7375 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7376 s0.setRooted( true );
7377 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7378 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7379 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7380 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7381 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7382 g0.setRooted( true );
7383 TaxonomyAssigner.execute( g0, s0 );
7384 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7387 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7390 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7393 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7396 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7399 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7400 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7401 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7402 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7403 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7404 g0.setRooted( true );
7405 TaxonomyAssigner.execute( g0, s0 );
7406 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7409 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7412 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7415 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7418 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7421 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7422 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7423 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7424 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7425 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7426 g0.setRooted( true );
7427 TaxonomyAssigner.execute( g0, s0 );
7428 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7431 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7434 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7437 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7440 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7443 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7444 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7445 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7446 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7447 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7448 g0.setRooted( true );
7449 TaxonomyAssigner.execute( g0, s0 );
7450 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7453 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7456 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7459 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7462 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7465 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7466 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7467 g0.setRooted( true );
7468 TaxonomyAssigner.execute( g0, s0 );
7469 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7472 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7475 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7478 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7479 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7480 g0.setRooted( true );
7481 TaxonomyAssigner.execute( g0, s0 );
7482 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7485 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7488 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7491 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7492 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7493 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7494 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7495 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7496 g0.setRooted( true );
7497 TaxonomyAssigner.execute( g0, s0 );
7498 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7501 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7504 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7507 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7510 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7513 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7516 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7519 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7520 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7521 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7522 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7523 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7524 g0.setRooted( true );
7525 TaxonomyAssigner.execute( g0, s0 );
7526 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7529 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7532 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7535 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7538 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7541 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7544 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7547 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7548 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7549 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7550 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7551 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7552 g0.setRooted( true );
7553 TaxonomyAssigner.execute( g0, s0 );
7554 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7557 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7560 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7563 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7566 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7569 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7572 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7575 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7576 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7577 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7578 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7579 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7580 g0.setRooted( true );
7581 TaxonomyAssigner.execute( g0, s0 );
7582 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7585 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7588 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7591 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7594 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7597 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7600 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7603 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7604 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7605 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7606 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7607 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7608 s0.setRooted( true );
7609 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7610 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7611 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7612 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7613 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7614 g0.setRooted( true );
7615 TaxonomyAssigner.execute( g0, s0 );
7616 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7619 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7623 catch ( final Exception e ) {
7624 e.printStackTrace( System.out );
7630 private static boolean testUniprotTaxonomySearch() {
7632 List<UniProtTaxonomy> results = UniProtWsTools
7633 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7634 if ( results.size() != 1 ) {
7637 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7640 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7643 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7646 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7649 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7653 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7654 if ( results.size() != 1 ) {
7657 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7660 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7663 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7666 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7669 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7673 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7674 if ( results.size() != 1 ) {
7677 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7680 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7683 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7686 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7689 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7693 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7694 if ( results.size() != 1 ) {
7697 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7700 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7703 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7706 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7709 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7712 if ( !results.get( 0 ).getLineage()[ 0 ].equals( "Eukaryota" ) ) {
7715 if ( !results.get( 0 ).getLineage()[ 1 ].equals( "Metazoa" ) ) {
7718 if ( !results.get( 0 ).getLineage()[ results.get( 0 ).getLineage().length - 1 ].equals( "Nematostella" ) ) {
7722 catch ( final IOException e ) {
7723 System.out.println();
7724 System.out.println( "the following might be due to absence internet connection:" );
7725 e.printStackTrace( System.out );
7728 catch ( final Exception e ) {
7734 private static boolean testUniprotEntryRetrieval() {
7736 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7737 if ( !entry.getAccession().equals( "P12345" ) ) {
7740 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7743 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7746 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7749 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7753 catch ( final IOException e ) {
7754 System.out.println();
7755 System.out.println( "the following might be due to absence internet connection:" );
7756 e.printStackTrace( System.out );
7759 catch ( final Exception e ) {
7765 private static boolean testWabiTxSearch() {
7768 result = TxSearch.searchSimple( "nematostella" );
7769 result = TxSearch.getTxId( "nematostella" );
7770 if ( !result.equals( "45350" ) ) {
7773 result = TxSearch.getTxName( "45350" );
7774 if ( !result.equals( "Nematostella" ) ) {
7777 result = TxSearch.getTxId( "nematostella vectensis" );
7778 if ( !result.equals( "45351" ) ) {
7781 result = TxSearch.getTxName( "45351" );
7782 if ( !result.equals( "Nematostella vectensis" ) ) {
7785 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7786 if ( !result.equals( "536089" ) ) {
7789 result = TxSearch.getTxName( "536089" );
7790 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7793 final List<String> queries = new ArrayList<String>();
7794 queries.add( "Campylobacter coli" );
7795 queries.add( "Escherichia coli" );
7796 queries.add( "Arabidopsis" );
7797 queries.add( "Trichoplax" );
7798 queries.add( "Samanea saman" );
7799 queries.add( "Kluyveromyces marxianus" );
7800 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7801 queries.add( "Bornavirus parrot/PDD/2008" );
7802 final List<RANKS> ranks = new ArrayList<RANKS>();
7803 ranks.add( RANKS.SUPERKINGDOM );
7804 ranks.add( RANKS.KINGDOM );
7805 ranks.add( RANKS.FAMILY );
7806 ranks.add( RANKS.GENUS );
7807 ranks.add( RANKS.TRIBE );
7808 result = TxSearch.searchLineage( queries, ranks );
7809 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7810 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7812 catch ( final Exception e ) {
7813 System.out.println();
7814 System.out.println( "the following might be due to absence internet connection:" );
7815 e.printStackTrace( System.out );
7821 private static boolean testAminoAcidSequence() {
7823 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
7824 if ( aa1.getLength() != 13 ) {
7827 if ( aa1.getResidueAt( 0 ) != 'A' ) {
7830 if ( aa1.getResidueAt( 2 ) != 'K' ) {
7833 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
7836 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
7837 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
7840 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
7841 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
7844 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
7845 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
7849 catch ( final Exception e ) {
7850 e.printStackTrace();
7856 private static boolean testCreateBalancedPhylogeny() {
7858 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
7859 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
7862 if ( p0.getNumberOfExternalNodes() != 15625 ) {
7865 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
7866 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
7869 if ( p1.getNumberOfExternalNodes() != 100 ) {
7873 catch ( final Exception e ) {
7874 e.printStackTrace();
7880 private static boolean testFastaParser() {
7882 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
7885 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
7888 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
7889 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
7892 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
7895 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
7898 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
7901 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
7904 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
7908 catch ( final Exception e ) {
7909 e.printStackTrace();
7915 private static boolean testGeneralMsaParser() {
7917 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
7918 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
7919 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
7920 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
7921 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
7922 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
7923 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
7924 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
7925 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
7926 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7929 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7932 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7935 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
7936 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
7939 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
7942 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
7945 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
7946 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
7949 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
7952 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
7956 catch ( final Exception e ) {
7957 e.printStackTrace();
7963 private static boolean testMafft() {
7965 final List<String> opts = new ArrayList<String>();
7966 opts.add( "--maxiterate" );
7968 opts.add( "--localpair" );
7969 opts.add( "--quiet" );
7971 final MsaInferrer mafft = Mafft.createInstance();
7972 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
7973 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
7977 catch ( final Exception e ) {
7978 e.printStackTrace( System.out );