2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.test;
28 import java.io.ByteArrayInputStream;
30 import java.io.FileInputStream;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Date;
34 import java.util.HashSet;
35 import java.util.Iterator;
36 import java.util.List;
37 import java.util.Locale;
40 import org.forester.application.support_transfer;
41 import org.forester.development.DevelopmentTools;
42 import org.forester.evoinference.TestPhylogenyReconstruction;
43 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
44 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
45 import org.forester.go.TestGo;
46 import org.forester.io.parsers.FastaParser;
47 import org.forester.io.parsers.GeneralMsaParser;
48 import org.forester.io.parsers.HmmscanPerDomainTableParser;
49 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
50 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
51 import org.forester.io.parsers.nexus.NexusCharactersParser;
52 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
53 import org.forester.io.parsers.nhx.NHXParser;
54 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
55 import org.forester.io.parsers.tol.TolParser;
56 import org.forester.io.writers.PhylogenyWriter;
57 import org.forester.msa.Mafft;
58 import org.forester.msa.Msa;
59 import org.forester.msa.MsaInferrer;
60 import org.forester.pccx.TestPccx;
61 import org.forester.phylogeny.Phylogeny;
62 import org.forester.phylogeny.PhylogenyBranch;
63 import org.forester.phylogeny.PhylogenyMethods;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.data.BinaryCharacters;
66 import org.forester.phylogeny.data.BranchWidth;
67 import org.forester.phylogeny.data.Confidence;
68 import org.forester.phylogeny.data.Distribution;
69 import org.forester.phylogeny.data.DomainArchitecture;
70 import org.forester.phylogeny.data.Event;
71 import org.forester.phylogeny.data.Identifier;
72 import org.forester.phylogeny.data.PhylogenyData;
73 import org.forester.phylogeny.data.Polygon;
74 import org.forester.phylogeny.data.PropertiesMap;
75 import org.forester.phylogeny.data.Property;
76 import org.forester.phylogeny.data.Property.AppliesTo;
77 import org.forester.phylogeny.data.ProteinDomain;
78 import org.forester.phylogeny.data.Taxonomy;
79 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
80 import org.forester.phylogeny.factories.PhylogenyFactory;
81 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
82 import org.forester.sdi.SDI;
83 import org.forester.sdi.SDIR;
84 import org.forester.sdi.SDIse;
85 import org.forester.sdi.TaxonomyAssigner;
86 import org.forester.sdi.TestGSDI;
87 import org.forester.sequence.BasicSequence;
88 import org.forester.sequence.Sequence;
89 import org.forester.surfacing.Protein;
90 import org.forester.surfacing.TestSurfacing;
91 import org.forester.tools.ConfidenceAssessor;
92 import org.forester.tools.SupportCount;
93 import org.forester.tools.TreeSplitMatrix;
94 import org.forester.util.AsciiHistogram;
95 import org.forester.util.BasicDescriptiveStatistics;
96 import org.forester.util.BasicTable;
97 import org.forester.util.BasicTableParser;
98 import org.forester.util.DescriptiveStatistics;
99 import org.forester.util.ForesterConstants;
100 import org.forester.util.ForesterUtil;
101 import org.forester.util.GeneralTable;
102 import org.forester.ws.uniprot.DatabaseTools;
103 import org.forester.ws.uniprot.SequenceDatabaseEntry;
104 import org.forester.ws.uniprot.UniProtTaxonomy;
105 import org.forester.ws.uniprot.UniProtWsTools;
106 import org.forester.ws.wabi.TxSearch;
107 import org.forester.ws.wabi.TxSearch.RANKS;
108 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
109 import org.forester.ws.wabi.TxSearch.TAX_RANK;
111 @SuppressWarnings( "unused")
112 public final class Test {
114 private final static double ZERO_DIFF = 1.0E-9;
115 private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
116 + ForesterUtil.getFileSeparator() + "test_data"
117 + ForesterUtil.getFileSeparator();
118 private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
119 + ForesterUtil.getFileSeparator() + "resources"
120 + ForesterUtil.getFileSeparator();
121 private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
122 private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
123 + ForesterConstants.PHYLO_XML_VERSION + "/"
124 + ForesterConstants.PHYLO_XML_XSD;
125 private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
126 + ForesterConstants.PHYLO_XML_VERSION + "/"
127 + ForesterConstants.PHYLO_XML_XSD;
129 private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
130 final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
134 private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
135 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
136 return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
139 public static boolean isEqual( final double a, final double b ) {
140 return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
143 public static void main( final String[] args ) {
144 System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
145 System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
147 Locale.setDefault( Locale.US );
148 System.out.println( "[Locale: " + Locale.getDefault() + "]" );
151 System.out.print( "[Test if directory with files for testing exists/is readable: " );
152 if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
153 System.out.println( "OK.]" );
156 System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
157 System.out.println( "Testing aborted." );
160 System.out.print( "[Test if resources directory exists/is readable: " );
161 if ( testDir( PATH_TO_RESOURCES ) ) {
162 System.out.println( "OK.]" );
165 System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
166 System.out.println( "Testing aborted." );
169 final long start_time = new Date().getTime();
170 System.out.print( "Hmmscan output parser: " );
171 if ( testHmmscanOutputParser() ) {
172 System.out.println( "OK." );
176 System.out.println( "failed." );
179 System.out.print( "Basic node methods: " );
180 if ( Test.testBasicNodeMethods() ) {
181 System.out.println( "OK." );
185 System.out.println( "failed." );
188 System.out.print( "Basic node construction and parsing of NHX (node level): " );
189 if ( Test.testNHXNodeParsing() ) {
190 System.out.println( "OK." );
194 System.out.println( "failed." );
197 System.out.print( "NH parsing: " );
198 if ( Test.testNHParsing() ) {
199 System.out.println( "OK." );
203 System.out.println( "failed." );
206 System.out.print( "Conversion to NHX (node level): " );
207 if ( Test.testNHXconversion() ) {
208 System.out.println( "OK." );
212 System.out.println( "failed." );
215 System.out.print( "NHX parsing: " );
216 if ( Test.testNHXParsing() ) {
217 System.out.println( "OK." );
221 System.out.println( "failed." );
224 System.out.print( "NHX parsing with quotes: " );
225 if ( Test.testNHXParsingQuotes() ) {
226 System.out.println( "OK." );
230 System.out.println( "failed." );
233 System.out.print( "NHX parsing (MrBayes): " );
234 if ( Test.testNHXParsingMB() ) {
235 System.out.println( "OK." );
239 System.out.println( "failed." );
242 System.out.print( "Nexus characters parsing: " );
243 if ( Test.testNexusCharactersParsing() ) {
244 System.out.println( "OK." );
248 System.out.println( "failed." );
251 System.out.print( "Nexus tree parsing: " );
252 if ( Test.testNexusTreeParsing() ) {
253 System.out.println( "OK." );
257 System.out.println( "failed." );
260 System.out.print( "Nexus tree parsing (translating): " );
261 if ( Test.testNexusTreeParsingTranslating() ) {
262 System.out.println( "OK." );
266 System.out.println( "failed." );
269 System.out.print( "Nexus matrix parsing: " );
270 if ( Test.testNexusMatrixParsing() ) {
271 System.out.println( "OK." );
275 System.out.println( "failed." );
278 System.out.print( "Basic phyloXML parsing: " );
279 if ( Test.testBasicPhyloXMLparsing() ) {
280 System.out.println( "OK." );
284 System.out.println( "failed." );
287 System.out.print( "Basic phyloXML parsing (validating against schema): " );
288 if ( testBasicPhyloXMLparsingValidating() ) {
289 System.out.println( "OK." );
293 System.out.println( "failed." );
296 System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
297 if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
298 System.out.println( "OK." );
302 System.out.println( "failed." );
305 System.out.print( "phyloXML Distribution Element: " );
306 if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
307 System.out.println( "OK." );
311 System.out.println( "failed." );
314 System.out.print( "Tol XML parsing: " );
315 if ( Test.testBasicTolXMLparsing() ) {
316 System.out.println( "OK." );
320 System.out.println( "failed." );
323 System.out.print( "Copying of node data: " );
324 if ( Test.testCopyOfNodeData() ) {
325 System.out.println( "OK." );
329 System.out.println( "failed." );
332 System.out.print( "Basic tree methods: " );
333 if ( Test.testBasicTreeMethods() ) {
334 System.out.println( "OK." );
338 System.out.println( "failed." );
341 System.out.print( "Postorder Iterator: " );
342 if ( Test.testPostOrderIterator() ) {
343 System.out.println( "OK." );
347 System.out.println( "failed." );
350 System.out.print( "Preorder Iterator: " );
351 if ( Test.testPreOrderIterator() ) {
352 System.out.println( "OK." );
356 System.out.println( "failed." );
359 System.out.print( "Levelorder Iterator: " );
360 if ( Test.testLevelOrderIterator() ) {
361 System.out.println( "OK." );
365 System.out.println( "failed." );
368 System.out.print( "Re-id methods: " );
369 if ( Test.testReIdMethods() ) {
370 System.out.println( "OK." );
374 System.out.println( "failed." );
377 System.out.print( "Methods on last external nodes: " );
378 if ( Test.testLastExternalNodeMethods() ) {
379 System.out.println( "OK." );
383 System.out.println( "failed." );
386 System.out.print( "Methods on external nodes: " );
387 if ( Test.testExternalNodeRelatedMethods() ) {
388 System.out.println( "OK." );
392 System.out.println( "failed." );
395 System.out.print( "Deletion of external nodes: " );
396 if ( Test.testDeletionOfExternalNodes() ) {
397 System.out.println( "OK." );
401 System.out.println( "failed." );
404 System.out.print( "Subtree deletion: " );
405 if ( Test.testSubtreeDeletion() ) {
406 System.out.println( "OK." );
410 System.out.println( "failed." );
413 System.out.print( "Phylogeny branch: " );
414 if ( Test.testPhylogenyBranch() ) {
415 System.out.println( "OK." );
419 System.out.println( "failed." );
422 System.out.print( "Rerooting: " );
423 if ( Test.testRerooting() ) {
424 System.out.println( "OK." );
428 System.out.println( "failed." );
431 System.out.print( "Mipoint rooting: " );
432 if ( Test.testMidpointrooting() ) {
433 System.out.println( "OK." );
437 System.out.println( "failed." );
440 System.out.print( "Support count: " );
441 if ( Test.testSupportCount() ) {
442 System.out.println( "OK." );
446 System.out.println( "failed." );
449 System.out.print( "Support transfer: " );
450 if ( Test.testSupportTransfer() ) {
451 System.out.println( "OK." );
455 System.out.println( "failed." );
458 System.out.print( "Finding of LCA: " );
459 if ( Test.testGetLCA() ) {
460 System.out.println( "OK." );
464 System.out.println( "failed." );
467 System.out.print( "Calculation of distance between nodes: " );
468 if ( Test.testGetDistance() ) {
469 System.out.println( "OK." );
473 System.out.println( "failed." );
476 System.out.print( "SDIse: " );
477 if ( Test.testSDIse() ) {
478 System.out.println( "OK." );
482 System.out.println( "failed." );
485 System.out.print( "Taxonomy assigner: " );
486 if ( Test.testTaxonomyAssigner() ) {
487 System.out.println( "OK." );
491 System.out.println( "failed." );
494 System.out.print( "SDIunrooted: " );
495 if ( Test.testSDIunrooted() ) {
496 System.out.println( "OK." );
500 System.out.println( "failed." );
503 System.out.print( "GSDI: " );
504 if ( TestGSDI.test() ) {
505 System.out.println( "OK." );
509 System.out.println( "failed." );
512 System.out.print( "Descriptive statistics: " );
513 if ( Test.testDescriptiveStatistics() ) {
514 System.out.println( "OK." );
518 System.out.println( "failed." );
521 System.out.print( "Data objects and methods: " );
522 if ( Test.testDataObjects() ) {
523 System.out.println( "OK." );
527 System.out.println( "failed." );
530 System.out.print( "Properties map: " );
531 if ( Test.testPropertiesMap() ) {
532 System.out.println( "OK." );
536 System.out.println( "failed." );
539 System.out.print( "Phylogeny reconstruction:" );
540 System.out.println();
541 if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
542 System.out.println( "OK." );
546 System.out.println( "failed." );
549 System.out.print( "Analysis of domain architectures: " );
550 System.out.println();
551 if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
552 System.out.println( "OK." );
556 System.out.println( "failed." );
559 System.out.print( "GO: " );
560 System.out.println();
561 if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
562 System.out.println( "OK." );
566 System.out.println( "failed." );
569 System.out.print( "Modeling tools: " );
570 if ( TestPccx.test() ) {
571 System.out.println( "OK." );
575 System.out.println( "failed." );
578 System.out.print( "Split Matrix strict: " );
579 if ( Test.testSplitStrict() ) {
580 System.out.println( "OK." );
584 System.out.println( "failed." );
587 System.out.print( "Split Matrix: " );
588 if ( Test.testSplit() ) {
589 System.out.println( "OK." );
593 System.out.println( "failed." );
596 System.out.print( "Confidence Assessor: " );
597 if ( Test.testConfidenceAssessor() ) {
598 System.out.println( "OK." );
602 System.out.println( "failed." );
605 System.out.print( "Basic table: " );
606 if ( Test.testBasicTable() ) {
607 System.out.println( "OK." );
611 System.out.println( "failed." );
614 System.out.print( "General table: " );
615 if ( Test.testGeneralTable() ) {
616 System.out.println( "OK." );
620 System.out.println( "failed." );
623 System.out.print( "Amino acid sequence: " );
624 if ( Test.testAminoAcidSequence() ) {
625 System.out.println( "OK." );
629 System.out.println( "failed." );
632 System.out.print( "General MSA parser: " );
633 if ( Test.testGeneralMsaParser() ) {
634 System.out.println( "OK." );
638 System.out.println( "failed." );
641 System.out.print( "Fasta parser for msa: " );
642 if ( Test.testFastaParser() ) {
643 System.out.println( "OK." );
647 System.out.println( "failed." );
650 System.out.print( "Creation of balanced phylogeny: " );
651 if ( Test.testCreateBalancedPhylogeny() ) {
652 System.out.println( "OK." );
656 System.out.println( "failed." );
659 System.out.print( "EMBL Entry Retrieval: " );
660 if ( Test.testEmblEntryRetrieval() ) {
661 System.out.println( "OK." );
665 System.out.println( "failed." );
668 System.out.print( "Uniprot Entry Retrieval: " );
669 if ( Test.testUniprotEntryRetrieval() ) {
670 System.out.println( "OK." );
674 System.out.println( "failed." );
677 System.out.print( "Uniprot Taxonomy Search: " );
678 if ( Test.testUniprotTaxonomySearch() ) {
679 System.out.println( "OK." );
683 System.out.println( "failed." );
686 if ( Mafft.isInstalled() ) {
687 System.out.print( "MAFFT (external program): " );
688 if ( Test.testMafft() ) {
689 System.out.println( "OK." );
693 System.out.println( "failed [will not count towards failed tests]" );
696 System.out.print( "Next nodes with collapsed: " );
697 if ( Test.testNextNodeWithCollapsing() ) {
698 System.out.println( "OK." );
702 System.out.println( "failed." );
705 // System.out.print( "WABI TxSearch: " );
706 // if ( Test.testWabiTxSearch() ) {
707 // System.out.println( "OK." );
712 // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
714 System.out.println();
715 final Runtime rt = java.lang.Runtime.getRuntime();
716 final long free_memory = rt.freeMemory() / 1000000;
717 final long total_memory = rt.totalMemory() / 1000000;
718 System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
719 + free_memory + "MB, total memory: " + total_memory + "MB)" );
720 System.out.println();
721 System.out.println( "Successful tests: " + succeeded );
722 System.out.println( "Failed tests: " + failed );
723 System.out.println();
725 System.out.println( "OK." );
728 System.out.println( "Not OK." );
730 // System.out.println();
731 // Development.setTime( true );
733 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
734 // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
735 // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
736 // final String multi = Test.PATH_TO_EXAMPLE_FILES +
737 // "multifurcations_ex_1.nhx";
738 // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
739 // final Phylogeny t1 = factory.create( new File( domains ), new
740 // NHXParser() )[ 0 ];
741 // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
743 // catch ( final Exception e ) {
744 // e.printStackTrace();
746 // t1.getRoot().preorderPrint();
747 // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
751 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
752 // + "\\AtNBSpos.nhx" ) );
754 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
755 // new NHXParser() );
756 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
757 // + "\\AtNBSpos.nhx" ) );
759 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
760 // new NHXParser() );
763 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
764 // + "\\big_tree.nhx" ) );
765 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
766 // + "\\big_tree.nhx" ) );
768 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
769 // new NHXParser() );
771 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
772 // new NHXParser() );
774 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
775 // + "\\big_tree.nhx" ) );
776 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
777 // + "\\big_tree.nhx" ) );
780 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
781 // new NHXParser() );
783 // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
784 // new NHXParser() );
786 // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
787 // + "\\AtNBSpos.nhx" ) );
789 // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
790 // new NHXParser() );
793 // catch ( IOException e ) {
794 // // TODO Auto-generated catch block
795 // e.printStackTrace();
799 private static boolean testBasicNodeMethods() {
801 if ( PhylogenyNode.getNodeCount() != 0 ) {
804 final PhylogenyNode n1 = new PhylogenyNode();
805 final PhylogenyNode n2 = PhylogenyNode
806 .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
807 final PhylogenyNode n3 = PhylogenyNode
808 .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
809 final PhylogenyNode n4 = PhylogenyNode
810 .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
811 if ( n1.isHasAssignedEvent() ) {
814 if ( PhylogenyNode.getNodeCount() != 4 ) {
817 if ( n3.getIndicator() != 0 ) {
820 if ( n3.getNumberOfExternalNodes() != 1 ) {
823 if ( !n3.isExternal() ) {
826 if ( !n3.isRoot() ) {
829 if ( !n4.getName().equals( "n4" ) ) {
833 catch ( final Exception e ) {
834 e.printStackTrace( System.out );
840 private static boolean testBasicPhyloXMLparsing() {
842 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
843 final PhyloXmlParser xml_parser = new PhyloXmlParser();
844 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
846 if ( xml_parser.getErrorCount() > 0 ) {
847 System.out.println( xml_parser.getErrorMessages().toString() );
850 if ( phylogenies_0.length != 4 ) {
853 final Phylogeny t1 = phylogenies_0[ 0 ];
854 final Phylogeny t2 = phylogenies_0[ 1 ];
855 final Phylogeny t3 = phylogenies_0[ 2 ];
856 final Phylogeny t4 = phylogenies_0[ 3 ];
857 if ( t1.getNumberOfExternalNodes() != 1 ) {
860 if ( !t1.isRooted() ) {
863 if ( t1.isRerootable() ) {
866 if ( !t1.getType().equals( "gene_tree" ) ) {
869 if ( t2.getNumberOfExternalNodes() != 2 ) {
872 if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
875 if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
878 if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
881 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
884 if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
887 if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
890 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
891 .startsWith( "actgtgggggt" ) ) {
894 if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
895 .startsWith( "ctgtgatgcat" ) ) {
898 if ( t3.getNumberOfExternalNodes() != 4 ) {
901 if ( !t1.getName().equals( "t1" ) ) {
904 if ( !t2.getName().equals( "t2" ) ) {
907 if ( !t3.getName().equals( "t3" ) ) {
910 if ( !t4.getName().equals( "t4" ) ) {
913 if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
916 if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
919 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
922 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
923 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
926 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
929 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
932 if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
935 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
936 .equals( "apoptosis" ) ) {
939 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
940 .equals( "GO:0006915" ) ) {
943 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
944 .equals( "UniProtKB" ) ) {
947 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
948 .equals( "experimental" ) ) {
951 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
952 .equals( "function" ) ) {
955 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
959 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
960 .getType().equals( "ml" ) ) {
963 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
964 .equals( "apoptosis" ) ) {
967 if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
968 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
971 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
972 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
975 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
976 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
979 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
980 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
983 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
984 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
987 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
988 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
991 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
992 .equals( "GO:0005829" ) ) {
995 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
996 .equals( "intracellular organelle" ) ) {
999 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1002 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1003 .equals( "UniProt link" ) ) ) {
1006 if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1009 //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
1012 // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
1015 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
1018 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1021 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1024 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1027 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1030 // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
1033 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1036 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
1037 // .equals( "B" ) ) {
1040 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
1043 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1046 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
1049 // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1050 // .getConfidence() != 2144 ) {
1053 // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1054 // .equals( "pfam" ) ) {
1057 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1060 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1063 // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1066 // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1069 // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1070 // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1074 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1077 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1080 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1083 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1086 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1089 // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1092 // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1095 // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1097 // if ( xml_parser.getErrorCount() > 0 ) {
1098 // System.out.println( xml_parser.getErrorMessages().toString() );
1101 // if ( phylogenies_1.length != 2 ) {
1104 // final Phylogeny a = phylogenies_1[ 0 ];
1105 // if ( !a.getName().equals( "tree 4" ) ) {
1108 // if ( a.getNumberOfExternalNodes() != 3 ) {
1111 // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1114 // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1118 catch ( final Exception e ) {
1119 e.printStackTrace( System.out );
1125 private static boolean testBasicPhyloXMLparsingRoundtrip() {
1127 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1128 final PhyloXmlParser xml_parser = new PhyloXmlParser();
1129 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1130 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1133 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1135 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1137 if ( xml_parser.getErrorCount() > 0 ) {
1138 System.out.println( xml_parser.getErrorMessages().toString() );
1141 if ( phylogenies_0.length != 4 ) {
1144 final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
1145 final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
1146 if ( phylogenies_t1.length != 1 ) {
1149 final Phylogeny t1_rt = phylogenies_t1[ 0 ];
1150 if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
1153 if ( !t1_rt.isRooted() ) {
1156 if ( t1_rt.isRerootable() ) {
1159 if ( !t1_rt.getType().equals( "gene_tree" ) ) {
1162 final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
1163 final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
1164 final Phylogeny t2_rt = phylogenies_t2[ 0 ];
1165 if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
1168 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
1171 if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
1174 if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
1177 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
1178 .startsWith( "actgtgggggt" ) ) {
1181 if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
1182 .startsWith( "ctgtgatgcat" ) ) {
1185 final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
1186 final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
1187 final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
1188 final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
1189 if ( phylogenies_1.length != 1 ) {
1192 final Phylogeny t3_rt = phylogenies_1[ 0 ];
1193 if ( !t3_rt.getName().equals( "t3" ) ) {
1196 if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
1199 if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
1202 if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
1205 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
1208 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
1209 .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
1212 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
1215 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
1218 if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
1219 .equals( "UniProtKB" ) ) {
1222 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1223 .equals( "apoptosis" ) ) {
1226 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
1227 .equals( "GO:0006915" ) ) {
1230 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
1231 .equals( "UniProtKB" ) ) {
1234 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
1235 .equals( "experimental" ) ) {
1238 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
1239 .equals( "function" ) ) {
1242 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1243 .getValue() != 1 ) {
1246 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
1247 .getType().equals( "ml" ) ) {
1250 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
1251 .equals( "apoptosis" ) ) {
1254 if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1255 .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
1258 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1259 .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
1262 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1263 .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
1266 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1267 .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
1270 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1271 .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
1274 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
1275 .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
1278 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
1279 .equals( "GO:0005829" ) ) {
1282 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
1283 .equals( "intracellular organelle" ) ) {
1286 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
1289 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
1290 .equals( "UniProt link" ) ) ) {
1293 if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
1296 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
1299 if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
1300 .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." ) ) ) {
1303 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
1306 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
1309 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
1312 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
1315 if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
1316 .equals( "ncbi" ) ) {
1319 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
1322 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1323 .getName().equals( "B" ) ) {
1326 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1327 .getFrom() != 21 ) {
1330 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
1333 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1334 .getLength() != 24 ) {
1337 if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
1338 .getConfidence() != 2144 ) {
1341 if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
1342 .equals( "pfam" ) ) {
1345 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
1348 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1351 if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
1354 if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
1357 final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
1358 if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
1361 if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
1364 if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
1367 if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
1370 if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
1373 if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
1376 if ( taxbb.getSynonyms().size() != 2 ) {
1379 if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
1382 if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
1385 if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
1388 if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
1391 if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
1394 if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
1395 .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
1399 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
1402 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
1405 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
1408 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
1411 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
1414 if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
1417 if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
1421 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
1424 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
1425 .equalsIgnoreCase( "435" ) ) {
1428 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
1431 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
1432 .equalsIgnoreCase( "443.7" ) ) {
1435 if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
1438 if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
1441 if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
1442 .equalsIgnoreCase( "433" ) ) {
1446 catch ( final Exception e ) {
1447 e.printStackTrace( System.out );
1453 private static boolean testBasicPhyloXMLparsingValidating() {
1455 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1456 PhyloXmlParser xml_parser = null;
1458 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1460 catch ( final Exception e ) {
1461 // Do nothing -- means were not running from jar.
1463 if ( xml_parser == null ) {
1464 xml_parser = new PhyloXmlParser();
1465 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
1466 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
1469 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
1472 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
1474 if ( xml_parser.getErrorCount() > 0 ) {
1475 System.out.println( xml_parser.getErrorMessages().toString() );
1478 if ( phylogenies_0.length != 4 ) {
1481 final Phylogeny t1 = phylogenies_0[ 0 ];
1482 final Phylogeny t2 = phylogenies_0[ 1 ];
1483 final Phylogeny t3 = phylogenies_0[ 2 ];
1484 final Phylogeny t4 = phylogenies_0[ 3 ];
1485 if ( !t1.getName().equals( "t1" ) ) {
1488 if ( !t2.getName().equals( "t2" ) ) {
1491 if ( !t3.getName().equals( "t3" ) ) {
1494 if ( !t4.getName().equals( "t4" ) ) {
1497 if ( t1.getNumberOfExternalNodes() != 1 ) {
1500 if ( t2.getNumberOfExternalNodes() != 2 ) {
1503 if ( t3.getNumberOfExternalNodes() != 4 ) {
1506 final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
1507 final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
1508 if ( xml_parser.getErrorCount() > 0 ) {
1509 System.out.println( "errors:" );
1510 System.out.println( xml_parser.getErrorMessages().toString() );
1513 if ( phylogenies_1.length != 4 ) {
1516 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
1518 if ( xml_parser.getErrorCount() > 0 ) {
1519 System.out.println( "errors:" );
1520 System.out.println( xml_parser.getErrorMessages().toString() );
1523 if ( phylogenies_2.length != 1 ) {
1526 if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
1529 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
1531 if ( xml_parser.getErrorCount() > 0 ) {
1532 System.out.println( xml_parser.getErrorMessages().toString() );
1535 if ( phylogenies_3.length != 2 ) {
1538 final Phylogeny a = phylogenies_3[ 0 ];
1539 if ( !a.getName().equals( "tree 4" ) ) {
1542 if ( a.getNumberOfExternalNodes() != 3 ) {
1545 if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
1548 if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
1551 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
1553 if ( xml_parser.getErrorCount() > 0 ) {
1554 System.out.println( xml_parser.getErrorMessages().toString() );
1557 if ( phylogenies_4.length != 1 ) {
1560 final Phylogeny s = phylogenies_4[ 0 ];
1561 if ( s.getNumberOfExternalNodes() != 6 ) {
1564 s.getNode( "first" );
1566 s.getNode( "\"<a'b&c'd\">\"" );
1567 s.getNode( "'''\"" );
1568 s.getNode( "\"\"\"" );
1569 s.getNode( "dick & doof" );
1571 catch ( final Exception e ) {
1572 e.printStackTrace( System.out );
1578 private static boolean testBasicTable() {
1580 final BasicTable<String> t0 = new BasicTable<String>();
1581 if ( t0.getNumberOfColumns() != 0 ) {
1584 if ( t0.getNumberOfRows() != 0 ) {
1587 t0.setValue( 3, 2, "23" );
1588 t0.setValue( 10, 1, "error" );
1589 t0.setValue( 10, 1, "110" );
1590 t0.setValue( 9, 1, "19" );
1591 t0.setValue( 1, 10, "101" );
1592 t0.setValue( 10, 10, "1010" );
1593 t0.setValue( 100, 10, "10100" );
1594 t0.setValue( 0, 0, "00" );
1595 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
1598 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
1601 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
1604 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
1607 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
1610 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
1613 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
1616 if ( t0.getNumberOfColumns() != 101 ) {
1619 if ( t0.getNumberOfRows() != 11 ) {
1622 if ( t0.getValueAsString( 49, 4 ) != null ) {
1625 final String l = ForesterUtil.getLineSeparator();
1626 final StringBuffer source = new StringBuffer();
1627 source.append( "" + l );
1628 source.append( "# 1 1 1 1 1 1 1 1" + l );
1629 source.append( " 00 01 02 03" + l );
1630 source.append( " 10 11 12 13 " + l );
1631 source.append( "20 21 22 23 " + l );
1632 source.append( " 30 31 32 33" + l );
1633 source.append( "40 41 42 43" + l );
1634 source.append( " # 1 1 1 1 1 " + l );
1635 source.append( "50 51 52 53 54" + l );
1636 final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
1637 if ( t1.getNumberOfColumns() != 5 ) {
1640 if ( t1.getNumberOfRows() != 6 ) {
1643 if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
1646 if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
1649 if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
1652 if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
1655 final StringBuffer source1 = new StringBuffer();
1656 source1.append( "" + l );
1657 source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1658 source1.append( " 00; 01 ;02;03" + l );
1659 source1.append( " 10; 11; 12; 13 " + l );
1660 source1.append( "20; 21; 22; 23 " + l );
1661 source1.append( " 30; 31; 32; 33" + l );
1662 source1.append( "40;41;42;43" + l );
1663 source1.append( " # 1 1 1 1 1 " + l );
1664 source1.append( ";;;50 ; ;52; 53;;54 " + l );
1665 final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
1666 if ( t2.getNumberOfColumns() != 5 ) {
1669 if ( t2.getNumberOfRows() != 6 ) {
1672 if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
1675 if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
1678 if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
1681 if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
1684 if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
1687 if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
1690 final StringBuffer source2 = new StringBuffer();
1691 source2.append( "" + l );
1692 source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
1693 source2.append( " 00; 01 ;02;03" + l );
1694 source2.append( " 10; 11; 12; 13 " + l );
1695 source2.append( "20; 21; 22; 23 " + l );
1696 source2.append( " " + l );
1697 source2.append( " 30; 31; 32; 33" + l );
1698 source2.append( "40;41;42;43" + l );
1699 source2.append( " comment: 1 1 1 1 1 " + l );
1700 source2.append( ";;;50 ; 52; 53;;54 " + l );
1701 final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
1706 if ( tl.size() != 2 ) {
1709 final BasicTable<String> t3 = tl.get( 0 );
1710 final BasicTable<String> t4 = tl.get( 1 );
1711 if ( t3.getNumberOfColumns() != 4 ) {
1714 if ( t3.getNumberOfRows() != 3 ) {
1717 if ( t4.getNumberOfColumns() != 4 ) {
1720 if ( t4.getNumberOfRows() != 3 ) {
1723 if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
1726 if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
1730 catch ( final Exception e ) {
1731 e.printStackTrace( System.out );
1737 private static boolean testBasicTolXMLparsing() {
1739 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1740 final TolParser parser = new TolParser();
1741 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
1742 if ( parser.getErrorCount() > 0 ) {
1743 System.out.println( parser.getErrorMessages().toString() );
1746 if ( phylogenies_0.length != 1 ) {
1749 final Phylogeny t1 = phylogenies_0[ 0 ];
1750 if ( t1.getNumberOfExternalNodes() != 5 ) {
1753 if ( !t1.isRooted() ) {
1756 if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
1759 if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
1762 if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
1765 if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
1768 final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
1769 if ( parser.getErrorCount() > 0 ) {
1770 System.out.println( parser.getErrorMessages().toString() );
1773 if ( phylogenies_1.length != 1 ) {
1776 final Phylogeny t2 = phylogenies_1[ 0 ];
1777 if ( t2.getNumberOfExternalNodes() != 664 ) {
1780 if ( !t2.isRooted() ) {
1783 if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
1786 if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
1789 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1792 if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
1795 if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
1798 if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
1799 .equals( "Aquifex" ) ) {
1802 final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
1803 if ( parser.getErrorCount() > 0 ) {
1804 System.out.println( parser.getErrorMessages().toString() );
1807 if ( phylogenies_2.length != 1 ) {
1810 final Phylogeny t3 = phylogenies_2[ 0 ];
1811 if ( t3.getNumberOfExternalNodes() != 184 ) {
1814 if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
1817 if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
1820 if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
1823 final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
1824 if ( parser.getErrorCount() > 0 ) {
1825 System.out.println( parser.getErrorMessages().toString() );
1828 if ( phylogenies_3.length != 1 ) {
1831 final Phylogeny t4 = phylogenies_3[ 0 ];
1832 if ( t4.getNumberOfExternalNodes() != 1 ) {
1835 if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
1838 if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
1841 if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
1844 final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
1845 if ( parser.getErrorCount() > 0 ) {
1846 System.out.println( parser.getErrorMessages().toString() );
1849 if ( phylogenies_4.length != 1 ) {
1852 final Phylogeny t5 = phylogenies_4[ 0 ];
1853 if ( t5.getNumberOfExternalNodes() != 13 ) {
1856 if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
1859 if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
1862 if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
1866 catch ( final Exception e ) {
1867 e.printStackTrace( System.out );
1873 private static boolean testBasicTreeMethods() {
1875 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1876 final Phylogeny t1 = factory.create();
1877 if ( !t1.isEmpty() ) {
1880 final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
1881 if ( t2.getNumberOfExternalNodes() != 4 ) {
1884 if ( t2.getHeight() != 8.5 ) {
1887 if ( !t2.isCompletelyBinary() ) {
1890 if ( t2.isEmpty() ) {
1893 final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
1894 if ( t3.getNumberOfExternalNodes() != 5 ) {
1897 if ( t3.getHeight() != 11 ) {
1900 if ( t3.isCompletelyBinary() ) {
1903 final PhylogenyNode n = t3.getNode( "ABC" );
1904 PhylogenyNodeIterator it;
1905 for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
1908 for( it.reset(); it.hasNext(); ) {
1911 final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
1912 if ( !it2.next().getName().equals( "A" ) ) {
1915 if ( !it2.next().getName().equals( "B" ) ) {
1918 if ( !it2.next().getName().equals( "C" ) ) {
1921 if ( it2.hasNext() ) {
1924 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 ];
1925 if ( t4.getNumberOfExternalNodes() != 9 ) {
1928 if ( t4.getHeight() != 11 ) {
1931 if ( t4.isCompletelyBinary() ) {
1934 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)" );
1935 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
1936 if ( t5.getNumberOfExternalNodes() != 8 ) {
1939 if ( t5.getHeight() != 15 ) {
1942 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)" );
1943 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
1944 if ( t6.getHeight() != 15 ) {
1947 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)" );
1948 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
1949 if ( t7.getHeight() != 15 ) {
1952 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)" );
1953 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
1954 if ( t8.getNumberOfExternalNodes() != 10 ) {
1957 if ( t8.getHeight() != 15 ) {
1960 final char[] a9 = new char[] {};
1961 final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
1962 if ( t9.getHeight() != 0 ) {
1965 final char[] a10 = new char[] { 'a', ':', '6' };
1966 final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
1967 if ( t10.getHeight() != 6 ) {
1971 catch ( final Exception e ) {
1972 e.printStackTrace( System.out );
1978 private static boolean testConfidenceAssessor() {
1980 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
1981 final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1982 final Phylogeny[] ev0 = factory
1983 .create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
1985 ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
1986 if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1989 if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
1992 final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
1993 final Phylogeny[] ev1 = factory
1994 .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)));",
1996 ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
1997 if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
2000 if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2003 final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2004 final Phylogeny[] ev_b = factory
2005 .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",
2007 ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
2008 // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
2009 if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
2012 if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2016 final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
2017 final Phylogeny[] ev1x = factory
2018 .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)));",
2020 ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
2021 if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2024 if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
2027 final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
2028 final Phylogeny[] ev_bx = factory
2029 .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",
2031 ConfidenceAssessor.evaluate( "bootstrap", ev_bx, t_bx, true, 1 );
2032 if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2035 if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2039 final Phylogeny[] t2 = factory
2040 .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);",
2042 final Phylogeny[] ev2 = factory
2043 .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);",
2045 for( final Phylogeny target : t2 ) {
2046 ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
2049 final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
2050 new NHXParser() )[ 0 ];
2051 final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
2052 ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
2053 if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2056 if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
2059 if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
2063 catch ( final Exception e ) {
2064 e.printStackTrace();
2070 private static boolean testCopyOfNodeData() {
2072 final PhylogenyNode n1 = PhylogenyNode
2073 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
2074 final PhylogenyNode n2 = n1.copyNodeData();
2075 if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
2079 catch ( final Exception e ) {
2080 e.printStackTrace();
2086 private static boolean testDataObjects() {
2088 final Confidence s0 = new Confidence();
2089 final Confidence s1 = new Confidence();
2090 if ( !s0.isEqual( s1 ) ) {
2093 final Confidence s2 = new Confidence( 0.23, "bootstrap" );
2094 final Confidence s3 = new Confidence( 0.23, "bootstrap" );
2095 if ( s2.isEqual( s1 ) ) {
2098 if ( !s2.isEqual( s3 ) ) {
2101 final Confidence s4 = ( Confidence ) s3.copy();
2102 if ( !s4.isEqual( s3 ) ) {
2109 final Taxonomy t1 = new Taxonomy();
2110 final Taxonomy t2 = new Taxonomy();
2111 final Taxonomy t3 = new Taxonomy();
2112 final Taxonomy t4 = new Taxonomy();
2113 final Taxonomy t5 = new Taxonomy();
2114 t1.setIdentifier( new Identifier( "ecoli" ) );
2115 t1.setTaxonomyCode( "ECOLI" );
2116 t1.setScientificName( "E. coli" );
2117 t1.setCommonName( "coli" );
2118 final Taxonomy t0 = ( Taxonomy ) t1.copy();
2119 if ( !t1.isEqual( t0 ) ) {
2122 t2.setIdentifier( new Identifier( "ecoli" ) );
2123 t2.setTaxonomyCode( "other" );
2124 t2.setScientificName( "what" );
2125 t2.setCommonName( "something" );
2126 if ( !t1.isEqual( t2 ) ) {
2129 t2.setIdentifier( new Identifier( "nemve" ) );
2130 if ( t1.isEqual( t2 ) ) {
2133 t1.setIdentifier( null );
2134 t3.setTaxonomyCode( "ECOLI" );
2135 t3.setScientificName( "what" );
2136 t3.setCommonName( "something" );
2137 if ( !t1.isEqual( t3 ) ) {
2140 t1.setIdentifier( null );
2141 t1.setTaxonomyCode( "" );
2142 t4.setScientificName( "E. ColI" );
2143 t4.setCommonName( "something" );
2144 if ( !t1.isEqual( t4 ) ) {
2147 t4.setScientificName( "B. subtilis" );
2148 t4.setCommonName( "something" );
2149 if ( t1.isEqual( t4 ) ) {
2152 t1.setIdentifier( null );
2153 t1.setTaxonomyCode( "" );
2154 t1.setScientificName( "" );
2155 t5.setCommonName( "COLI" );
2156 if ( !t1.isEqual( t5 ) ) {
2159 t5.setCommonName( "vibrio" );
2160 if ( t1.isEqual( t5 ) ) {
2165 final Identifier id0 = new Identifier( "123", "pfam" );
2166 final Identifier id1 = ( Identifier ) id0.copy();
2167 if ( !id1.isEqual( id1 ) ) {
2170 if ( !id1.isEqual( id0 ) ) {
2173 if ( !id0.isEqual( id1 ) ) {
2180 final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
2181 final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
2182 if ( !pd1.isEqual( pd1 ) ) {
2185 if ( !pd1.isEqual( pd0 ) ) {
2190 final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
2191 final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
2192 if ( !pd3.isEqual( pd3 ) ) {
2195 if ( !pd2.isEqual( pd3 ) ) {
2198 if ( !pd0.isEqual( pd3 ) ) {
2203 // DomainArchitecture
2204 // ------------------
2205 final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
2206 final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
2207 final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
2208 final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
2209 final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
2210 final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
2215 final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
2216 if ( ds0.getNumberOfDomains() != 4 ) {
2219 final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
2220 if ( !ds0.isEqual( ds0 ) ) {
2223 if ( !ds0.isEqual( ds1 ) ) {
2226 if ( ds1.getNumberOfDomains() != 4 ) {
2229 final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
2234 final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
2235 if ( ds0.isEqual( ds2 ) ) {
2241 final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
2242 if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
2243 System.out.println( ds3.toNHX() );
2246 if ( ds3.getNumberOfDomains() != 3 ) {
2251 final Event e1 = new Event( Event.EventType.fusion );
2252 if ( e1.isDuplication() ) {
2255 if ( !e1.isFusion() ) {
2258 if ( !e1.asText().toString().equals( "fusion" ) ) {
2261 if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
2264 final Event e11 = new Event( Event.EventType.fusion );
2265 if ( !e11.isEqual( e1 ) ) {
2268 if ( !e11.toNHX().toString().equals( "" ) ) {
2271 final Event e2 = new Event( Event.EventType.speciation_or_duplication );
2272 if ( e2.isDuplication() ) {
2275 if ( !e2.isSpeciationOrDuplication() ) {
2278 if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
2281 if ( !e2.asSimpleText().toString().equals( "?" ) ) {
2284 if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
2287 if ( e11.isEqual( e2 ) ) {
2290 final Event e2c = ( Event ) e2.copy();
2291 if ( !e2c.isEqual( e2 ) ) {
2294 Event e3 = new Event( 1, 2, 3 );
2295 if ( e3.isDuplication() ) {
2298 if ( e3.isSpeciation() ) {
2301 if ( e3.isGeneLoss() ) {
2304 if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2307 final Event e3c = ( Event ) e3.copy();
2308 final Event e3cc = ( Event ) e3c.copy();
2309 if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
2313 if ( !e3c.isEqual( e3cc ) ) {
2316 Event e4 = new Event( 1, 2, 3 );
2317 if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2320 if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
2323 final Event e4c = ( Event ) e4.copy();
2325 final Event e4cc = ( Event ) e4c.copy();
2326 if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
2329 if ( !e4c.isEqual( e4cc ) ) {
2332 final Event e5 = new Event();
2333 if ( !e5.isUnassigned() ) {
2336 if ( !e5.asText().toString().equals( "unassigned" ) ) {
2339 if ( !e5.asSimpleText().toString().equals( "" ) ) {
2342 final Event e6 = new Event( 1, 0, 0 );
2343 if ( !e6.asText().toString().equals( "duplication" ) ) {
2346 if ( !e6.asSimpleText().toString().equals( "D" ) ) {
2349 final Event e7 = new Event( 0, 1, 0 );
2350 if ( !e7.asText().toString().equals( "speciation" ) ) {
2353 if ( !e7.asSimpleText().toString().equals( "S" ) ) {
2356 final Event e8 = new Event( 0, 0, 1 );
2357 if ( !e8.asText().toString().equals( "gene-loss" ) ) {
2360 if ( !e8.asSimpleText().toString().equals( "L" ) ) {
2364 catch ( final Exception e ) {
2365 e.printStackTrace( System.out );
2371 private static boolean testDeletionOfExternalNodes() {
2373 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2374 final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
2375 final PhylogenyWriter w = new PhylogenyWriter();
2376 if ( t0.isEmpty() ) {
2379 if ( t0.getNumberOfExternalNodes() != 1 ) {
2382 t0.deleteSubtree( t0.getNode( "A" ), false );
2383 if ( t0.getNumberOfExternalNodes() != 0 ) {
2386 if ( !t0.isEmpty() ) {
2389 final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
2390 if ( t1.getNumberOfExternalNodes() != 2 ) {
2393 t1.deleteSubtree( t1.getNode( "A" ), false );
2394 if ( t1.getNumberOfExternalNodes() != 1 ) {
2397 if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
2400 t1.deleteSubtree( t1.getNode( "B" ), false );
2401 if ( t1.getNumberOfExternalNodes() != 1 ) {
2404 t1.deleteSubtree( t1.getNode( "r" ), false );
2405 if ( !t1.isEmpty() ) {
2408 final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
2409 if ( t2.getNumberOfExternalNodes() != 3 ) {
2412 t2.deleteSubtree( t2.getNode( "B" ), false );
2413 if ( t2.getNumberOfExternalNodes() != 2 ) {
2416 t2.toNewHampshireX();
2417 PhylogenyNode n = t2.getNode( "A" );
2418 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2421 t2.deleteSubtree( t2.getNode( "A" ), false );
2422 if ( t2.getNumberOfExternalNodes() != 2 ) {
2425 t2.deleteSubtree( t2.getNode( "C" ), true );
2426 if ( t2.getNumberOfExternalNodes() != 1 ) {
2429 final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2430 if ( t3.getNumberOfExternalNodes() != 4 ) {
2433 t3.deleteSubtree( t3.getNode( "B" ), true );
2434 if ( t3.getNumberOfExternalNodes() != 3 ) {
2437 n = t3.getNode( "A" );
2438 if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
2441 n = n.getNextExternalNode();
2442 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2445 t3.deleteSubtree( t3.getNode( "A" ), true );
2446 if ( t3.getNumberOfExternalNodes() != 2 ) {
2449 n = t3.getNode( "C" );
2450 if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
2453 t3.deleteSubtree( t3.getNode( "C" ), true );
2454 if ( t3.getNumberOfExternalNodes() != 1 ) {
2457 t3.deleteSubtree( t3.getNode( "D" ), true );
2458 if ( t3.getNumberOfExternalNodes() != 0 ) {
2461 final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2462 if ( t4.getNumberOfExternalNodes() != 6 ) {
2465 t4.deleteSubtree( t4.getNode( "B2" ), true );
2466 if ( t4.getNumberOfExternalNodes() != 5 ) {
2469 String s = w.toNewHampshire( t4, false, true ).toString();
2470 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2473 t4.deleteSubtree( t4.getNode( "B11" ), true );
2474 if ( t4.getNumberOfExternalNodes() != 4 ) {
2477 t4.deleteSubtree( t4.getNode( "C" ), true );
2478 if ( t4.getNumberOfExternalNodes() != 3 ) {
2481 n = t4.getNode( "A" );
2482 n = n.getNextExternalNode();
2483 if ( !n.getName().equals( "B12" ) ) {
2486 n = n.getNextExternalNode();
2487 if ( !n.getName().equals( "D" ) ) {
2490 s = w.toNewHampshire( t4, false, true ).toString();
2491 if ( !s.equals( "((A,B12),D);" ) ) {
2494 final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2495 t5.deleteSubtree( t5.getNode( "A" ), true );
2496 if ( t5.getNumberOfExternalNodes() != 5 ) {
2499 s = w.toNewHampshire( t5, false, true ).toString();
2500 if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
2503 final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2504 t6.deleteSubtree( t6.getNode( "B11" ), true );
2505 if ( t6.getNumberOfExternalNodes() != 5 ) {
2508 s = w.toNewHampshire( t6, false, false ).toString();
2509 if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
2512 final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2513 t7.deleteSubtree( t7.getNode( "B12" ), true );
2514 if ( t7.getNumberOfExternalNodes() != 5 ) {
2517 s = w.toNewHampshire( t7, false, true ).toString();
2518 if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
2521 final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2522 t8.deleteSubtree( t8.getNode( "B2" ), true );
2523 if ( t8.getNumberOfExternalNodes() != 5 ) {
2526 s = w.toNewHampshire( t8, false, false ).toString();
2527 if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
2530 final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2531 t9.deleteSubtree( t9.getNode( "C" ), true );
2532 if ( t9.getNumberOfExternalNodes() != 5 ) {
2535 s = w.toNewHampshire( t9, false, true ).toString();
2536 if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
2539 final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
2540 t10.deleteSubtree( t10.getNode( "D" ), true );
2541 if ( t10.getNumberOfExternalNodes() != 5 ) {
2544 s = w.toNewHampshire( t10, false, true ).toString();
2545 if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
2548 final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
2549 t11.deleteSubtree( t11.getNode( "A" ), true );
2550 if ( t11.getNumberOfExternalNodes() != 2 ) {
2553 s = w.toNewHampshire( t11, false, true ).toString();
2554 if ( !s.equals( "(B,C);" ) ) {
2557 t11.deleteSubtree( t11.getNode( "C" ), true );
2558 if ( t11.getNumberOfExternalNodes() != 1 ) {
2561 s = w.toNewHampshire( t11, false, false ).toString();
2562 if ( !s.equals( "B;" ) ) {
2565 final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
2566 t12.deleteSubtree( t12.getNode( "B2" ), true );
2567 if ( t12.getNumberOfExternalNodes() != 8 ) {
2570 s = w.toNewHampshire( t12, false, true ).toString();
2571 if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
2574 t12.deleteSubtree( t12.getNode( "B3" ), true );
2575 if ( t12.getNumberOfExternalNodes() != 7 ) {
2578 s = w.toNewHampshire( t12, false, true ).toString();
2579 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
2582 t12.deleteSubtree( t12.getNode( "C3" ), true );
2583 if ( t12.getNumberOfExternalNodes() != 6 ) {
2586 s = w.toNewHampshire( t12, false, true ).toString();
2587 if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
2590 t12.deleteSubtree( t12.getNode( "A1" ), true );
2591 if ( t12.getNumberOfExternalNodes() != 5 ) {
2594 s = w.toNewHampshire( t12, false, true ).toString();
2595 if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
2598 t12.deleteSubtree( t12.getNode( "B1" ), true );
2599 if ( t12.getNumberOfExternalNodes() != 4 ) {
2602 s = w.toNewHampshire( t12, false, true ).toString();
2603 if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
2606 t12.deleteSubtree( t12.getNode( "A3" ), true );
2607 if ( t12.getNumberOfExternalNodes() != 3 ) {
2610 s = w.toNewHampshire( t12, false, true ).toString();
2611 if ( !s.equals( "(A2,(C1,C2));" ) ) {
2614 t12.deleteSubtree( t12.getNode( "A2" ), true );
2615 if ( t12.getNumberOfExternalNodes() != 2 ) {
2618 s = w.toNewHampshire( t12, false, true ).toString();
2619 if ( !s.equals( "(C1,C2);" ) ) {
2622 final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
2623 t13.deleteSubtree( t13.getNode( "D" ), true );
2624 if ( t13.getNumberOfExternalNodes() != 4 ) {
2627 s = w.toNewHampshire( t13, false, true ).toString();
2628 if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
2631 final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
2632 t14.deleteSubtree( t14.getNode( "E" ), true );
2633 if ( t14.getNumberOfExternalNodes() != 5 ) {
2636 s = w.toNewHampshire( t14, false, true ).toString();
2637 if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
2640 final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
2641 t15.deleteSubtree( t15.getNode( "B2" ), true );
2642 if ( t15.getNumberOfExternalNodes() != 11 ) {
2645 t15.deleteSubtree( t15.getNode( "B1" ), true );
2646 if ( t15.getNumberOfExternalNodes() != 10 ) {
2649 t15.deleteSubtree( t15.getNode( "B3" ), true );
2650 if ( t15.getNumberOfExternalNodes() != 9 ) {
2653 t15.deleteSubtree( t15.getNode( "B4" ), true );
2654 if ( t15.getNumberOfExternalNodes() != 8 ) {
2657 t15.deleteSubtree( t15.getNode( "A1" ), true );
2658 if ( t15.getNumberOfExternalNodes() != 7 ) {
2661 t15.deleteSubtree( t15.getNode( "C4" ), true );
2662 if ( t15.getNumberOfExternalNodes() != 6 ) {
2666 catch ( final Exception e ) {
2667 e.printStackTrace( System.out );
2673 private static boolean testDescriptiveStatistics() {
2675 final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
2676 dss1.addValue( 82 );
2677 dss1.addValue( 78 );
2678 dss1.addValue( 70 );
2679 dss1.addValue( 58 );
2680 dss1.addValue( 42 );
2681 if ( dss1.getN() != 5 ) {
2684 if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
2687 if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
2690 if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
2693 if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
2696 if ( !Test.isEqual( dss1.median(), 70 ) ) {
2699 if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
2702 if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
2705 if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
2708 if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
2711 if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
2714 if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
2717 dss1.addValue( 123 );
2718 if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
2721 if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
2724 if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
2727 final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
2728 dss2.addValue( -1.85 );
2729 dss2.addValue( 57.5 );
2730 dss2.addValue( 92.78 );
2731 dss2.addValue( 57.78 );
2732 if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
2735 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
2738 final double[] a = dss2.getDataAsDoubleArray();
2739 if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
2742 dss2.addValue( -100 );
2743 if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
2746 if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
2749 final double[] ds = new double[ 14 ];
2764 final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
2765 if ( bins.length != 4 ) {
2768 if ( bins[ 0 ] != 2 ) {
2771 if ( bins[ 1 ] != 3 ) {
2774 if ( bins[ 2 ] != 4 ) {
2777 if ( bins[ 3 ] != 5 ) {
2780 final double[] ds1 = new double[ 9 ];
2790 final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
2791 if ( bins1.length != 4 ) {
2794 if ( bins1[ 0 ] != 2 ) {
2797 if ( bins1[ 1 ] != 3 ) {
2800 if ( bins1[ 2 ] != 0 ) {
2803 if ( bins1[ 3 ] != 4 ) {
2806 final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
2807 if ( bins1_1.length != 3 ) {
2810 if ( bins1_1[ 0 ] != 3 ) {
2813 if ( bins1_1[ 1 ] != 2 ) {
2816 if ( bins1_1[ 2 ] != 4 ) {
2819 final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
2820 if ( bins1_2.length != 3 ) {
2823 if ( bins1_2[ 0 ] != 2 ) {
2826 if ( bins1_2[ 1 ] != 2 ) {
2829 if ( bins1_2[ 2 ] != 2 ) {
2832 final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
2846 dss3.addValue( 10 );
2847 dss3.addValue( 10 );
2848 dss3.addValue( 10 );
2849 final AsciiHistogram histo = new AsciiHistogram( dss3 );
2850 histo.toStringBuffer( 10, '=', 40, 5 );
2851 histo.toStringBuffer( 3, 8, 10, '=', 40, 5 );
2853 catch ( final Exception e ) {
2854 e.printStackTrace( System.out );
2860 private static boolean testDir( final String file ) {
2862 final File f = new File( file );
2863 if ( !f.exists() ) {
2866 if ( !f.isDirectory() ) {
2869 if ( !f.canRead() ) {
2873 catch ( final Exception e ) {
2879 private static boolean testExternalNodeRelatedMethods() {
2881 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2882 final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2883 PhylogenyNode n = t1.getNode( "A" );
2884 n = n.getNextExternalNode();
2885 if ( !n.getName().equals( "B" ) ) {
2888 n = n.getNextExternalNode();
2889 if ( !n.getName().equals( "C" ) ) {
2892 n = n.getNextExternalNode();
2893 if ( !n.getName().equals( "D" ) ) {
2896 n = t1.getNode( "B" );
2897 while ( !n.isLastExternalNode() ) {
2898 n = n.getNextExternalNode();
2900 final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
2901 n = t2.getNode( "A" );
2902 n = n.getNextExternalNode();
2903 if ( !n.getName().equals( "B" ) ) {
2906 n = n.getNextExternalNode();
2907 if ( !n.getName().equals( "C" ) ) {
2910 n = n.getNextExternalNode();
2911 if ( !n.getName().equals( "D" ) ) {
2914 n = t2.getNode( "B" );
2915 while ( !n.isLastExternalNode() ) {
2916 n = n.getNextExternalNode();
2918 final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2919 n = t3.getNode( "A" );
2920 n = n.getNextExternalNode();
2921 if ( !n.getName().equals( "B" ) ) {
2924 n = n.getNextExternalNode();
2925 if ( !n.getName().equals( "C" ) ) {
2928 n = n.getNextExternalNode();
2929 if ( !n.getName().equals( "D" ) ) {
2932 n = n.getNextExternalNode();
2933 if ( !n.getName().equals( "E" ) ) {
2936 n = n.getNextExternalNode();
2937 if ( !n.getName().equals( "F" ) ) {
2940 n = n.getNextExternalNode();
2941 if ( !n.getName().equals( "G" ) ) {
2944 n = n.getNextExternalNode();
2945 if ( !n.getName().equals( "H" ) ) {
2948 n = t3.getNode( "B" );
2949 while ( !n.isLastExternalNode() ) {
2950 n = n.getNextExternalNode();
2952 final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
2953 for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
2954 final PhylogenyNode node = iter.next();
2956 final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
2957 for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
2958 final PhylogenyNode node = iter.next();
2961 catch ( final Exception e ) {
2962 e.printStackTrace( System.out );
2968 private static boolean testGeneralTable() {
2970 final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
2971 t0.setValue( 3, 2, "23" );
2972 t0.setValue( 10, 1, "error" );
2973 t0.setValue( 10, 1, "110" );
2974 t0.setValue( 9, 1, "19" );
2975 t0.setValue( 1, 10, "101" );
2976 t0.setValue( 10, 10, "1010" );
2977 t0.setValue( 100, 10, "10100" );
2978 t0.setValue( 0, 0, "00" );
2979 if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
2982 if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
2985 if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
2988 if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
2991 if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
2994 if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
2997 if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
3000 if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
3003 if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
3006 final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
3007 t1.setValue( "3", "2", "23" );
3008 t1.setValue( "10", "1", "error" );
3009 t1.setValue( "10", "1", "110" );
3010 t1.setValue( "9", "1", "19" );
3011 t1.setValue( "1", "10", "101" );
3012 t1.setValue( "10", "10", "1010" );
3013 t1.setValue( "100", "10", "10100" );
3014 t1.setValue( "0", "0", "00" );
3015 t1.setValue( "qwerty", "zxcvbnm", "asdef" );
3016 if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
3019 if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
3022 if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
3025 if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
3028 if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
3031 if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
3034 if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
3037 if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
3040 if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
3043 if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
3047 catch ( final Exception e ) {
3048 e.printStackTrace( System.out );
3054 private static boolean testGetDistance() {
3056 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3057 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",
3058 new NHXParser() )[ 0 ];
3059 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3060 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
3063 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
3066 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
3069 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
3072 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
3075 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
3078 if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
3081 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
3084 if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
3087 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
3090 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
3093 if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
3096 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
3099 if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
3102 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
3105 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
3108 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
3111 if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
3114 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
3117 if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
3120 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
3123 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
3126 if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
3129 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
3132 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
3135 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
3138 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
3141 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
3144 if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
3147 if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
3150 if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
3153 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",
3154 new NHXParser() )[ 0 ];
3155 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
3158 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
3161 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
3164 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
3167 if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
3170 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
3173 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
3176 if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
3179 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
3182 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
3185 if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
3189 catch ( final Exception e ) {
3190 e.printStackTrace( System.out );
3196 private static boolean testGetLCA() {
3198 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3199 final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
3200 new NHXParser() )[ 0 ];
3201 final PhylogenyMethods pm = PhylogenyMethods.getInstance();
3202 final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
3203 if ( !A.getName().equals( "A" ) ) {
3206 final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
3207 if ( !gh.getName().equals( "gh" ) ) {
3210 final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
3211 if ( !ab.getName().equals( "ab" ) ) {
3214 final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
3215 if ( !ab2.getName().equals( "ab" ) ) {
3218 final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
3219 if ( !gh2.getName().equals( "gh" ) ) {
3222 final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
3223 if ( !gh3.getName().equals( "gh" ) ) {
3226 final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
3227 if ( !abc.getName().equals( "abc" ) ) {
3230 final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
3231 if ( !abc2.getName().equals( "abc" ) ) {
3234 final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
3235 if ( !abcd.getName().equals( "abcd" ) ) {
3238 final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
3239 if ( !abcd2.getName().equals( "abcd" ) ) {
3242 final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
3243 if ( !abcdef.getName().equals( "abcdef" ) ) {
3246 final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
3247 if ( !abcdef2.getName().equals( "abcdef" ) ) {
3250 final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
3251 if ( !abcdef3.getName().equals( "abcdef" ) ) {
3254 final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
3255 if ( !abcdef4.getName().equals( "abcdef" ) ) {
3258 final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
3259 if ( !abcde.getName().equals( "abcde" ) ) {
3262 final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
3263 if ( !abcde2.getName().equals( "abcde" ) ) {
3266 final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
3267 if ( !r.getName().equals( "abcdefgh" ) ) {
3270 final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
3271 if ( !r2.getName().equals( "abcdefgh" ) ) {
3274 final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
3275 if ( !r3.getName().equals( "abcdefgh" ) ) {
3278 final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
3279 if ( !abcde3.getName().equals( "abcde" ) ) {
3282 final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
3283 if ( !abcde4.getName().equals( "abcde" ) ) {
3286 final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
3287 if ( !ab3.getName().equals( "ab" ) ) {
3290 final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
3291 if ( !ab4.getName().equals( "ab" ) ) {
3294 final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
3295 final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
3296 if ( !cd.getName().equals( "cd" ) ) {
3299 final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
3300 if ( !cd2.getName().equals( "cd" ) ) {
3303 final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
3304 if ( !cde.getName().equals( "cde" ) ) {
3307 final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
3308 if ( !cde2.getName().equals( "cde" ) ) {
3311 final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
3312 if ( !cdef.getName().equals( "cdef" ) ) {
3315 final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
3316 if ( !cdef2.getName().equals( "cdef" ) ) {
3319 final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
3320 if ( !cdef3.getName().equals( "cdef" ) ) {
3323 final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
3324 if ( !rt.getName().equals( "r" ) ) {
3327 final Phylogeny p3 = factory
3328 .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
3329 new NHXParser() )[ 0 ];
3330 final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
3331 if ( !bc_3.getName().equals( "bc" ) ) {
3334 final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
3335 if ( !ac_3.getName().equals( "abc" ) ) {
3338 final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
3339 if ( !ad_3.getName().equals( "abcde" ) ) {
3342 final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
3343 if ( !af_3.getName().equals( "abcdef" ) ) {
3346 final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
3347 if ( !ag_3.getName().equals( "" ) ) {
3350 if ( !ag_3.isRoot() ) {
3353 final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
3354 if ( !al_3.getName().equals( "" ) ) {
3357 if ( !al_3.isRoot() ) {
3360 final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
3361 if ( !kl_3.getName().equals( "" ) ) {
3364 if ( !kl_3.isRoot() ) {
3367 final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
3368 if ( !fl_3.getName().equals( "" ) ) {
3371 if ( !fl_3.isRoot() ) {
3374 final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
3375 if ( !gk_3.getName().equals( "ghijk" ) ) {
3378 final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
3379 final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
3380 if ( !r_4.getName().equals( "r" ) ) {
3383 final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
3384 final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
3385 if ( !r_5.getName().equals( "root" ) ) {
3388 final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
3389 final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
3390 if ( !r_6.getName().equals( "rot" ) ) {
3393 final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
3394 final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
3395 if ( !r_7.getName().equals( "rott" ) ) {
3399 catch ( final Exception e ) {
3400 e.printStackTrace( System.out );
3406 private static boolean testHmmscanOutputParser() {
3407 final String test_dir = Test.PATH_TO_TEST_DATA;
3409 final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
3410 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3412 final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
3413 + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
3414 final List<Protein> proteins = parser2.parse();
3415 if ( parser2.getProteinsEncountered() != 4 ) {
3418 if ( proteins.size() != 4 ) {
3421 if ( parser2.getDomainsEncountered() != 69 ) {
3424 if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
3427 if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
3430 final Protein p1 = proteins.get( 0 );
3431 if ( p1.getNumberOfProteinDomains() != 15 ) {
3434 final Protein p2 = proteins.get( 1 );
3435 if ( p2.getNumberOfProteinDomains() != 51 ) {
3438 final Protein p3 = proteins.get( 2 );
3439 if ( p3.getNumberOfProteinDomains() != 2 ) {
3442 final Protein p4 = proteins.get( 3 );
3443 if ( p4.getNumberOfProteinDomains() != 1 ) {
3446 if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
3449 if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
3452 if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
3455 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
3458 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
3461 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
3464 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
3467 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
3470 if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
3474 catch ( final Exception e ) {
3475 e.printStackTrace( System.out );
3481 private static boolean testLastExternalNodeMethods() {
3483 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3484 final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
3485 final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
3486 final PhylogenyNode n1 = t0.getNode( "A" );
3487 if ( n1.isLastExternalNode() ) {
3490 final PhylogenyNode n2 = t0.getNode( "B" );
3491 if ( n2.isLastExternalNode() ) {
3494 final PhylogenyNode n3 = t0.getNode( "C" );
3495 if ( n3.isLastExternalNode() ) {
3498 final PhylogenyNode n4 = t0.getNode( "D" );
3499 if ( !n4.isLastExternalNode() ) {
3503 catch ( final Exception e ) {
3504 e.printStackTrace( System.out );
3510 private static boolean testLevelOrderIterator() {
3512 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3513 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
3514 PhylogenyNodeIterator it0;
3515 for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
3518 for( it0.reset(); it0.hasNext(); ) {
3521 final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
3522 if ( !it.next().getName().equals( "r" ) ) {
3525 if ( !it.next().getName().equals( "ab" ) ) {
3528 if ( !it.next().getName().equals( "cd" ) ) {
3531 if ( !it.next().getName().equals( "A" ) ) {
3534 if ( !it.next().getName().equals( "B" ) ) {
3537 if ( !it.next().getName().equals( "C" ) ) {
3540 if ( !it.next().getName().equals( "D" ) ) {
3543 if ( it.hasNext() ) {
3546 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",
3547 new NHXParser() )[ 0 ];
3548 PhylogenyNodeIterator it2;
3549 for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
3552 for( it2.reset(); it2.hasNext(); ) {
3555 final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
3556 if ( !it3.next().getName().equals( "r" ) ) {
3559 if ( !it3.next().getName().equals( "abc" ) ) {
3562 if ( !it3.next().getName().equals( "defg" ) ) {
3565 if ( !it3.next().getName().equals( "A" ) ) {
3568 if ( !it3.next().getName().equals( "B" ) ) {
3571 if ( !it3.next().getName().equals( "C" ) ) {
3574 if ( !it3.next().getName().equals( "D" ) ) {
3577 if ( !it3.next().getName().equals( "E" ) ) {
3580 if ( !it3.next().getName().equals( "F" ) ) {
3583 if ( !it3.next().getName().equals( "G" ) ) {
3586 if ( !it3.next().getName().equals( "1" ) ) {
3589 if ( !it3.next().getName().equals( "2" ) ) {
3592 if ( !it3.next().getName().equals( "3" ) ) {
3595 if ( !it3.next().getName().equals( "4" ) ) {
3598 if ( !it3.next().getName().equals( "5" ) ) {
3601 if ( !it3.next().getName().equals( "6" ) ) {
3604 if ( !it3.next().getName().equals( "f1" ) ) {
3607 if ( !it3.next().getName().equals( "f2" ) ) {
3610 if ( !it3.next().getName().equals( "f3" ) ) {
3613 if ( !it3.next().getName().equals( "a" ) ) {
3616 if ( !it3.next().getName().equals( "b" ) ) {
3619 if ( !it3.next().getName().equals( "f21" ) ) {
3622 if ( !it3.next().getName().equals( "X" ) ) {
3625 if ( !it3.next().getName().equals( "Y" ) ) {
3628 if ( !it3.next().getName().equals( "Z" ) ) {
3631 if ( it3.hasNext() ) {
3634 final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
3635 PhylogenyNodeIterator it4;
3636 for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
3639 for( it4.reset(); it4.hasNext(); ) {
3642 final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
3643 if ( !it5.next().getName().equals( "r" ) ) {
3646 if ( !it5.next().getName().equals( "A" ) ) {
3649 if ( !it5.next().getName().equals( "B" ) ) {
3652 if ( !it5.next().getName().equals( "C" ) ) {
3655 if ( !it5.next().getName().equals( "D" ) ) {
3658 final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
3659 PhylogenyNodeIterator it6;
3660 for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
3663 for( it6.reset(); it6.hasNext(); ) {
3666 final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
3667 if ( !it7.next().getName().equals( "A" ) ) {
3670 if ( it.hasNext() ) {
3674 catch ( final Exception e ) {
3675 e.printStackTrace( System.out );
3681 private static boolean testMidpointrooting() {
3683 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3684 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",
3685 new NHXParser() )[ 0 ];
3686 if ( !t1.isRooted() ) {
3689 PhylogenyMethods.midpointRoot( t1 );
3690 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3693 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3696 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3699 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3702 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3705 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3708 t1.reRoot( t1.getNode( "A" ) );
3709 PhylogenyMethods.midpointRoot( t1 );
3710 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
3713 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
3716 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
3719 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
3722 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
3725 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
3729 catch ( final Exception e ) {
3730 e.printStackTrace( System.out );
3736 private static boolean testNexusCharactersParsing() {
3738 final NexusCharactersParser parser = new NexusCharactersParser();
3739 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
3741 String[] labels = parser.getCharStateLabels();
3742 if ( labels.length != 7 ) {
3745 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3748 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3751 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3754 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3757 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3760 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3763 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3766 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3768 labels = parser.getCharStateLabels();
3769 if ( labels.length != 7 ) {
3772 if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3775 if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3778 if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3781 if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3784 if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3787 if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3790 if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3794 catch ( final Exception e ) {
3795 e.printStackTrace( System.out );
3801 private static boolean testNexusMatrixParsing() {
3803 final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
3804 parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
3806 final CharacterStateMatrix<BinaryStates> m = parser.getMatrix();
3807 if ( m.getNumberOfCharacters() != 9 ) {
3810 if ( m.getNumberOfIdentifiers() != 5 ) {
3813 if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
3816 if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
3819 if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
3822 if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
3825 if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
3828 if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
3831 if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
3834 // if ( labels.length != 7 ) {
3837 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3840 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3843 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3846 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3849 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3852 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3855 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3858 // parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
3860 // labels = parser.getCharStateLabels();
3861 // if ( labels.length != 7 ) {
3864 // if ( !labels[ 0 ].equals( "14-3-3" ) ) {
3867 // if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
3870 // if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
3873 // if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
3876 // if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
3879 // if ( !labels[ 5 ].equals( "3-HAO" ) ) {
3882 // if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
3886 catch ( final Exception e ) {
3887 e.printStackTrace( System.out );
3893 private static boolean testNexusTreeParsing() {
3895 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
3896 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
3897 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
3898 if ( phylogenies.length != 1 ) {
3901 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
3904 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3908 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
3909 if ( phylogenies.length != 1 ) {
3912 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3915 if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
3919 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
3920 if ( phylogenies.length != 1 ) {
3923 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
3926 if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
3929 if ( phylogenies[ 0 ].isRooted() ) {
3933 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
3934 if ( phylogenies.length != 18 ) {
3937 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
3940 if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
3943 if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
3946 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
3949 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
3952 if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
3955 if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
3958 if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
3961 if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
3964 if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
3967 if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
3970 if ( phylogenies[ 8 ].isRooted() ) {
3973 if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
3976 if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
3979 if ( !phylogenies[ 9 ].isRooted() ) {
3982 if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
3985 if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
3988 if ( !phylogenies[ 10 ].isRooted() ) {
3991 if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
3994 if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
3997 if ( phylogenies[ 11 ].isRooted() ) {
4000 if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
4003 if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
4006 if ( !phylogenies[ 12 ].isRooted() ) {
4009 if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
4012 if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
4015 if ( !phylogenies[ 13 ].isRooted() ) {
4018 if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
4021 if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
4024 if ( !phylogenies[ 14 ].isRooted() ) {
4027 if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
4030 if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
4033 if ( phylogenies[ 15 ].isRooted() ) {
4036 if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
4039 if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
4042 if ( !phylogenies[ 16 ].isRooted() ) {
4045 if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
4048 if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
4051 if ( phylogenies[ 17 ].isRooted() ) {
4054 if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
4058 catch ( final Exception e ) {
4059 e.printStackTrace( System.out );
4065 private static boolean testNexusTreeParsingTranslating() {
4067 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4068 final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
4069 Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
4070 if ( phylogenies.length != 1 ) {
4073 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4076 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4079 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4082 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4085 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4086 .equals( "Aranaeus" ) ) {
4090 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
4091 if ( phylogenies.length != 3 ) {
4094 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4097 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4100 if ( phylogenies[ 0 ].isRooted() ) {
4103 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4106 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4109 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4110 .equals( "Aranaeus" ) ) {
4113 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4116 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4119 if ( phylogenies[ 1 ].isRooted() ) {
4122 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4125 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4128 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4129 .equals( "Aranaeus" ) ) {
4132 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4135 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4138 if ( !phylogenies[ 2 ].isRooted() ) {
4141 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4144 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4147 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4148 .equals( "Aranaeus" ) ) {
4152 phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
4153 if ( phylogenies.length != 3 ) {
4156 if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
4159 if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
4162 if ( phylogenies[ 0 ].isRooted() ) {
4165 if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4168 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4171 if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4172 .equals( "Aranaeus" ) ) {
4175 if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
4178 if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
4181 if ( phylogenies[ 1 ].isRooted() ) {
4184 if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4187 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4190 if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4191 .equals( "Aranaeus" ) ) {
4194 if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
4197 if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
4200 if ( !phylogenies[ 2 ].isRooted() ) {
4203 if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
4206 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
4209 if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
4210 .equals( "Aranaeus" ) ) {
4214 catch ( final Exception e ) {
4215 e.printStackTrace( System.out );
4221 private static boolean testNHParsing() {
4223 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4224 final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
4225 if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
4228 final NHXParser nhxp = new NHXParser();
4229 nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
4230 nhxp.setReplaceUnderscores( true );
4231 final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
4232 if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
4235 if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
4238 final Phylogeny p1b = factory
4239 .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 ",
4240 new NHXParser() )[ 0 ];
4241 if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
4244 if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
4247 final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
4248 final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
4249 final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
4250 final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
4251 final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
4252 final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
4253 final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
4254 final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
4255 final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
4256 final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
4257 final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
4258 + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
4259 + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
4261 if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
4264 if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
4267 if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
4270 if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
4273 final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
4274 final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
4275 final String p16_S = "((A,B),C)";
4276 final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
4277 if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
4280 final String p17_S = "(C,(A,B))";
4281 final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
4282 if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
4285 final String p18_S = "((A,B),(C,D))";
4286 final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
4287 if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
4290 final String p19_S = "(((A,B),C),D)";
4291 final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
4292 if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
4295 final String p20_S = "(A,(B,(C,D)))";
4296 final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
4297 if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
4300 final String p21_S = "(A,(B,(C,(D,E))))";
4301 final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
4302 if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
4305 final String p22_S = "((((A,B),C),D),E)";
4306 final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
4307 if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
4310 final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4311 final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
4312 if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
4315 final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4316 final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
4317 if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
4320 final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4321 final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4322 final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
4323 if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
4326 if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
4329 final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
4330 + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
4331 + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
4332 + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
4333 + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
4334 + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
4335 + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
4336 + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
4337 final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
4338 if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
4341 final String p26_S = "(A,B)ab";
4342 final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
4343 if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
4346 final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4347 final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
4349 if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
4352 final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
4353 final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
4354 final String p28_S3 = "(A,B)ab";
4355 final String p28_S4 = "((((A,B),C),D),;E;)";
4356 final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
4358 if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
4361 if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
4364 if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
4367 if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
4370 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";
4371 final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
4372 if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
4375 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";
4376 final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
4377 if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
4380 final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
4381 final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
4382 if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
4385 final String p33_S = "A";
4386 final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
4387 if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
4390 final String p34_S = "B;";
4391 final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
4392 if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
4395 final String p35_S = "B:0.2";
4396 final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
4397 if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
4400 final String p36_S = "(A)";
4401 final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
4402 if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
4405 final String p37_S = "((A))";
4406 final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
4407 if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
4410 final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4411 final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
4412 if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
4415 final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
4416 final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
4417 if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
4420 final String p40_S = "(A,B,C)";
4421 final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
4422 if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
4425 final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
4426 final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
4427 if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
4430 final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
4431 final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
4432 if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
4435 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)";
4436 final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
4437 if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
4440 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)))";
4441 final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
4442 if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
4445 final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
4446 final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
4447 if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
4450 final String p46_S = "";
4451 final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
4452 if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
4456 catch ( final Exception e ) {
4457 e.printStackTrace( System.out );
4463 private static boolean testNHXconversion() {
4465 final PhylogenyNode n1 = new PhylogenyNode();
4466 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4467 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4468 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4469 final PhylogenyNode n5 = PhylogenyNode
4470 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
4471 final PhylogenyNode n6 = PhylogenyNode
4472 .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
4473 if ( !n1.toNewHampshireX().equals( "" ) ) {
4476 if ( !n2.toNewHampshireX().equals( "" ) ) {
4479 if ( !n3.toNewHampshireX().equals( "n3" ) ) {
4482 if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
4485 if ( !n5.toNewHampshireX()
4486 .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]" ) ) {
4489 if ( !n6.toNewHampshireX()
4490 .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]" ) ) {
4494 catch ( final Exception e ) {
4495 e.printStackTrace( System.out );
4501 private static boolean testNHXNodeParsing() {
4503 final PhylogenyNode n1 = new PhylogenyNode();
4504 final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
4505 final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
4506 final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
4507 final PhylogenyNode n5 = PhylogenyNode
4508 .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
4509 if ( !n3.getName().equals( "n3" ) ) {
4512 if ( n3.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4515 if ( n3.isDuplication() ) {
4518 if ( n3.isHasAssignedEvent() ) {
4521 if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
4524 if ( !n4.getName().equals( "n4" ) ) {
4527 if ( n4.getDistanceToParent() != 0.01 ) {
4530 if ( !n5.getName().equals( "n5" ) ) {
4533 if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
4536 if ( n5.getDistanceToParent() != 0.1 ) {
4539 if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
4542 if ( !n5.isDuplication() ) {
4545 if ( !n5.isHasAssignedEvent() ) {
4548 if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
4551 if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
4554 final PhylogenyNode n8 = PhylogenyNode
4555 .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
4556 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4557 if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
4560 if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
4563 final PhylogenyNode n9 = PhylogenyNode
4564 .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
4565 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4566 if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
4569 if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
4572 final PhylogenyNode n10 = PhylogenyNode
4573 .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4574 if ( !n10.getName().equals( "n10.ECOLI" ) ) {
4577 final PhylogenyNode n20 = PhylogenyNode
4578 .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4579 if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
4582 if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
4585 final PhylogenyNode n20x = PhylogenyNode
4586 .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4587 if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
4590 if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
4593 final PhylogenyNode n20xx = PhylogenyNode
4594 .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4595 if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
4598 if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
4601 final PhylogenyNode n20xxx = PhylogenyNode
4602 .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4603 if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
4606 if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
4609 final PhylogenyNode n20xxxx = PhylogenyNode
4610 .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4611 if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
4614 if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
4617 final PhylogenyNode n21 = PhylogenyNode
4618 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
4619 if ( !n21.getName().equals( "n21_PIG" ) ) {
4622 if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
4625 final PhylogenyNode n21x = PhylogenyNode
4626 .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4627 if ( !n21x.getName().equals( "n21_PIG" ) ) {
4630 if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
4633 final PhylogenyNode n22 = PhylogenyNode
4634 .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4635 if ( !n22.getName().equals( "n22/PIG" ) ) {
4638 if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
4641 final PhylogenyNode n23 = PhylogenyNode
4642 .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4643 if ( !n23.getName().equals( "n23/PIG_1" ) ) {
4646 if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
4649 if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
4650 final PhylogenyNode a = PhylogenyNode
4651 .createInstanceFromNhxString( "n10_ECOLI/1-2",
4652 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4653 if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
4656 if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
4659 final PhylogenyNode b = PhylogenyNode
4660 .createInstanceFromNhxString( "n10_ECOLI1/1-2",
4661 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4662 if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
4665 if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
4668 final PhylogenyNode c = PhylogenyNode
4669 .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
4670 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4671 if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
4674 if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
4677 final PhylogenyNode d = PhylogenyNode
4678 .createInstanceFromNhxString( "n10_RAT1/1-2",
4679 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4680 if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
4683 if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
4686 final PhylogenyNode e = PhylogenyNode
4687 .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4688 if ( !e.getName().equals( "n10_RAT1" ) ) {
4691 if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
4695 final PhylogenyNode n11 = PhylogenyNode
4696 .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
4697 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4698 if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
4701 if ( n11.getDistanceToParent() != 0.4 ) {
4704 if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
4707 final PhylogenyNode n12 = PhylogenyNode
4708 .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
4709 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4710 if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
4713 if ( n12.getDistanceToParent() != 0.4 ) {
4716 if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
4719 final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
4720 final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
4721 if ( !tvu1.getRef().equals( "tag1" ) ) {
4724 if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
4727 if ( !tvu1.getUnit().equals( "unit1" ) ) {
4730 if ( !tvu1.getValue().equals( "value1" ) ) {
4733 if ( !tvu3.getRef().equals( "tag3" ) ) {
4736 if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
4739 if ( !tvu3.getUnit().equals( "unit3" ) ) {
4742 if ( !tvu3.getValue().equals( "value3" ) ) {
4745 if ( n1.getName().compareTo( "" ) != 0 ) {
4748 if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4751 if ( n1.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4754 if ( n2.getName().compareTo( "" ) != 0 ) {
4757 if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4760 if ( n2.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
4763 final PhylogenyNode n00 = PhylogenyNode
4764 .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
4765 if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
4768 if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
4771 if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
4774 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
4777 if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
4780 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
4783 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
4786 if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
4789 final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
4790 if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
4793 final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
4794 if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
4797 final PhylogenyNode n13 = PhylogenyNode
4798 .createInstanceFromNhxString( "blah_12345/1-2",
4799 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4800 if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
4803 if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
4806 final PhylogenyNode n14 = PhylogenyNode
4807 .createInstanceFromNhxString( "blah_12X45/1-2",
4808 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4809 if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
4812 if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
4815 final PhylogenyNode n15 = PhylogenyNode
4816 .createInstanceFromNhxString( "something_wicked[123]",
4817 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4818 if ( !n15.getName().equals( "something_wicked" ) ) {
4821 if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
4824 if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
4827 final PhylogenyNode n16 = PhylogenyNode
4828 .createInstanceFromNhxString( "something_wicked2[9]",
4829 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4830 if ( !n16.getName().equals( "something_wicked2" ) ) {
4833 if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
4836 if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
4839 final PhylogenyNode n17 = PhylogenyNode
4840 .createInstanceFromNhxString( "something_wicked3[a]",
4841 PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4842 if ( !n17.getName().equals( "something_wicked3" ) ) {
4845 if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
4848 final PhylogenyNode n18 = PhylogenyNode
4849 .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
4850 if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
4853 if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
4856 if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
4860 catch ( final Exception e ) {
4861 e.printStackTrace( System.out );
4867 private static boolean testNHXParsing() {
4869 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4870 final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
4871 if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
4874 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]";
4875 final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
4876 if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4879 final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
4880 final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
4881 if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
4884 final Phylogeny[] p3 = factory
4885 .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]",
4887 if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4890 final Phylogeny[] p4 = factory
4891 .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(]",
4893 if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4896 final Phylogeny[] p5 = factory
4897 .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(((]",
4899 if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
4902 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)";
4903 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)";
4904 final Phylogeny[] p6 = factory.create( p6_S_C, new NHXParser() );
4905 if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
4908 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)))";
4909 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)))";
4910 final Phylogeny[] p7 = factory.create( p7_S_C, new NHXParser() );
4911 if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
4914 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]) ))[,,, ])))))))";
4915 final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
4916 final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
4917 if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
4920 final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
4921 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]" ) ) {
4924 final Phylogeny p10 = factory
4925 .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]",
4926 new NHXParser() )[ 0 ];
4927 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]" ) ) {
4931 catch ( final Exception e ) {
4932 e.printStackTrace( System.out );
4938 private static boolean testNHXParsingQuotes() {
4940 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
4941 final NHXParser p = new NHXParser();
4942 final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
4943 if ( phylogenies_0.length != 5 ) {
4946 final Phylogeny phy = phylogenies_0[ 4 ];
4947 if ( phy.getNumberOfExternalNodes() != 7 ) {
4950 if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
4953 if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
4956 if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
4957 .getScientificName().equals( "hsapiens" ) ) {
4960 if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
4963 if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
4966 if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
4969 if ( phy.getNodes( "noquotes" ).size() != 1 ) {
4972 if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
4975 final NHXParser p1p = new NHXParser();
4976 p1p.setIgnoreQuotes( true );
4977 final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
4978 if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
4981 final NHXParser p2p = new NHXParser();
4982 p1p.setIgnoreQuotes( false );
4983 final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
4984 if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
4987 final NHXParser p3p = new NHXParser();
4988 p3p.setIgnoreQuotes( false );
4989 final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
4990 if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
4993 final NHXParser p4p = new NHXParser();
4994 p4p.setIgnoreQuotes( false );
4995 final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
4996 if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
4999 final Phylogeny p10 = factory
5000 .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]",
5001 new NHXParser() )[ 0 ];
5002 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]";
5003 if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
5006 final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
5007 if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
5011 final Phylogeny p12 = factory
5012 .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]",
5013 new NHXParser() )[ 0 ];
5014 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]";
5015 if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
5018 final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
5019 if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
5022 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;";
5023 if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
5026 final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
5027 if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
5031 catch ( final Exception e ) {
5032 e.printStackTrace( System.out );
5038 private static boolean testNHXParsingMB() {
5040 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5041 final Phylogeny p1 = factory.create( "(1[&prob=1.000000000000000e+00,prob_stddev=0.000000000000000e+00,"
5042 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5043 + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
5044 + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
5045 + "5.026800000000000e-02}],2[&prob=1.000000000000000e+00,prob_stddev=0.000000000000000e+00,"
5046 + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
5047 + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
5048 + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
5049 + "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
5050 if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
5051 System.out.println( p1.getNode( "1" ).getDistanceToParent() );
5055 // if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
5059 catch ( final Exception e ) {
5060 e.printStackTrace( System.out );
5067 private static boolean testPhylogenyBranch() {
5069 final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
5070 final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
5071 final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
5072 final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
5073 if ( !a1b1.equals( a1b1 ) ) {
5076 if ( !a1b1.equals( b1a1 ) ) {
5079 if ( !b1a1.equals( a1b1 ) ) {
5082 final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
5083 final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
5084 final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
5085 if ( a1_b1.equals( b1_a1 ) ) {
5088 if ( a1_b1.equals( a1_b1_ ) ) {
5091 final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
5092 if ( !a1_b1.equals( b1_a1_ ) ) {
5095 if ( a1_b1_.equals( b1_a1_ ) ) {
5098 if ( !a1_b1_.equals( b1_a1 ) ) {
5102 catch ( final Exception e ) {
5103 e.printStackTrace( System.out );
5109 private static boolean testPhyloXMLparsingOfDistributionElement() {
5111 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5112 PhyloXmlParser xml_parser = null;
5114 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
5116 catch ( final Exception e ) {
5117 // Do nothing -- means were not running from jar.
5119 if ( xml_parser == null ) {
5120 xml_parser = new PhyloXmlParser();
5121 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
5122 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
5125 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
5128 final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
5130 if ( xml_parser.getErrorCount() > 0 ) {
5131 System.out.println( xml_parser.getErrorMessages().toString() );
5134 if ( phylogenies_0.length != 1 ) {
5137 final Phylogeny t1 = phylogenies_0[ 0 ];
5138 PhylogenyNode n = null;
5139 Distribution d = null;
5140 n = t1.getNode( "root node" );
5141 if ( !n.getNodeData().isHasDistribution() ) {
5144 if ( n.getNodeData().getDistributions().size() != 1 ) {
5147 d = n.getNodeData().getDistribution();
5148 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5151 if ( d.getPoints().size() != 1 ) {
5154 if ( d.getPolygons() != null ) {
5157 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5160 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5163 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5166 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5169 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5172 n = t1.getNode( "node a" );
5173 if ( !n.getNodeData().isHasDistribution() ) {
5176 if ( n.getNodeData().getDistributions().size() != 2 ) {
5179 d = n.getNodeData().getDistribution( 1 );
5180 if ( !d.getDesc().equals( "San Diego" ) ) {
5183 if ( d.getPoints().size() != 1 ) {
5186 if ( d.getPolygons() != null ) {
5189 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5192 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5195 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5198 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5201 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5204 n = t1.getNode( "node bb" );
5205 if ( !n.getNodeData().isHasDistribution() ) {
5208 if ( n.getNodeData().getDistributions().size() != 1 ) {
5211 d = n.getNodeData().getDistribution( 0 );
5212 if ( d.getPoints().size() != 3 ) {
5215 if ( d.getPolygons().size() != 2 ) {
5218 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5221 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5224 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5227 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5230 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5233 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5236 Polygon p = d.getPolygons().get( 0 );
5237 if ( p.getPoints().size() != 3 ) {
5240 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5243 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5246 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5249 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5252 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5255 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5258 p = d.getPolygons().get( 1 );
5259 if ( p.getPoints().size() != 3 ) {
5262 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5265 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5268 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5272 final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
5273 final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
5274 if ( rt.length != 1 ) {
5277 final Phylogeny t1_rt = rt[ 0 ];
5278 n = t1_rt.getNode( "root node" );
5279 if ( !n.getNodeData().isHasDistribution() ) {
5282 if ( n.getNodeData().getDistributions().size() != 1 ) {
5285 d = n.getNodeData().getDistribution();
5286 if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
5289 if ( d.getPoints().size() != 1 ) {
5292 if ( d.getPolygons() != null ) {
5295 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
5298 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5301 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5304 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
5307 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
5310 n = t1_rt.getNode( "node a" );
5311 if ( !n.getNodeData().isHasDistribution() ) {
5314 if ( n.getNodeData().getDistributions().size() != 2 ) {
5317 d = n.getNodeData().getDistribution( 1 );
5318 if ( !d.getDesc().equals( "San Diego" ) ) {
5321 if ( d.getPoints().size() != 1 ) {
5324 if ( d.getPolygons() != null ) {
5327 if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
5330 if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
5333 if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
5336 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
5339 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
5342 n = t1_rt.getNode( "node bb" );
5343 if ( !n.getNodeData().isHasDistribution() ) {
5346 if ( n.getNodeData().getDistributions().size() != 1 ) {
5349 d = n.getNodeData().getDistribution( 0 );
5350 if ( d.getPoints().size() != 3 ) {
5353 if ( d.getPolygons().size() != 2 ) {
5356 if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
5359 if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
5362 if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
5365 if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
5368 if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
5371 if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
5374 p = d.getPolygons().get( 0 );
5375 if ( p.getPoints().size() != 3 ) {
5378 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
5381 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
5384 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5387 if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
5390 if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
5393 if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
5396 p = d.getPolygons().get( 1 );
5397 if ( p.getPoints().size() != 3 ) {
5400 if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
5403 if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
5406 if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
5410 catch ( final Exception e ) {
5411 e.printStackTrace( System.out );
5417 private static boolean testPostOrderIterator() {
5419 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5420 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5421 PhylogenyNodeIterator it0;
5422 for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
5425 for( it0.reset(); it0.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 final PhylogenyNodeIterator it = t1.iteratorPostorder();
5430 if ( !it.next().getName().equals( "A" ) ) {
5433 if ( !it.next().getName().equals( "B" ) ) {
5436 if ( !it.next().getName().equals( "ab" ) ) {
5439 if ( !it.next().getName().equals( "C" ) ) {
5442 if ( !it.next().getName().equals( "D" ) ) {
5445 if ( !it.next().getName().equals( "cd" ) ) {
5448 if ( !it.next().getName().equals( "abcd" ) ) {
5451 if ( !it.next().getName().equals( "E" ) ) {
5454 if ( !it.next().getName().equals( "F" ) ) {
5457 if ( !it.next().getName().equals( "ef" ) ) {
5460 if ( !it.next().getName().equals( "G" ) ) {
5463 if ( !it.next().getName().equals( "H" ) ) {
5466 if ( !it.next().getName().equals( "gh" ) ) {
5469 if ( !it.next().getName().equals( "efgh" ) ) {
5472 if ( !it.next().getName().equals( "r" ) ) {
5475 if ( it.hasNext() ) {
5479 catch ( final Exception e ) {
5480 e.printStackTrace( System.out );
5486 private static boolean testPreOrderIterator() {
5488 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5489 final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
5490 PhylogenyNodeIterator it0;
5491 for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
5494 for( it0.reset(); it0.hasNext(); ) {
5497 PhylogenyNodeIterator it = t0.iteratorPreorder();
5498 if ( !it.next().getName().equals( "r" ) ) {
5501 if ( !it.next().getName().equals( "ab" ) ) {
5504 if ( !it.next().getName().equals( "A" ) ) {
5507 if ( !it.next().getName().equals( "B" ) ) {
5510 if ( !it.next().getName().equals( "cd" ) ) {
5513 if ( !it.next().getName().equals( "C" ) ) {
5516 if ( !it.next().getName().equals( "D" ) ) {
5519 if ( it.hasNext() ) {
5522 final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
5523 it = t1.iteratorPreorder();
5524 if ( !it.next().getName().equals( "r" ) ) {
5527 if ( !it.next().getName().equals( "abcd" ) ) {
5530 if ( !it.next().getName().equals( "ab" ) ) {
5533 if ( !it.next().getName().equals( "A" ) ) {
5536 if ( !it.next().getName().equals( "B" ) ) {
5539 if ( !it.next().getName().equals( "cd" ) ) {
5542 if ( !it.next().getName().equals( "C" ) ) {
5545 if ( !it.next().getName().equals( "D" ) ) {
5548 if ( !it.next().getName().equals( "efgh" ) ) {
5551 if ( !it.next().getName().equals( "ef" ) ) {
5554 if ( !it.next().getName().equals( "E" ) ) {
5557 if ( !it.next().getName().equals( "F" ) ) {
5560 if ( !it.next().getName().equals( "gh" ) ) {
5563 if ( !it.next().getName().equals( "G" ) ) {
5566 if ( !it.next().getName().equals( "H" ) ) {
5569 if ( it.hasNext() ) {
5573 catch ( final Exception e ) {
5574 e.printStackTrace( System.out );
5580 private static boolean testPropertiesMap() {
5582 final PropertiesMap pm = new PropertiesMap();
5583 final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5584 final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
5585 final Property p2 = new Property( "something:else",
5587 "improbable:research",
5590 pm.addProperty( p0 );
5591 pm.addProperty( p1 );
5592 pm.addProperty( p2 );
5593 if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
5596 if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
5599 if ( pm.getProperties().size() != 3 ) {
5602 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
5605 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5608 if ( pm.getProperties().size() != 3 ) {
5611 pm.removeProperty( "dimensions:diameter" );
5612 if ( pm.getProperties().size() != 2 ) {
5615 if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
5618 if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
5622 catch ( final Exception e ) {
5623 e.printStackTrace( System.out );
5629 private static boolean testReIdMethods() {
5631 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5632 final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
5633 final int count = PhylogenyNode.getNodeCount();
5635 if ( p.getNode( "r" ).getId() != count ) {
5638 if ( p.getNode( "A" ).getId() != count + 1 ) {
5641 if ( p.getNode( "B" ).getId() != count + 1 ) {
5644 if ( p.getNode( "C" ).getId() != count + 1 ) {
5647 if ( p.getNode( "1" ).getId() != count + 2 ) {
5650 if ( p.getNode( "2" ).getId() != count + 2 ) {
5653 if ( p.getNode( "3" ).getId() != count + 2 ) {
5656 if ( p.getNode( "4" ).getId() != count + 2 ) {
5659 if ( p.getNode( "5" ).getId() != count + 2 ) {
5662 if ( p.getNode( "6" ).getId() != count + 2 ) {
5665 if ( p.getNode( "a" ).getId() != count + 3 ) {
5668 if ( p.getNode( "b" ).getId() != count + 3 ) {
5671 if ( p.getNode( "X" ).getId() != count + 4 ) {
5674 if ( p.getNode( "Y" ).getId() != count + 4 ) {
5677 if ( p.getNode( "Z" ).getId() != count + 4 ) {
5681 catch ( final Exception e ) {
5682 e.printStackTrace( System.out );
5688 private static boolean testRerooting() {
5690 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5691 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",
5692 new NHXParser() )[ 0 ];
5693 if ( !t1.isRooted() ) {
5696 t1.reRoot( t1.getNode( "D" ) );
5697 t1.reRoot( t1.getNode( "CD" ) );
5698 t1.reRoot( t1.getNode( "A" ) );
5699 t1.reRoot( t1.getNode( "B" ) );
5700 t1.reRoot( t1.getNode( "AB" ) );
5701 t1.reRoot( t1.getNode( "D" ) );
5702 t1.reRoot( t1.getNode( "C" ) );
5703 t1.reRoot( t1.getNode( "CD" ) );
5704 t1.reRoot( t1.getNode( "A" ) );
5705 t1.reRoot( t1.getNode( "B" ) );
5706 t1.reRoot( t1.getNode( "AB" ) );
5707 t1.reRoot( t1.getNode( "D" ) );
5708 t1.reRoot( t1.getNode( "D" ) );
5709 t1.reRoot( t1.getNode( "C" ) );
5710 t1.reRoot( t1.getNode( "A" ) );
5711 t1.reRoot( t1.getNode( "B" ) );
5712 t1.reRoot( t1.getNode( "AB" ) );
5713 t1.reRoot( t1.getNode( "C" ) );
5714 t1.reRoot( t1.getNode( "D" ) );
5715 t1.reRoot( t1.getNode( "CD" ) );
5716 t1.reRoot( t1.getNode( "D" ) );
5717 t1.reRoot( t1.getNode( "A" ) );
5718 t1.reRoot( t1.getNode( "B" ) );
5719 t1.reRoot( t1.getNode( "AB" ) );
5720 t1.reRoot( t1.getNode( "C" ) );
5721 t1.reRoot( t1.getNode( "D" ) );
5722 t1.reRoot( t1.getNode( "CD" ) );
5723 t1.reRoot( t1.getNode( "D" ) );
5724 if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
5727 if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
5730 if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
5733 if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
5736 if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
5739 if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
5742 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",
5743 new NHXParser() )[ 0 ];
5744 t2.reRoot( t2.getNode( "A" ) );
5745 t2.reRoot( t2.getNode( "D" ) );
5746 t2.reRoot( t2.getNode( "ABC" ) );
5747 t2.reRoot( t2.getNode( "A" ) );
5748 t2.reRoot( t2.getNode( "B" ) );
5749 t2.reRoot( t2.getNode( "D" ) );
5750 t2.reRoot( t2.getNode( "C" ) );
5751 t2.reRoot( t2.getNode( "ABC" ) );
5752 t2.reRoot( t2.getNode( "A" ) );
5753 t2.reRoot( t2.getNode( "B" ) );
5754 t2.reRoot( t2.getNode( "AB" ) );
5755 t2.reRoot( t2.getNode( "AB" ) );
5756 t2.reRoot( t2.getNode( "D" ) );
5757 t2.reRoot( t2.getNode( "C" ) );
5758 t2.reRoot( t2.getNode( "B" ) );
5759 t2.reRoot( t2.getNode( "AB" ) );
5760 t2.reRoot( t2.getNode( "D" ) );
5761 t2.reRoot( t2.getNode( "D" ) );
5762 t2.reRoot( t2.getNode( "ABC" ) );
5763 t2.reRoot( t2.getNode( "A" ) );
5764 t2.reRoot( t2.getNode( "B" ) );
5765 t2.reRoot( t2.getNode( "AB" ) );
5766 t2.reRoot( t2.getNode( "D" ) );
5767 t2.reRoot( t2.getNode( "C" ) );
5768 t2.reRoot( t2.getNode( "ABC" ) );
5769 t2.reRoot( t2.getNode( "A" ) );
5770 t2.reRoot( t2.getNode( "B" ) );
5771 t2.reRoot( t2.getNode( "AB" ) );
5772 t2.reRoot( t2.getNode( "D" ) );
5773 t2.reRoot( t2.getNode( "D" ) );
5774 t2.reRoot( t2.getNode( "C" ) );
5775 t2.reRoot( t2.getNode( "A" ) );
5776 t2.reRoot( t2.getNode( "B" ) );
5777 t2.reRoot( t2.getNode( "AB" ) );
5778 t2.reRoot( t2.getNode( "C" ) );
5779 t2.reRoot( t2.getNode( "D" ) );
5780 t2.reRoot( t2.getNode( "ABC" ) );
5781 t2.reRoot( t2.getNode( "D" ) );
5782 t2.reRoot( t2.getNode( "A" ) );
5783 t2.reRoot( t2.getNode( "B" ) );
5784 t2.reRoot( t2.getNode( "AB" ) );
5785 t2.reRoot( t2.getNode( "C" ) );
5786 t2.reRoot( t2.getNode( "D" ) );
5787 t2.reRoot( t2.getNode( "ABC" ) );
5788 t2.reRoot( t2.getNode( "D" ) );
5789 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5792 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5795 t2.reRoot( t2.getNode( "ABC" ) );
5796 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5799 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5802 t2.reRoot( t2.getNode( "AB" ) );
5803 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5806 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5809 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5812 t2.reRoot( t2.getNode( "AB" ) );
5813 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5816 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5819 if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5822 t2.reRoot( t2.getNode( "D" ) );
5823 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5826 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5829 t2.reRoot( t2.getNode( "ABC" ) );
5830 if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
5833 if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
5836 final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
5837 new NHXParser() )[ 0 ];
5838 t3.reRoot( t3.getNode( "B" ) );
5839 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5842 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5845 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5848 t3.reRoot( t3.getNode( "B" ) );
5849 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5852 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5855 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5858 t3.reRoot( t3.getRoot() );
5859 if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5862 if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
5865 if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
5869 catch ( final Exception e ) {
5870 e.printStackTrace( System.out );
5876 private static boolean testSDIse() {
5878 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
5879 final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
5880 final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
5881 gene1.setRooted( true );
5882 species1.setRooted( true );
5883 final SDI sdi = new SDIse( gene1, species1 );
5884 if ( !gene1.getRoot().isDuplication() ) {
5887 final Phylogeny species2 = factory
5888 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5889 new NHXParser() )[ 0 ];
5890 final Phylogeny gene2 = factory
5891 .create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5892 new NHXParser() )[ 0 ];
5893 species2.setRooted( true );
5894 gene2.setRooted( true );
5895 final SDI sdi2 = new SDIse( gene2, species2 );
5896 if ( sdi2.getDuplicationsSum() != 0 ) {
5899 if ( !gene2.getNode( "ab" ).isSpeciation() ) {
5902 if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
5905 if ( !gene2.getNode( "abc" ).isSpeciation() ) {
5908 if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
5911 if ( !gene2.getNode( "r" ).isSpeciation() ) {
5914 if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
5917 final Phylogeny species3 = factory
5918 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5919 new NHXParser() )[ 0 ];
5920 final Phylogeny gene3 = factory
5921 .create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5922 new NHXParser() )[ 0 ];
5923 species3.setRooted( true );
5924 gene3.setRooted( true );
5925 final SDI sdi3 = new SDIse( gene3, species3 );
5926 if ( sdi3.getDuplicationsSum() != 1 ) {
5929 if ( !gene3.getNode( "aa" ).isDuplication() ) {
5932 if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
5935 final Phylogeny species4 = factory
5936 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5937 new NHXParser() )[ 0 ];
5938 final Phylogeny gene4 = factory
5939 .create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5940 new NHXParser() )[ 0 ];
5941 species4.setRooted( true );
5942 gene4.setRooted( true );
5943 final SDI sdi4 = new SDIse( gene4, species4 );
5944 if ( sdi4.getDuplicationsSum() != 1 ) {
5947 if ( !gene4.getNode( "ac" ).isSpeciation() ) {
5950 if ( !gene4.getNode( "abc" ).isDuplication() ) {
5953 if ( gene4.getNode( "abcd" ).isDuplication() ) {
5956 if ( species4.getNumberOfExternalNodes() != 6 ) {
5959 if ( gene4.getNumberOfExternalNodes() != 6 ) {
5962 final Phylogeny species5 = factory
5963 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
5964 new NHXParser() )[ 0 ];
5965 final Phylogeny gene5 = factory
5966 .create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
5967 new NHXParser() )[ 0 ];
5968 species5.setRooted( true );
5969 gene5.setRooted( true );
5970 final SDI sdi5 = new SDIse( gene5, species5 );
5971 if ( sdi5.getDuplicationsSum() != 2 ) {
5974 if ( !gene5.getNode( "ad" ).isSpeciation() ) {
5977 if ( !gene5.getNode( "adc" ).isDuplication() ) {
5980 if ( !gene5.getNode( "abcd" ).isDuplication() ) {
5983 if ( species5.getNumberOfExternalNodes() != 6 ) {
5986 if ( gene5.getNumberOfExternalNodes() != 6 ) {
5989 // Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
5990 // Conjecture for Comparing Molecular Phylogenies"
5991 // J. of Comput Bio. Vol. 4, No 2, pp.177-187
5992 final Phylogeny species6 = factory
5993 .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,"
5994 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
5995 new NHXParser() )[ 0 ];
5996 final Phylogeny gene6 = factory
5997 .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,"
5998 + "((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,"
5999 + "(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;",
6000 new NHXParser() )[ 0 ];
6001 species6.setRooted( true );
6002 gene6.setRooted( true );
6003 final SDI sdi6 = new SDIse( gene6, species6 );
6004 if ( sdi6.getDuplicationsSum() != 3 ) {
6007 if ( !gene6.getNode( "r" ).isDuplication() ) {
6010 if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
6013 if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
6016 if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
6019 if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
6022 if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
6025 if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
6028 if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
6031 sdi6.computeMappingCostL();
6032 if ( sdi6.computeMappingCostL() != 17 ) {
6035 if ( species6.getNumberOfExternalNodes() != 9 ) {
6038 if ( gene6.getNumberOfExternalNodes() != 9 ) {
6041 final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
6042 + "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
6043 + "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
6044 + "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
6045 + "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
6046 species7.setRooted( true );
6047 final Phylogeny gene7_1 = Test
6048 .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])" );
6049 gene7_1.setRooted( true );
6050 final SDI sdi7 = new SDIse( gene7_1, species7 );
6051 if ( sdi7.getDuplicationsSum() != 0 ) {
6054 if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
6057 if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
6060 if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
6063 if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
6066 if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
6069 if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
6072 if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
6075 if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
6078 final Phylogeny gene7_2 = Test
6079 .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])" );
6080 gene7_2.setRooted( true );
6081 final SDI sdi7_2 = new SDIse( gene7_2, species7 );
6082 if ( sdi7_2.getDuplicationsSum() != 1 ) {
6085 if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
6088 if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
6091 if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
6094 if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
6097 if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
6100 if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
6103 if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
6106 if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
6109 if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
6113 catch ( final Exception e ) {
6119 private static boolean testSDIunrooted() {
6121 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6122 final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
6123 final List<PhylogenyBranch> l = SDIR.getBranchesInPreorder( p0 );
6124 final Iterator<PhylogenyBranch> iter = l.iterator();
6125 PhylogenyBranch br = iter.next();
6126 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
6129 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
6133 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6136 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6140 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
6143 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
6147 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6150 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6154 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6157 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6161 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
6164 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
6168 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6171 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6175 if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6178 if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6182 if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6185 if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6189 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
6192 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
6196 if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6199 if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6203 if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
6206 if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
6210 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
6213 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
6217 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
6220 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
6224 if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
6227 if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
6230 if ( iter.hasNext() ) {
6233 final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
6234 final List<PhylogenyBranch> l1 = SDIR.getBranchesInPreorder( p1 );
6235 final Iterator<PhylogenyBranch> iter1 = l1.iterator();
6237 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6240 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6244 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6247 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6251 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6254 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6257 if ( iter1.hasNext() ) {
6260 final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
6261 final List<PhylogenyBranch> l2 = SDIR.getBranchesInPreorder( p2 );
6262 final Iterator<PhylogenyBranch> iter2 = l2.iterator();
6264 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
6267 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
6271 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
6274 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
6278 if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
6281 if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
6284 if ( iter2.hasNext() ) {
6287 final Phylogeny species0 = factory
6288 .create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
6289 new NHXParser() )[ 0 ];
6290 final Phylogeny gene1 = factory
6291 .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])",
6292 new NHXParser() )[ 0 ];
6293 species0.setRooted( true );
6294 gene1.setRooted( true );
6295 final SDIR sdi_unrooted = new SDIR();
6296 sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
6297 if ( sdi_unrooted.getCount() != 1 ) {
6300 if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
6303 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
6306 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
6309 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6312 final Phylogeny gene2 = factory
6313 .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])",
6314 new NHXParser() )[ 0 ];
6315 gene2.setRooted( true );
6316 sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
6317 if ( sdi_unrooted.getCount() != 1 ) {
6320 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6323 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6326 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
6329 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6332 final Phylogeny species6 = factory
6333 .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,"
6334 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6335 new NHXParser() )[ 0 ];
6336 final Phylogeny gene6 = factory
6337 .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],"
6338 + "(((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],"
6339 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6340 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6341 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6342 new NHXParser() )[ 0 ];
6343 species6.setRooted( true );
6344 gene6.setRooted( true );
6345 Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
6346 if ( sdi_unrooted.getCount() != 1 ) {
6349 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6352 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6355 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6358 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6361 if ( !p6[ 0 ].getRoot().isDuplication() ) {
6364 if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6367 if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6370 if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
6373 if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6376 if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
6379 if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
6382 if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6386 final Phylogeny species7 = factory
6387 .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,"
6388 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6389 new NHXParser() )[ 0 ];
6390 final Phylogeny gene7 = factory
6391 .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],"
6392 + "(((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],"
6393 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6394 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6395 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6396 new NHXParser() )[ 0 ];
6397 species7.setRooted( true );
6398 gene7.setRooted( true );
6399 Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
6400 if ( sdi_unrooted.getCount() != 1 ) {
6403 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6406 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6409 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6412 if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
6415 if ( !p7[ 0 ].getRoot().isDuplication() ) {
6418 if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6421 if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6424 if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
6427 if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6430 if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
6433 if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
6436 if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6440 final Phylogeny species8 = factory
6441 .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,"
6442 + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
6443 new NHXParser() )[ 0 ];
6444 final Phylogeny gene8 = factory
6445 .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],"
6446 + "(((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],"
6447 + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
6448 + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
6449 + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
6450 new NHXParser() )[ 0 ];
6451 species8.setRooted( true );
6452 gene8.setRooted( true );
6453 Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
6454 if ( sdi_unrooted.getCount() != 1 ) {
6457 if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
6460 if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
6463 if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
6466 if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
6469 if ( !p8[ 0 ].getRoot().isDuplication() ) {
6472 if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
6475 if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
6478 if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
6481 if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
6484 if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
6487 if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
6490 if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
6495 catch ( final Exception e ) {
6496 e.printStackTrace( System.out );
6502 private static boolean testSplit() {
6504 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6505 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6506 //Archaeopteryx.createApplication( p0 );
6507 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6508 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6509 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6510 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6511 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6512 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6513 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6514 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6515 ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6516 ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6517 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
6518 // System.out.println( s0.toString() );
6520 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6521 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6522 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6523 if ( s0.match( query_nodes ) ) {
6526 query_nodes = new HashSet<PhylogenyNode>();
6527 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6528 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6529 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6530 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6531 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6532 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6533 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6534 if ( !s0.match( query_nodes ) ) {
6538 query_nodes = new HashSet<PhylogenyNode>();
6539 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6540 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6541 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6542 if ( !s0.match( query_nodes ) ) {
6546 query_nodes = new HashSet<PhylogenyNode>();
6547 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6548 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6549 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6550 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6551 if ( !s0.match( query_nodes ) ) {
6555 query_nodes = new HashSet<PhylogenyNode>();
6556 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6557 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6558 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6559 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6560 if ( !s0.match( query_nodes ) ) {
6564 query_nodes = new HashSet<PhylogenyNode>();
6565 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6566 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6567 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6568 if ( !s0.match( query_nodes ) ) {
6572 query_nodes = new HashSet<PhylogenyNode>();
6573 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6574 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6575 if ( !s0.match( query_nodes ) ) {
6579 query_nodes = new HashSet<PhylogenyNode>();
6580 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6581 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6582 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6583 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6584 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6585 if ( !s0.match( query_nodes ) ) {
6589 query_nodes = new HashSet<PhylogenyNode>();
6590 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6591 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6592 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6593 if ( !s0.match( query_nodes ) ) {
6597 query_nodes = new HashSet<PhylogenyNode>();
6598 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6599 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6600 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6601 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6602 if ( !s0.match( query_nodes ) ) {
6606 query_nodes = new HashSet<PhylogenyNode>();
6607 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6608 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6609 if ( s0.match( query_nodes ) ) {
6613 query_nodes = new HashSet<PhylogenyNode>();
6614 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6615 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6616 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6617 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6618 if ( s0.match( query_nodes ) ) {
6622 query_nodes = new HashSet<PhylogenyNode>();
6623 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6624 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6625 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6626 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6627 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6628 if ( s0.match( query_nodes ) ) {
6632 query_nodes = new HashSet<PhylogenyNode>();
6633 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6634 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6635 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6636 if ( s0.match( query_nodes ) ) {
6640 query_nodes = new HashSet<PhylogenyNode>();
6641 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6642 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6643 if ( s0.match( query_nodes ) ) {
6647 query_nodes = new HashSet<PhylogenyNode>();
6648 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6649 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6650 if ( s0.match( query_nodes ) ) {
6654 query_nodes = new HashSet<PhylogenyNode>();
6655 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6656 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6657 if ( s0.match( query_nodes ) ) {
6661 query_nodes = new HashSet<PhylogenyNode>();
6662 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6663 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6664 if ( s0.match( query_nodes ) ) {
6668 query_nodes = new HashSet<PhylogenyNode>();
6669 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6670 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6671 if ( s0.match( query_nodes ) ) {
6675 query_nodes = new HashSet<PhylogenyNode>();
6676 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6677 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6678 if ( s0.match( query_nodes ) ) {
6682 query_nodes = new HashSet<PhylogenyNode>();
6683 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6684 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6685 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6686 if ( s0.match( query_nodes ) ) {
6690 query_nodes = new HashSet<PhylogenyNode>();
6691 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6692 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6693 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6694 if ( s0.match( query_nodes ) ) {
6698 query_nodes = new HashSet<PhylogenyNode>();
6699 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6700 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6701 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6702 if ( s0.match( query_nodes ) ) {
6706 query_nodes = new HashSet<PhylogenyNode>();
6707 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6708 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6709 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6710 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6711 if ( s0.match( query_nodes ) ) {
6715 // query_nodes = new HashSet<PhylogenyNode>();
6716 // query_nodes.add( new PhylogenyNode( "X" ) );
6717 // query_nodes.add( new PhylogenyNode( "Y" ) );
6718 // query_nodes.add( new PhylogenyNode( "A" ) );
6719 // query_nodes.add( new PhylogenyNode( "B" ) );
6720 // query_nodes.add( new PhylogenyNode( "C" ) );
6721 // query_nodes.add( new PhylogenyNode( "D" ) );
6722 // query_nodes.add( new PhylogenyNode( "E" ) );
6723 // query_nodes.add( new PhylogenyNode( "F" ) );
6724 // query_nodes.add( new PhylogenyNode( "G" ) );
6725 // if ( !s0.match( query_nodes ) ) {
6728 // query_nodes = new HashSet<PhylogenyNode>();
6729 // query_nodes.add( new PhylogenyNode( "X" ) );
6730 // query_nodes.add( new PhylogenyNode( "Y" ) );
6731 // query_nodes.add( new PhylogenyNode( "A" ) );
6732 // query_nodes.add( new PhylogenyNode( "B" ) );
6733 // query_nodes.add( new PhylogenyNode( "C" ) );
6734 // if ( !s0.match( query_nodes ) ) {
6738 // query_nodes = new HashSet<PhylogenyNode>();
6739 // query_nodes.add( new PhylogenyNode( "X" ) );
6740 // query_nodes.add( new PhylogenyNode( "Y" ) );
6741 // query_nodes.add( new PhylogenyNode( "D" ) );
6742 // query_nodes.add( new PhylogenyNode( "E" ) );
6743 // query_nodes.add( new PhylogenyNode( "F" ) );
6744 // query_nodes.add( new PhylogenyNode( "G" ) );
6745 // if ( !s0.match( query_nodes ) ) {
6749 // query_nodes = new HashSet<PhylogenyNode>();
6750 // query_nodes.add( new PhylogenyNode( "X" ) );
6751 // query_nodes.add( new PhylogenyNode( "Y" ) );
6752 // query_nodes.add( new PhylogenyNode( "A" ) );
6753 // query_nodes.add( new PhylogenyNode( "B" ) );
6754 // query_nodes.add( new PhylogenyNode( "C" ) );
6755 // query_nodes.add( new PhylogenyNode( "D" ) );
6756 // if ( !s0.match( query_nodes ) ) {
6760 // query_nodes = new HashSet<PhylogenyNode>();
6761 // query_nodes.add( new PhylogenyNode( "X" ) );
6762 // query_nodes.add( new PhylogenyNode( "Y" ) );
6763 // query_nodes.add( new PhylogenyNode( "E" ) );
6764 // query_nodes.add( new PhylogenyNode( "F" ) );
6765 // query_nodes.add( new PhylogenyNode( "G" ) );
6766 // if ( !s0.match( query_nodes ) ) {
6770 // query_nodes = new HashSet<PhylogenyNode>();
6771 // query_nodes.add( new PhylogenyNode( "X" ) );
6772 // query_nodes.add( new PhylogenyNode( "Y" ) );
6773 // query_nodes.add( new PhylogenyNode( "F" ) );
6774 // query_nodes.add( new PhylogenyNode( "G" ) );
6775 // if ( !s0.match( query_nodes ) ) {
6779 query_nodes = new HashSet<PhylogenyNode>();
6780 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6781 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6782 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6783 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6784 if ( s0.match( query_nodes ) ) {
6788 query_nodes = new HashSet<PhylogenyNode>();
6789 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6790 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6791 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6792 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6793 if ( s0.match( query_nodes ) ) {
6796 ///////////////////////////
6798 query_nodes = new HashSet<PhylogenyNode>();
6799 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6800 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6801 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6802 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6803 if ( s0.match( query_nodes ) ) {
6807 query_nodes = new HashSet<PhylogenyNode>();
6808 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6809 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6810 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6811 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6812 if ( s0.match( query_nodes ) ) {
6816 query_nodes = new HashSet<PhylogenyNode>();
6817 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6818 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6819 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6820 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6821 if ( s0.match( query_nodes ) ) {
6825 query_nodes = new HashSet<PhylogenyNode>();
6826 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6827 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6828 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6829 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6830 if ( s0.match( query_nodes ) ) {
6834 query_nodes = new HashSet<PhylogenyNode>();
6835 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6836 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6837 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6838 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6839 if ( s0.match( query_nodes ) ) {
6843 query_nodes = new HashSet<PhylogenyNode>();
6844 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6845 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6846 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6847 if ( s0.match( query_nodes ) ) {
6851 query_nodes = new HashSet<PhylogenyNode>();
6852 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6853 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6854 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6855 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6856 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6857 if ( s0.match( query_nodes ) ) {
6861 query_nodes = new HashSet<PhylogenyNode>();
6862 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6863 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6864 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6865 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6866 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6867 if ( s0.match( query_nodes ) ) {
6871 query_nodes = new HashSet<PhylogenyNode>();
6872 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6873 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6874 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6875 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6876 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6877 if ( s0.match( query_nodes ) ) {
6881 query_nodes = new HashSet<PhylogenyNode>();
6882 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
6883 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
6884 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6885 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6886 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6887 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6888 if ( s0.match( query_nodes ) ) {
6892 catch ( final Exception e ) {
6893 e.printStackTrace();
6899 private static boolean testSplitStrict() {
6901 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
6902 final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
6903 final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
6904 ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6905 ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6906 ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6907 ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6908 ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6909 ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6910 ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6911 final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
6912 Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
6913 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6914 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6915 if ( s0.match( query_nodes ) ) {
6918 query_nodes = new HashSet<PhylogenyNode>();
6919 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6920 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6921 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6922 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6923 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6924 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6925 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6926 if ( !s0.match( query_nodes ) ) {
6930 query_nodes = new HashSet<PhylogenyNode>();
6931 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6932 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6933 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6934 if ( !s0.match( query_nodes ) ) {
6938 query_nodes = new HashSet<PhylogenyNode>();
6939 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6940 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6941 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6942 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6943 if ( !s0.match( query_nodes ) ) {
6947 query_nodes = new HashSet<PhylogenyNode>();
6948 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6949 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6950 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6951 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6952 if ( !s0.match( query_nodes ) ) {
6956 query_nodes = new HashSet<PhylogenyNode>();
6957 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6958 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6959 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6960 if ( !s0.match( query_nodes ) ) {
6964 query_nodes = new HashSet<PhylogenyNode>();
6965 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6966 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6967 if ( !s0.match( query_nodes ) ) {
6971 query_nodes = new HashSet<PhylogenyNode>();
6972 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6973 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6974 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
6975 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
6976 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
6977 if ( !s0.match( query_nodes ) ) {
6981 query_nodes = new HashSet<PhylogenyNode>();
6982 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6983 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6984 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6985 if ( !s0.match( query_nodes ) ) {
6989 query_nodes = new HashSet<PhylogenyNode>();
6990 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
6991 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
6992 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
6993 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
6994 if ( !s0.match( query_nodes ) ) {
6998 query_nodes = new HashSet<PhylogenyNode>();
6999 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7000 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7001 if ( s0.match( query_nodes ) ) {
7005 query_nodes = new HashSet<PhylogenyNode>();
7006 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7007 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7008 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7009 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7010 if ( s0.match( query_nodes ) ) {
7014 query_nodes = new HashSet<PhylogenyNode>();
7015 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7016 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7017 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7018 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7019 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7020 if ( s0.match( query_nodes ) ) {
7024 query_nodes = new HashSet<PhylogenyNode>();
7025 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7026 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7027 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7028 if ( s0.match( query_nodes ) ) {
7032 query_nodes = new HashSet<PhylogenyNode>();
7033 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7034 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7035 if ( s0.match( query_nodes ) ) {
7039 query_nodes = new HashSet<PhylogenyNode>();
7040 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7041 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7042 if ( s0.match( query_nodes ) ) {
7046 query_nodes = new HashSet<PhylogenyNode>();
7047 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7048 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
7049 if ( s0.match( query_nodes ) ) {
7053 query_nodes = new HashSet<PhylogenyNode>();
7054 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7055 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7056 if ( s0.match( query_nodes ) ) {
7060 query_nodes = new HashSet<PhylogenyNode>();
7061 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7062 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7063 if ( s0.match( query_nodes ) ) {
7067 query_nodes = new HashSet<PhylogenyNode>();
7068 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7069 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7070 if ( s0.match( query_nodes ) ) {
7074 query_nodes = new HashSet<PhylogenyNode>();
7075 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7076 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
7077 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7078 if ( s0.match( query_nodes ) ) {
7082 query_nodes = new HashSet<PhylogenyNode>();
7083 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7084 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
7085 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7086 if ( s0.match( query_nodes ) ) {
7090 query_nodes = new HashSet<PhylogenyNode>();
7091 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7092 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7093 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7094 if ( s0.match( query_nodes ) ) {
7098 query_nodes = new HashSet<PhylogenyNode>();
7099 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
7100 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
7101 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
7102 query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
7103 if ( s0.match( query_nodes ) ) {
7107 catch ( final Exception e ) {
7108 e.printStackTrace();
7114 private static boolean testSubtreeDeletion() {
7116 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7117 final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7118 t1.deleteSubtree( t1.getNode( "A" ), false );
7119 if ( t1.getNumberOfExternalNodes() != 5 ) {
7122 t1.toNewHampshireX();
7123 t1.deleteSubtree( t1.getNode( "E" ), false );
7124 if ( t1.getNumberOfExternalNodes() != 4 ) {
7127 t1.toNewHampshireX();
7128 t1.deleteSubtree( t1.getNode( "F" ), false );
7129 if ( t1.getNumberOfExternalNodes() != 3 ) {
7132 t1.toNewHampshireX();
7133 t1.deleteSubtree( t1.getNode( "D" ), false );
7134 t1.toNewHampshireX();
7135 if ( t1.getNumberOfExternalNodes() != 3 ) {
7138 t1.deleteSubtree( t1.getNode( "def" ), false );
7139 t1.toNewHampshireX();
7140 if ( t1.getNumberOfExternalNodes() != 2 ) {
7143 t1.deleteSubtree( t1.getNode( "B" ), false );
7144 t1.toNewHampshireX();
7145 if ( t1.getNumberOfExternalNodes() != 1 ) {
7148 t1.deleteSubtree( t1.getNode( "C" ), false );
7149 t1.toNewHampshireX();
7150 if ( t1.getNumberOfExternalNodes() != 1 ) {
7153 t1.deleteSubtree( t1.getNode( "abc" ), false );
7154 t1.toNewHampshireX();
7155 if ( t1.getNumberOfExternalNodes() != 1 ) {
7158 t1.deleteSubtree( t1.getNode( "r" ), false );
7159 if ( t1.getNumberOfExternalNodes() != 0 ) {
7162 if ( !t1.isEmpty() ) {
7165 final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
7166 t2.deleteSubtree( t2.getNode( "A" ), false );
7167 t2.toNewHampshireX();
7168 if ( t2.getNumberOfExternalNodes() != 5 ) {
7171 t2.deleteSubtree( t2.getNode( "abc" ), false );
7172 t2.toNewHampshireX();
7173 if ( t2.getNumberOfExternalNodes() != 3 ) {
7176 t2.deleteSubtree( t2.getNode( "def" ), false );
7177 t2.toNewHampshireX();
7178 if ( t2.getNumberOfExternalNodes() != 1 ) {
7182 catch ( final Exception e ) {
7183 e.printStackTrace( System.out );
7189 private static boolean testSupportCount() {
7191 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7192 final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
7193 final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
7194 + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
7195 + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
7196 + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
7197 + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
7199 SupportCount.count( t0_1, phylogenies_1, true, false );
7200 final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
7201 final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
7202 + "(((((A,B),C),D),E),((F,G),X))"
7203 + "(((((A,Y),B),C),D),((F,G),E))"
7204 + "(((((A,B),C),D),E),(F,G))"
7205 + "(((((A,B),C),D),E),(F,G))"
7206 + "(((((A,B),C),D),E),(F,G))"
7207 + "(((((A,B),C),D),E),(F,G),Z)"
7208 + "(((((A,B),C),D),E),(F,G))"
7209 + "((((((A,B),C),D),E),F),G)"
7210 + "(((((X,Y),F,G),E),((A,B),C)),D)",
7212 SupportCount.count( t0_2, phylogenies_2, true, false );
7213 final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
7214 while ( it.hasNext() ) {
7215 final PhylogenyNode n = it.next();
7216 if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
7220 final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
7221 final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
7222 + "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
7223 SupportCount.count( t0_3, phylogenies_3, true, false );
7224 t0_3.reRoot( t0_3.getNode( "def" ).getId() );
7225 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
7228 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
7231 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
7234 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
7237 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
7240 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
7243 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
7246 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
7249 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
7252 if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
7255 final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7256 final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
7257 + "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
7258 SupportCount.count( t0_4, phylogenies_4, true, false );
7259 t0_4.reRoot( t0_4.getNode( "F" ).getId() );
7260 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
7263 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
7266 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
7269 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
7272 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
7275 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
7278 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
7281 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
7284 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
7287 if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
7290 Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7291 final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7292 double d = SupportCount.compare( b1, a, true, true, true );
7293 if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
7296 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7297 final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7298 d = SupportCount.compare( b2, a, true, true, true );
7299 if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
7302 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
7303 final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
7304 d = SupportCount.compare( b3, a, true, true, true );
7305 if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
7308 a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
7309 final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
7310 d = SupportCount.compare( b4, a, true, true, false );
7311 if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
7315 catch ( final Exception e ) {
7316 e.printStackTrace( System.out );
7322 private static boolean testSupportTransfer() {
7324 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
7325 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)",
7326 new NHXParser() )[ 0 ];
7327 final Phylogeny p2 = factory
7328 .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 ];
7329 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
7332 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
7335 support_transfer.moveBranchLengthsToBootstrap( p1 );
7336 support_transfer.transferSupportValues( p1, p2 );
7337 if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
7340 if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
7343 if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
7346 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
7349 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
7352 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
7355 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
7358 if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
7362 catch ( final Exception e ) {
7363 e.printStackTrace( System.out );
7369 private static boolean testTaxonomyAssigner() {
7371 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]";
7372 String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
7373 Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7374 Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7375 s0.setRooted( true );
7376 g0.setRooted( true );
7377 TaxonomyAssigner.execute( g0, s0 );
7378 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7381 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7384 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7387 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7388 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7389 g0.setRooted( true );
7390 TaxonomyAssigner.execute( g0, s0 );
7391 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7394 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7397 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7400 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7401 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7402 g0.setRooted( true );
7403 TaxonomyAssigner.execute( g0, s0 );
7404 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7407 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7410 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7413 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
7414 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7415 g0.setRooted( true );
7416 TaxonomyAssigner.execute( g0, s0 );
7417 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7420 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7423 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7426 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7427 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7428 g0.setRooted( true );
7429 TaxonomyAssigner.execute( g0, s0 );
7430 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
7433 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
7436 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7439 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
7440 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7441 g0.setRooted( true );
7442 TaxonomyAssigner.execute( g0, s0 );
7443 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7446 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7449 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7452 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7453 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7454 g0.setRooted( true );
7455 TaxonomyAssigner.execute( g0, s0 );
7456 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7459 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7462 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
7465 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
7466 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
7467 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
7468 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
7469 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7470 s0.setRooted( true );
7471 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7472 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
7473 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
7474 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
7475 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7476 g0.setRooted( true );
7477 TaxonomyAssigner.execute( g0, s0 );
7478 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7481 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7484 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7487 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7490 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7493 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7494 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7495 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
7496 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
7497 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7498 g0.setRooted( true );
7499 TaxonomyAssigner.execute( g0, s0 );
7500 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7503 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7506 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
7509 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
7512 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7515 g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
7516 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
7517 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7518 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
7519 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7520 g0.setRooted( true );
7521 TaxonomyAssigner.execute( g0, s0 );
7522 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7525 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
7528 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7531 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7534 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7537 g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
7538 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
7539 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
7540 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7541 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7542 g0.setRooted( true );
7543 TaxonomyAssigner.execute( g0, s0 );
7544 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7547 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7550 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7553 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7556 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7559 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
7560 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7561 g0.setRooted( true );
7562 TaxonomyAssigner.execute( g0, s0 );
7563 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7566 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7569 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7572 g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
7573 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7574 g0.setRooted( true );
7575 TaxonomyAssigner.execute( g0, s0 );
7576 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7579 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7582 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7585 g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
7586 + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7587 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7588 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7589 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7590 g0.setRooted( true );
7591 TaxonomyAssigner.execute( g0, s0 );
7592 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7595 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7598 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7601 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7604 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7607 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7610 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7613 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7614 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7615 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7616 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
7617 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7618 g0.setRooted( true );
7619 TaxonomyAssigner.execute( g0, s0 );
7620 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7623 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7626 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7629 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7632 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7635 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7638 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7641 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7642 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7643 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
7644 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7645 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7646 g0.setRooted( true );
7647 TaxonomyAssigner.execute( g0, s0 );
7648 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7651 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7654 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7657 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
7660 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7663 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7666 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7669 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7670 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7671 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7672 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7673 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7674 g0.setRooted( true );
7675 TaxonomyAssigner.execute( g0, s0 );
7676 if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7679 if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7682 if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7685 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7688 if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
7691 if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7694 if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
7697 s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
7698 + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
7699 + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
7700 + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
7701 s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
7702 s0.setRooted( true );
7703 g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
7704 + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
7705 + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
7706 + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
7707 g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
7708 g0.setRooted( true );
7709 TaxonomyAssigner.execute( g0, s0 );
7710 if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
7713 if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
7717 catch ( final Exception e ) {
7718 e.printStackTrace( System.out );
7724 private static boolean testUniprotTaxonomySearch() {
7726 List<UniProtTaxonomy> results = UniProtWsTools
7727 .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
7728 if ( results.size() != 1 ) {
7731 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7734 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7737 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7740 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7743 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7747 results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
7748 if ( results.size() != 1 ) {
7751 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7754 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7757 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7760 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7763 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7767 results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
7768 if ( results.size() != 1 ) {
7771 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7774 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7777 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7780 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7783 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7787 results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
7788 if ( results.size() != 1 ) {
7791 if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
7794 if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
7797 if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
7800 if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
7803 if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
7806 if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
7809 if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
7812 if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
7813 .equals( "Nematostella vectensis" ) ) {
7814 System.out.println( results.get( 0 ).getLineage() );
7818 catch ( final IOException e ) {
7819 System.out.println();
7820 System.out.println( "the following might be due to absence internet connection:" );
7821 e.printStackTrace( System.out );
7824 catch ( final Exception e ) {
7830 private static boolean testEmblEntryRetrieval() {
7831 //The format for GenBank Accession numbers are:
7832 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
7833 //Protein: 3 letters + 5 numerals
7834 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
7835 if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
7838 if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
7841 if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) {
7844 if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) {
7847 if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
7850 if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) {
7853 if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
7856 if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
7859 if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) {
7862 if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) {
7865 if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
7868 if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
7871 if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
7877 private static boolean testUniprotEntryRetrieval() {
7878 if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
7881 if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
7884 if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
7887 if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
7890 if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
7893 if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
7896 if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
7899 if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
7902 if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
7905 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
7908 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
7911 if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
7914 if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
7918 final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
7919 if ( !entry.getAccession().equals( "P12345" ) ) {
7922 if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
7925 if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
7928 if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
7931 if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
7935 catch ( final IOException e ) {
7936 System.out.println();
7937 System.out.println( "the following might be due to absence internet connection:" );
7938 e.printStackTrace( System.out );
7941 catch ( final Exception e ) {
7947 private static boolean testWabiTxSearch() {
7950 result = TxSearch.searchSimple( "nematostella" );
7951 result = TxSearch.getTxId( "nematostella" );
7952 if ( !result.equals( "45350" ) ) {
7955 result = TxSearch.getTxName( "45350" );
7956 if ( !result.equals( "Nematostella" ) ) {
7959 result = TxSearch.getTxId( "nematostella vectensis" );
7960 if ( !result.equals( "45351" ) ) {
7963 result = TxSearch.getTxName( "45351" );
7964 if ( !result.equals( "Nematostella vectensis" ) ) {
7967 result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
7968 if ( !result.equals( "536089" ) ) {
7971 result = TxSearch.getTxName( "536089" );
7972 if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
7975 final List<String> queries = new ArrayList<String>();
7976 queries.add( "Campylobacter coli" );
7977 queries.add( "Escherichia coli" );
7978 queries.add( "Arabidopsis" );
7979 queries.add( "Trichoplax" );
7980 queries.add( "Samanea saman" );
7981 queries.add( "Kluyveromyces marxianus" );
7982 queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
7983 queries.add( "Bornavirus parrot/PDD/2008" );
7984 final List<RANKS> ranks = new ArrayList<RANKS>();
7985 ranks.add( RANKS.SUPERKINGDOM );
7986 ranks.add( RANKS.KINGDOM );
7987 ranks.add( RANKS.FAMILY );
7988 ranks.add( RANKS.GENUS );
7989 ranks.add( RANKS.TRIBE );
7990 result = TxSearch.searchLineage( queries, ranks );
7991 result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
7992 result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
7994 catch ( final Exception e ) {
7995 System.out.println();
7996 System.out.println( "the following might be due to absence internet connection:" );
7997 e.printStackTrace( System.out );
8003 private static boolean testAminoAcidSequence() {
8005 final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
8006 if ( aa1.getLength() != 13 ) {
8009 if ( aa1.getResidueAt( 0 ) != 'A' ) {
8012 if ( aa1.getResidueAt( 2 ) != 'K' ) {
8015 if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
8018 final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
8019 if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
8022 final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
8023 if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
8026 final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
8027 if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
8031 catch ( final Exception e ) {
8032 e.printStackTrace();
8038 private static boolean testCreateBalancedPhylogeny() {
8040 final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
8041 if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
8044 if ( p0.getNumberOfExternalNodes() != 15625 ) {
8047 final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
8048 if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
8051 if ( p1.getNumberOfExternalNodes() != 100 ) {
8055 catch ( final Exception e ) {
8056 e.printStackTrace();
8062 private static boolean testFastaParser() {
8064 if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
8067 if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
8070 final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
8071 if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
8074 if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
8077 if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
8080 if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
8083 if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
8086 if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
8090 catch ( final Exception e ) {
8091 e.printStackTrace();
8097 private static boolean testGeneralMsaParser() {
8099 final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
8100 final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
8101 final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n";
8102 final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
8103 final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
8104 final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
8105 final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
8106 final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
8107 final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
8108 if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8111 if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8114 if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8117 final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
8118 if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
8121 if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
8124 if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
8127 final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
8128 if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
8131 if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
8134 if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
8138 catch ( final Exception e ) {
8139 e.printStackTrace();
8145 private static boolean testMafft() {
8147 final List<String> opts = new ArrayList<String>();
8148 opts.add( "--maxiterate" );
8150 opts.add( "--localpair" );
8151 opts.add( "--quiet" );
8153 final MsaInferrer mafft = Mafft.createInstance();
8154 msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts );
8155 if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) {
8159 catch ( final Exception e ) {
8160 e.printStackTrace( System.out );
8166 private static boolean testNextNodeWithCollapsing() {
8168 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
8170 List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
8171 final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8172 final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
8173 t0.getNode( "cd" ).setCollapse( true );
8174 t0.getNode( "cde" ).setCollapse( true );
8175 n = t0.getFirstExternalNode();
8176 while ( n != null ) {
8178 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8180 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8183 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8186 if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
8189 if ( !ext.get( 3 ).getName().equals( "f" ) ) {
8192 if ( !ext.get( 4 ).getName().equals( "g" ) ) {
8195 if ( !ext.get( 5 ).getName().equals( "h" ) ) {
8199 final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8200 final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
8201 t1.getNode( "ab" ).setCollapse( true );
8202 t1.getNode( "cd" ).setCollapse( true );
8203 t1.getNode( "cde" ).setCollapse( true );
8204 n = t1.getNode( "ab" );
8205 ext = new ArrayList<PhylogenyNode>();
8206 while ( n != null ) {
8208 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8210 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8213 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8216 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8219 if ( !ext.get( 3 ).getName().equals( "g" ) ) {
8222 if ( !ext.get( 4 ).getName().equals( "h" ) ) {
8228 final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8229 final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
8230 t2.getNode( "ab" ).setCollapse( true );
8231 t2.getNode( "cd" ).setCollapse( true );
8232 t2.getNode( "cde" ).setCollapse( true );
8233 t2.getNode( "c" ).setCollapse( true );
8234 t2.getNode( "d" ).setCollapse( true );
8235 t2.getNode( "e" ).setCollapse( true );
8236 t2.getNode( "gh" ).setCollapse( true );
8237 n = t2.getNode( "ab" );
8238 ext = new ArrayList<PhylogenyNode>();
8239 while ( n != null ) {
8241 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8243 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8246 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8249 if ( !ext.get( 2 ).getName().equals( "f" ) ) {
8252 if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
8258 final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8259 final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
8260 t3.getNode( "ab" ).setCollapse( true );
8261 t3.getNode( "cd" ).setCollapse( true );
8262 t3.getNode( "cde" ).setCollapse( true );
8263 t3.getNode( "c" ).setCollapse( true );
8264 t3.getNode( "d" ).setCollapse( true );
8265 t3.getNode( "e" ).setCollapse( true );
8266 t3.getNode( "gh" ).setCollapse( true );
8267 t3.getNode( "fgh" ).setCollapse( true );
8268 n = t3.getNode( "ab" );
8269 ext = new ArrayList<PhylogenyNode>();
8270 while ( n != null ) {
8272 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8274 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8277 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8280 if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
8286 final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8287 final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
8288 t4.getNode( "ab" ).setCollapse( true );
8289 t4.getNode( "cd" ).setCollapse( true );
8290 t4.getNode( "cde" ).setCollapse( true );
8291 t4.getNode( "c" ).setCollapse( true );
8292 t4.getNode( "d" ).setCollapse( true );
8293 t4.getNode( "e" ).setCollapse( true );
8294 t4.getNode( "gh" ).setCollapse( true );
8295 t4.getNode( "fgh" ).setCollapse( true );
8296 t4.getNode( "abcdefgh" ).setCollapse( true );
8297 n = t4.getNode( "abcdefgh" );
8298 if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
8303 final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8304 final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
8306 n = t5.getFirstExternalNode();
8307 while ( n != null ) {
8309 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8311 if ( ext.size() != 8 ) {
8314 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8317 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8320 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8323 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8326 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8329 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8332 if ( !ext.get( 6 ).getName().equals( "g" ) ) {
8335 if ( !ext.get( 7 ).getName().equals( "h" ) ) {
8340 final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8341 final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
8343 t6.getNode( "ab" ).setCollapse( true );
8344 n = t6.getNode( "ab" );
8345 while ( n != null ) {
8347 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8349 if ( ext.size() != 7 ) {
8352 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8355 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8358 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8361 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8364 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8367 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8370 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8375 final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8376 final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
8378 t7.getNode( "cd" ).setCollapse( true );
8379 n = t7.getNode( "a" );
8380 while ( n != null ) {
8382 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8384 if ( ext.size() != 7 ) {
8387 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8390 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8393 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8396 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8399 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8402 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8405 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8410 final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
8411 final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
8413 t8.getNode( "cd" ).setCollapse( true );
8414 t8.getNode( "c" ).setCollapse( true );
8415 t8.getNode( "d" ).setCollapse( true );
8416 n = t8.getNode( "a" );
8417 while ( n != null ) {
8419 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8421 if ( ext.size() != 7 ) {
8424 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8427 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8430 if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
8431 System.out.println( "2 fail" );
8434 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8437 if ( !ext.get( 4 ).getName().equals( "f" ) ) {
8440 if ( !ext.get( 5 ).getName().equals( "g" ) ) {
8443 if ( !ext.get( 6 ).getName().equals( "h" ) ) {
8448 final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8449 final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
8451 t9.getNode( "gh" ).setCollapse( true );
8452 n = t9.getNode( "a" );
8453 while ( n != null ) {
8455 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8457 if ( ext.size() != 7 ) {
8460 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8463 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8466 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8469 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8472 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8475 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8478 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8483 final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8484 final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
8486 t10.getNode( "gh" ).setCollapse( true );
8487 t10.getNode( "g" ).setCollapse( true );
8488 t10.getNode( "h" ).setCollapse( true );
8489 n = t10.getNode( "a" );
8490 while ( n != null ) {
8492 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8494 if ( ext.size() != 7 ) {
8497 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8500 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8503 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8506 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8509 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8512 if ( !ext.get( 5 ).getName().equals( "f" ) ) {
8515 if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
8520 final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8521 final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
8523 t11.getNode( "gh" ).setCollapse( true );
8524 t11.getNode( "fgh" ).setCollapse( true );
8525 n = t11.getNode( "a" );
8526 while ( n != null ) {
8528 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8530 if ( ext.size() != 6 ) {
8533 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8536 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8539 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8542 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8545 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8548 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8553 final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8554 final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
8556 t12.getNode( "gh" ).setCollapse( true );
8557 t12.getNode( "fgh" ).setCollapse( true );
8558 t12.getNode( "g" ).setCollapse( true );
8559 t12.getNode( "h" ).setCollapse( true );
8560 t12.getNode( "f" ).setCollapse( true );
8561 n = t12.getNode( "a" );
8562 while ( n != null ) {
8564 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8566 if ( ext.size() != 6 ) {
8569 if ( !ext.get( 0 ).getName().equals( "a" ) ) {
8572 if ( !ext.get( 1 ).getName().equals( "b" ) ) {
8575 if ( !ext.get( 2 ).getName().equals( "c" ) ) {
8578 if ( !ext.get( 3 ).getName().equals( "d" ) ) {
8581 if ( !ext.get( 4 ).getName().equals( "e" ) ) {
8584 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8589 final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
8590 final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
8592 t13.getNode( "ab" ).setCollapse( true );
8593 t13.getNode( "b" ).setCollapse( true );
8594 t13.getNode( "fgh" ).setCollapse( true );
8595 t13.getNode( "gh" ).setCollapse( true );
8596 n = t13.getNode( "ab" );
8597 while ( n != null ) {
8599 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8601 if ( ext.size() != 5 ) {
8604 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8607 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8610 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8613 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8616 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8621 final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8622 final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
8624 t14.getNode( "ab" ).setCollapse( true );
8625 t14.getNode( "a" ).setCollapse( true );
8626 t14.getNode( "fgh" ).setCollapse( true );
8627 t14.getNode( "gh" ).setCollapse( true );
8628 n = t14.getNode( "ab" );
8629 while ( n != null ) {
8631 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8633 if ( ext.size() != 5 ) {
8636 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8639 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8642 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8645 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8648 if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
8653 final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8654 final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
8656 t15.getNode( "ab" ).setCollapse( true );
8657 t15.getNode( "a" ).setCollapse( true );
8658 t15.getNode( "fgh" ).setCollapse( true );
8659 t15.getNode( "gh" ).setCollapse( true );
8660 n = t15.getNode( "ab" );
8661 while ( n != null ) {
8663 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8665 if ( ext.size() != 6 ) {
8668 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8671 if ( !ext.get( 1 ).getName().equals( "c" ) ) {
8674 if ( !ext.get( 2 ).getName().equals( "d" ) ) {
8677 if ( !ext.get( 3 ).getName().equals( "e" ) ) {
8680 if ( !ext.get( 4 ).getName().equals( "x" ) ) {
8683 if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
8688 final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
8689 final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
8691 t16.getNode( "ab" ).setCollapse( true );
8692 t16.getNode( "a" ).setCollapse( true );
8693 t16.getNode( "fgh" ).setCollapse( true );
8694 t16.getNode( "gh" ).setCollapse( true );
8695 t16.getNode( "cd" ).setCollapse( true );
8696 t16.getNode( "cde" ).setCollapse( true );
8697 t16.getNode( "d" ).setCollapse( true );
8698 t16.getNode( "x" ).setCollapse( true );
8699 n = t16.getNode( "ab" );
8700 while ( n != null ) {
8702 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
8704 if ( ext.size() != 4 ) {
8707 if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
8710 if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
8713 if ( !ext.get( 2 ).getName().equals( "x" ) ) {
8716 if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
8720 catch ( final Exception e ) {
8721 e.printStackTrace( System.out );